diff --git a/CHANGES.md b/CHANGES.md index 8f4e95e6..b326d0de 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -6,6 +6,13 @@ * #661: Fix a bug in index construction that, for some references, made the randstrobe with the smallest hash value impossible to find. Pre-generated index files (`.sti` files) need to be re-generated. +* #656: Report tandem duplications in single-end mode: an insertion of at least + `--dl` bases (default 50) is re-aligned against the reference on both sides of + the insertion point, and if it matches at least a fraction `--dm` (default + 0.80) of the inserted bases, the read is output as one record per copy instead + of as an insertion. `--dw` (default 20) is the bandwidth used for the two arms + and `--dl 0` turns detection off. Strobealign supports multiple records per + read with an `SA:Z` tag. ## v0.19.0 (2026-10-08) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 41385a2b..b112f6f6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -102,6 +102,7 @@ mapped reads. `X0`: Number of equally scored best alignments (greater than 1 for multimappers). For paired-end reads, the tag is output for both reads, but the value is identical and is the number of equally scored best alignment *pairs*. +`du`: Number of insertions re-interpreted as tandem duplications. ## Hidden command-line options diff --git a/src/aligner.rs b/src/aligner.rs index b12f38c0..6fdbea52 100644 --- a/src/aligner.rs +++ b/src/aligner.rs @@ -5,6 +5,7 @@ use std::cell::Cell; use crate::chainer::Anchor; use crate::cigar::{Cigar, CigarOperation}; use crate::piecewisealigner::PiecewiseAligner; +use crate::simdaligner::SplitReferenceAlignment; use crate::ssw::SswAligner; #[derive(Debug, Clone, Copy)] @@ -29,6 +30,22 @@ impl Default for Scores { } } +impl Scores { + pub fn score(&self, cigar: &Cigar) -> i32 { + cigar + .iter() + .map(|(op, len)| match op { + CigarOperation::Eq => self.match_ as i32 * len as i32, + CigarOperation::X => -(self.mismatch as i32) * len as i32, + CigarOperation::Insertion | CigarOperation::Deletion => { + -(self.gap_open as i32 + (len as i32 - 1) * self.gap_extend as i32) + } + _ => unreachable!("scoring a CIGAR that is not =/X/I/D: {len}{op}"), + }) + .sum() + } +} + #[derive(Debug)] pub struct AlignmentInfo { pub cigar: Cigar, @@ -174,6 +191,21 @@ impl Aligner { .expect("this Aligner was built for SSW extension only") .extend_piecewise(query, refseq, chain, padding) } + + pub fn realign_insertion( + &self, + inserted: &[u8], + left_reference: &[u8], + right_reference: &[u8], + band: usize, + ) -> Option { + Some(self.piecewise_aligner.as_ref()?.realign_insertion( + inserted, + left_reference, + right_reference, + band, + )) + } } pub fn hamming_distance(s: &[u8], t: &[u8]) -> Option { @@ -308,6 +340,21 @@ mod test { use crate::aligner::{ Aligner, Scores, hamming_align, hamming_align_global, highest_scoring_segment, }; + use crate::cigar::Cigar; + + #[test] + fn score_cigar() { + let scores = Scores { + match_: 2, + mismatch: 8, + gap_open: 12, + gap_extend: 1, + end_bonus: 10, + }; + let cigar: Cigar = "10X100=52D5=".parse().unwrap(); + + assert_eq!(scores.score(&cigar), 67); + } #[test] fn ssw_align_no_result() { diff --git a/src/cigar.rs b/src/cigar.rs index 8dbc2703..fdf428a3 100644 --- a/src/cigar.rs +++ b/src/cigar.rs @@ -155,6 +155,20 @@ impl Cigar { dist } + /// Bases matched exactly, zero for a CIGAR written with `M`. + pub fn matches(&self) -> usize { + self.ops + .iter() + .filter(|op_len| op_len.op == CigarOperation::Eq) + .map(|op_len| op_len.len) + .sum() + } + + /// Iterate over the operations as `(operation, length)` pairs. + pub fn iter(&self) -> impl ExactSizeIterator { + self.ops.iter().map(|oplen| (oplen.op, oplen.len)) + } + /// Return a new Cigar that uses = and X operations instead of M pub fn with_eqx(&self, query: &[u8], refseq: &[u8]) -> Cigar { let mut cigar = Cigar::new(); @@ -270,6 +284,20 @@ mod test { assert!(!cigar.is_empty()); } + #[test] + fn iter_yields_operations_and_lengths() { + let cigar = Cigar::from_str("10=2X3D5=").unwrap(); + assert_eq!( + cigar.iter().collect::>(), + vec![ + (CigarOperation::Eq, 10), + (CigarOperation::X, 2), + (CigarOperation::Deletion, 3), + (CigarOperation::Eq, 5), + ] + ); + } + #[test] fn construct() { let cigar = Cigar::new(); diff --git a/src/details.rs b/src/details.rs index 3f44f251..750aabfb 100644 --- a/src/details.rs +++ b/src/details.rs @@ -65,6 +65,9 @@ pub struct AlignmentDetails { /// No. of best alignments with same score pub best_alignments: usize, + /// No. of insertions re-interpreted as tandem duplications + pub duplications: usize, + pub time_extend: f64, } @@ -76,6 +79,7 @@ impl ops::AddAssign for AlignmentDetails { self.anchors += rhs.anchors; self.collisions += rhs.collisions; self.best_alignments += rhs.best_alignments; + self.duplications += rhs.duplications; self.time_extend += rhs.time_extend; } } diff --git a/src/duplications.rs b/src/duplications.rs new file mode 100644 index 00000000..2ddf32c0 --- /dev/null +++ b/src/duplications.rs @@ -0,0 +1,186 @@ +use crate::aligner::{Aligner, Scores}; +use crate::cigar::{Cigar, CigarOperation}; +use crate::modes::align::Alignment; +use crate::packed_seq::PackedSeqSlice; +use crate::read::Read; +use crate::refseq::RefSequence; +use crate::simdaligner::SplitReferenceAlignment; + +/// Cuts the alignment into one segment per copy wherever an insertion of at least `min_length` +/// bases turns out to be a tandem duplication. A `min_length` of zero turns this off. Always +/// returns at least the alignment it was given. +pub fn reinterpret_insertions( + aligner: &Aligner, + alignment: Alignment, + refseq: &RefSequence, + read: &Read, + min_length: usize, + min_matches: f32, + band: usize, +) -> Vec { + if min_length == 0 { + return vec![alignment]; + } + let query = if alignment.is_revcomp { + read.rc() + } else { + read.seq() + }; + let contig = refseq.contig(alignment.contig_id); + + let mut segments = Vec::new(); + let mut segment_cigar = Cigar::new(); + let mut segment_start = alignment.contig_start; + let mut segment_clip_left = alignment.soft_clip_left; + let mut ref_pos = alignment.contig_start; + let mut query_pos = alignment.soft_clip_left; + + for (op, len) in alignment.cigar.iter() { + if op == CigarOperation::Insertion + && len >= min_length + && let Some((copy_start, split)) = find_duplication( + aligner, + &contig, + &query[query_pos..query_pos + len], + ref_pos, + min_length, + min_matches, + band, + ) + { + // The right arm carries the segment being built on past the insertion point, and + // the left arm opens the next one at the second copy. + let mut upstream = segment_cigar.clone(); + upstream.extend(&split.right.cigar); + + if let Some(segment) = clip_segment( + &alignment, + upstream, + segment_start, + segment_clip_left, + query.len(), + &aligner.scores, + ) { + segments.push(segment); + segment_cigar = split.left.cigar; + segment_start = copy_start; + segment_clip_left = query_pos + split.left.query_start; + query_pos += len; + continue; + } + } + + segment_cigar.push(op, len); + let (query_len, ref_len) = query_ref_len(op, len); + query_pos += query_len; + ref_pos += ref_len; + } + + if segments.is_empty() { + return vec![alignment]; + } + + let Some(last) = clip_segment( + &alignment, + segment_cigar, + segment_start, + segment_clip_left, + query.len(), + &aligner.scores, + ) else { + return vec![alignment]; + }; + segments.push(last); + + segments +} + +/// Aligns the bases inserted at `ref_pos` against both references surrounding the +/// insertion region and returns a duplication pattern: 2 alignments bridging the +/// query region by jumping from one reference to the other. None when the +/// duplication pattern is not good enough to report. +fn find_duplication( + aligner: &Aligner, + contig: &PackedSeqSlice, + insertion: &[u8], + ref_pos: usize, + min_length: usize, + min_matches: f32, + band: usize, +) -> Option<(usize, SplitReferenceAlignment)> { + let len = insertion.len(); + let padding = len + band; + let left_start = ref_pos.saturating_sub(len + padding); + let right_end = (ref_pos + len + padding).min(contig.len()); + let left_reference = contig.decode(left_start, ref_pos); + let right_reference = contig.decode(ref_pos, right_end); + + let split = aligner.realign_insertion(insertion, &left_reference, &right_reference, band)?; + + let matched = split.left.cigar.matches() + split.right.cigar.matches(); + let copy_len = + (split.right.ref_end - split.right.ref_start) + (split.left.ref_end - split.left.ref_start); + + // The duplication must match most of the inserted sequence. + if (matched as f32) < min_matches * len as f32 || copy_len < min_length { + return None; + } + + Some((left_start + split.left.ref_start, split)) +} + +/// Builds the alignment of one segment from the cigar it covers, soft-clipping the read on +/// both sides and scoring the segment on its own. None if it scores zero or less. +fn clip_segment( + source: &Alignment, + cigar: Cigar, + ref_start: usize, + soft_clip_left: usize, + read_len: usize, + scores: &Scores, +) -> Option { + let (query_span, ref_span) = query_ref_span(&cigar); + let soft_clip_right = read_len - (soft_clip_left + query_span); + let unclipped_ends = (soft_clip_left == 0) as u32 + (soft_clip_right == 0) as u32; + let score = scores.score(&cigar) + (unclipped_ends * scores.end_bonus) as i32; + if score <= 0 { + return None; + } + + Some(Alignment { + contig_id: source.contig_id, + is_revcomp: source.is_revcomp, + contig_start: ref_start, + length: ref_span, + soft_clip_left, + soft_clip_right, + edit_distance: cigar.edit_distance(), + score: score as u32, + cigar, + gapped: source.gapped, + anchors: source.anchors, + collisions: source.collisions, + }) +} + +fn query_ref_span(cigar: &Cigar) -> (usize, usize) { + let mut query = 0; + let mut reference = 0; + + for (op, len) in cigar.iter() { + let (q, r) = query_ref_len(op, len); + query += q; + reference += r; + } + + (query, reference) +} + +fn query_ref_len(op: CigarOperation, len: usize) -> (usize, usize) { + match op { + CigarOperation::Match | CigarOperation::Eq | CigarOperation::X => (len, len), + CigarOperation::Insertion | CigarOperation::Softclip => (len, 0), + CigarOperation::Deletion | CigarOperation::Skip => (0, len), + CigarOperation::Hardclip | CigarOperation::Pad => (0, 0), + } +} diff --git a/src/io/sam.rs b/src/io/sam.rs index 86902b58..1cd7f7d4 100644 --- a/src/io/sam.rs +++ b/src/io/sam.rs @@ -35,6 +35,8 @@ pub struct SamRecord { pub alignment_score: Option, pub details: Option
, pub rg_id: Option, + /// Lists the alignments for a read split in multiple records + pub sa_tag: Option, /// Copied from FASTQ header pub extra: Option, } @@ -116,11 +118,12 @@ impl Display for SamRecord { if let Some(details) = &self.details { write!( f, - "\tna:i:{}\tal:i:{}\tga:i:{}\tX0:i:{}", + "\tna:i:{}\tal:i:{}\tga:i:{}\tX0:i:{}\tdu:i:{}", details.chain.n_chains, details.align.tried_alignment, details.align.gapped, details.align.best_alignments, + details.align.duplications, )?; if self.flags & PAIRED != 0 { write!(f, "\tmr:i:{}", details.align.mate_rescue)?; @@ -129,6 +132,9 @@ impl Display for SamRecord { if let Some(rg_id) = &self.rg_id { write!(f, "\tRG:Z:{}", rg_id)?; } + if let Some(sa_tag) = &self.sa_tag { + write!(f, "\tSA:Z:{}", sa_tag)?; + } if let Some(extra) = &self.extra { write!(f, "\t{}", extra)?; } diff --git a/src/lib.rs b/src/lib.rs index a109f894..d35cb535 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -3,6 +3,7 @@ pub mod chain; pub mod chainer; pub mod cigar; pub mod details; +pub mod duplications; pub mod hit; pub mod index; pub mod indexer; diff --git a/src/main.rs b/src/main.rs index b5c24feb..cc7d4304 100644 --- a/src/main.rs +++ b/src/main.rs @@ -287,6 +287,18 @@ struct Args { #[arg(long = "bw", default_value_t = 1024, value_name = "N", help_heading = "Alignment")] bandwidth: usize, + /// Minimum size for reported tandem duplications (single-end only), 0 to disable duplication detection + #[arg(long = "dl", default_value_t = MappingParameters::default().min_duplication_length, value_name = "N", help_heading = "Duplications")] + min_duplication_length: usize, + + /// Minimum fraction of matches for a valid duplication + #[arg(long = "dm", default_value_t = MappingParameters::default().min_duplication_matches, help_heading = "Duplications")] + min_duplication_matches: f32, + + /// Bandwidth of the two arms of a duplication split + #[arg(long = "dw", default_value_t = MappingParameters::default().duplication_band, value_name = "N", help_heading = "Duplications")] + duplication_band: usize, + /// Path to input reference (in FASTA format) ref_path: String, @@ -554,6 +566,9 @@ fn run() -> Result<(), CliError> { output_unmapped: !args.only_mapped, mcs_strategy: args.mcs_strategy, use_ssw: args.use_ssw, + min_duplication_length: args.min_duplication_length, + min_duplication_matches: args.min_duplication_matches, + duplication_band: args.duplication_band, }; let chaining_parameters = ChainingParameters { diff --git a/src/modes/align.rs b/src/modes/align.rs index 1c6c8251..f221eec2 100644 --- a/src/modes/align.rs +++ b/src/modes/align.rs @@ -18,12 +18,14 @@ use crate::chain::Chain; use crate::chainer::Anchor; use crate::cigar::{Cigar, CigarOperation}; use crate::details::{AlignmentDetails, ChainDetails, Details}; +use crate::duplications::reinterpret_insertions; use crate::hit::HitsDetails; use crate::index::StrobemerIndex; use crate::insertsize::InsertSizeDistribution; use crate::io::record::SequenceRecord; use crate::io::sam::{ - MREVERSE, MUNMAP, PAIRED, PROPER_PAIR, READ1, READ2, REVERSE, SECONDARY, SamRecord, UNMAP, + MREVERSE, MUNMAP, PAIRED, PROPER_PAIR, READ1, READ2, REVERSE, SECONDARY, SUPPLEMENTARY, + SamRecord, UNMAP, }; use crate::math::normal_pdf; use crate::mcsstrategy::McsStrategy; @@ -46,6 +48,9 @@ pub struct MappingParameters { pub mcs_strategy: McsStrategy, pub output_unmapped: bool, pub use_ssw: bool, + pub min_duplication_length: usize, + pub min_duplication_matches: f32, + pub duplication_band: usize, } impl Default for MappingParameters { @@ -59,6 +64,9 @@ impl Default for MappingParameters { mcs_strategy: McsStrategy::default(), output_unmapped: true, use_ssw: false, + min_duplication_length: 50, + min_duplication_matches: 0.80, + duplication_band: 20, } } } @@ -71,31 +79,80 @@ impl Default for MappingParameters { /// conversion from the flat position needs to be done anyway before aligning /// to ensure we don’t align across contigs. #[derive(Debug, Clone)] -struct Alignment { - contig_id: usize, - contig_start: usize, - cigar: Cigar, - edit_distance: usize, - soft_clip_left: usize, - soft_clip_right: usize, - score: u32, - length: usize, - is_revcomp: bool, +pub struct Alignment { + pub contig_id: usize, + pub contig_start: usize, + pub cigar: Cigar, + pub edit_distance: usize, + pub soft_clip_left: usize, + pub soft_clip_right: usize, + pub score: u32, + pub length: usize, + pub is_revcomp: bool, /// Whether a gapped alignment function was used to obtain this alignment /// (even if true, the alignment can still be without gaps) - gapped: bool, + pub gapped: bool, /// Number of anchors used - anchors: usize, + pub anchors: usize, /// Number of anchors removed because of hash collison - collisions: usize, + pub collisions: usize, } impl Alignment { fn global_edit_distance(&self) -> usize { self.edit_distance + self.soft_clip_left + self.soft_clip_right } + + fn sam_cigar(&self, cigar_eqx: bool) -> Cigar { + let mut cigar = Cigar::new(); + cigar.push(CigarOperation::Softclip, self.soft_clip_left); + cigar.extend(&self.cigar); + cigar.push(CigarOperation::Softclip, self.soft_clip_right); + if cigar_eqx { cigar } else { cigar.with_m() } + } + + fn sa_entry(&self, refseq: &RefSequence, mapq: u8, cigar_eqx: bool) -> String { + format!( + "{},{},{},{},{},{};", + refseq.names[self.contig_id], + self.contig_start + 1, + if self.is_revcomp { '-' } else { '+' }, + self.sam_cigar(cigar_eqx), + mapq, + self.edit_distance, + ) + } +} + +fn build_sa_tags( + segments: &[Alignment], + mapq: u8, + refseq: &RefSequence, + cigar_eqx: bool, +) -> Vec> { + if segments.len() < 2 { + return vec![None; segments.len()]; + } + + let mut entries = Vec::with_capacity(segments.len()); + for segment in segments { + entries.push(segment.sa_entry(refseq, mapq, cigar_eqx)); + } + + let mut tags = Vec::with_capacity(segments.len()); + for i in 0..entries.len() { + let mut tag = String::new(); + for (j, entry) in entries.iter().enumerate() { + if i != j { + tag.push_str(entry); + } + } + tags.push(Some(tag)); + } + + tags } impl AlignmentDetails { @@ -117,6 +174,7 @@ enum PairStatus { enum AlignmentStatus { Primary, Secondary, + Supplementary, } /// Conversion of an Alignment into a SamRecord @@ -160,6 +218,7 @@ impl SamOutput { mapq, alignment_status, details.clone(), + None, ), None => self.make_unmapped_record(record, details.clone()), } @@ -174,15 +233,20 @@ impl SamOutput { mut mapq: u8, alignment_status: AlignmentStatus, details: Details, + sa_tag: Option, ) -> SamRecord { let mut flags = 0; if alignment.is_revcomp { flags |= REVERSE; } - if alignment_status == AlignmentStatus::Secondary { - mapq = 0; - flags |= SECONDARY; + match alignment_status { + AlignmentStatus::Primary => {} + AlignmentStatus::Secondary => { + mapq = 0; + flags |= SECONDARY; + } + AlignmentStatus::Supplementary => flags |= SUPPLEMENTARY, } let query_sequence = if alignment.is_revcomp { @@ -200,10 +264,6 @@ impl SamOutput { } else { record.qualities.clone() }; - let mut cigar = Cigar::new(); - cigar.push(CigarOperation::Softclip, alignment.soft_clip_left); - cigar.extend(&alignment.cigar); - cigar.push(CigarOperation::Softclip, alignment.soft_clip_right); let reference_name = Some(refseq.names[alignment.contig_id].clone()); let pos = Some(ContigPosition(alignment.contig_start as u32)); let details = if self.show_details { @@ -211,11 +271,7 @@ impl SamOutput { } else { None }; - let cigar = if self.cigar_eqx { - Some(cigar) - } else { - Some(cigar.with_m()) - }; + let cigar = Some(alignment.sam_cigar(self.cigar_eqx)); let extra = if self.fastq_comments { record.comment.clone() } else { @@ -232,6 +288,7 @@ impl SamOutput { query_qualities, edit_distance: Some(alignment.edit_distance as u32), alignment_score: Some(alignment.score), + sa_tag, details, rg_id: self.rg_id.clone(), extra, @@ -476,23 +533,45 @@ pub fn align_single_end_read( alignments.push(alignment); } } - if best_alignment.is_none() { + let Some(best_alignment) = best_alignment else { return ( vec![sam_output.make_unmapped_record(record, details.clone())], details, ); - } + }; let mapq = (60 * (best_score - second_best_score)).div_ceil(best_score) as u8; - let best_alignment = best_alignment.unwrap(); - sam_records.push(sam_output.make_mapped_record( - &best_alignment, + let mut segments = reinterpret_insertions( + aligner, + best_alignment, refseq, - record, - mapq, - AlignmentStatus::Primary, - details.clone(), - )); + &read, + mapping_parameters.min_duplication_length, + mapping_parameters.min_duplication_matches, + mapping_parameters.duplication_band, + ); + details.align.duplications += segments.len() - 1; + + // The best scoring segment becomes the primary and the rest supplementary + segments.sort_by_key(|segment| Reverse(segment.score)); + let mut sa_tags = build_sa_tags(&segments, mapq, refseq, sam_output.cigar_eqx); + + for i in 0..segments.len() { + let status = if i == 0 { + AlignmentStatus::Primary + } else { + AlignmentStatus::Supplementary + }; + sam_records.push(sam_output.make_mapped_record( + &segments[i], + refseq, + record, + mapq, + status, + details.clone(), + sa_tags[i].take(), + )); + } // Secondary alignments if mapping_parameters.max_secondary > 0 { @@ -517,6 +596,7 @@ pub fn align_single_end_read( mapq, AlignmentStatus::Secondary, details.clone(), + None, )); } } @@ -1476,6 +1556,8 @@ fn top_dropoff(chains: &[Chain]) -> f32 { mod tests { use super::*; use crate::cigar::Cigar; + use crate::packed_seq::PackedSeq; + use std::str::FromStr; pub fn make_alignment(contig_start: usize, score: u32, is_revcomp: bool) -> Alignment { Alignment { @@ -1511,6 +1593,50 @@ mod tests { } } + #[test] + fn sa_tags_cross_reference_the_other_segments() { + let refseq = RefSequence::new( + PackedSeq::from_slice(b""), + vec![0], + vec!["chr1".to_string()], + ) + .unwrap(); + let first = Alignment { + contig_id: 0, + contig_start: 100, + cigar: Cigar::from_str("40=").unwrap(), + edit_distance: 0, + soft_clip_left: 0, + soft_clip_right: 70, + score: 60, + length: 40, + is_revcomp: false, + gapped: false, + anchors: 0, + collisions: 0, + }; + let second = Alignment { + contig_id: 0, + contig_start: 10, + cigar: Cigar::from_str("70=").unwrap(), + edit_distance: 0, + soft_clip_left: 40, + soft_clip_right: 0, + score: 55, + length: 70, + is_revcomp: true, + gapped: false, + anchors: 0, + collisions: 0, + }; + + let tags = build_sa_tags(&[first.clone(), second], 60, &refseq, true); + assert_eq!(tags[0].as_deref(), Some("chr1,11,-,40S70=,60,0;")); + assert_eq!(tags[1].as_deref(), Some("chr1,101,+,40=70S,60,0;")); + + assert_eq!(build_sa_tags(&[first], 60, &refseq, true), vec![None]); + } + #[test] fn count_best_alignment_pairs_works() { let mut pairs = vec![]; diff --git a/src/piecewisealigner.rs b/src/piecewisealigner.rs index ba02953c..13cb4c60 100644 --- a/src/piecewisealigner.rs +++ b/src/piecewisealigner.rs @@ -2,7 +2,7 @@ use crate::{ aligner::{AlignmentInfo, Scores, hamming_align_global}, chainer::Anchor, cigar::CigarOperation, - simdaligner::{AlignmentResult, SimdAligner}, + simdaligner::{AlignmentResult, SimdAligner, SplitReferenceAlignment}, }; use std::cell::RefCell; @@ -318,6 +318,21 @@ impl PiecewiseAligner { None } } + + pub fn realign_insertion( + &self, + inserted: &[u8], + left_reference: &[u8], + right_reference: &[u8], + band: usize, + ) -> SplitReferenceAlignment { + self.simd_aligner.borrow_mut().split_reference_alignment( + inserted, + left_reference, + right_reference, + Some(band), + ) + } } /// Removes spurious anchors from a chain of anchor points. diff --git a/tests/phix.dup.fastq b/tests/phix.dup.fastq new file mode 100644 index 00000000..678f5322 --- /dev/null +++ b/tests/phix.dup.fastq @@ -0,0 +1,16 @@ +@dup60 SRR1377138.1 dup=60 +NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC ++ +#8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# +@dup80 SRR1377138.7 dup=80 +NCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCAAAGCGGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGCTTAATAGAGGCCAAAGCGGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCC ++ +#8ACBGGGGGGEGGGEDEGFEGEGGGGGCFGGGGGFDGGCCFGGFCFDFEGGFEFFGFEGGGGGGGGGGGFEFFEGGGEGGGGGGGGGGGGGGGGGGFG8=FFFGGGGGGGGGGGGGGG9BA,.06<4AFFF?>008:64 +@dup30 SRR1377138.4 dup=30 +NACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC ++ +#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFFGFGGFGFGFFFFFFFFFFF1A@FFFF?5@EC?,(2/67;BFFFFFB???DFBFBFFF<2:>BF0 +@nodup SRR1377138.1 dup=0 +NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC ++ +#8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# diff --git a/tests/phix.dup.sam b/tests/phix.dup.sam new file mode 100644 index 00000000..f625d791 --- /dev/null +++ b/tests/phix.dup.sam @@ -0,0 +1,8 @@ +@HD VN:1.6 SO:unsorted +@SQ SN:NC_001422.1 LN:5386 +dup60 0 NC_001422.1 4163 60 180S181= * 0 0 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:0 AS:i:372 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:1 SA:Z:NC_001422.1,4043,+,1X179=181S,60,1; +dup60 2048 NC_001422.1 4043 60 1X179=181S * 0 0 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:360 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:1 SA:Z:NC_001422.1,4163,+,180S181=,60,0; +dup80 16 NC_001422.1 256 60 191=190S * 0 0 GGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGN 46:800>?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:0 AS:i:392 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:1 SA:Z:NC_001422.1,367,-,191S189=1X,60,1; +dup80 2064 NC_001422.1 367 60 191S189=1X * 0 0 GGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGN 46:800>?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:1 AS:i:380 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:1 SA:Z:NC_001422.1,256,-,191=190S,60,0; +dup30 0 NC_001422.1 3491 60 1X138=30I162= * 0 0 NACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFFGFGGFGFGFFFFFFFFFFF1A@FFFF?5@EC?,(2/67;BFFFFFB???DFBFBFFF<2:>BF0 NM:i:31 AS:i:571 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:0 +nodup 0 NC_001422.1 4043 60 1X300= * 0 0 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 diff --git a/tests/phix.pe.sam b/tests/phix.pe.sam index e0b55d7d..b4b2e445 100644 --- a/tests/phix.pe.sam +++ b/tests/phix.pe.sam @@ -1,93 +1,93 @@ @HD VN:1.6 SO:unsorted @SQ SN:NC_001422.1 LN:5386 @RG ID:1 SM:sample LB:library -SRR1377138.1 99 NC_001422.1 4043 60 1X300= = 4151 409 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.1 147 NC_001422.1 4151 60 300=1X = 4043 -409 TCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAN #####FFB?B:?<>??<9>>>BFFFFFFFF?A4BFA?:>FFFFDFFFFBFFFF?BAFFFFFB@FFFFECFFBAFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.2 83 NC_001422.1 1723 60 300=1X = 1568 -456 TAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCN 2BB=FG,4,,9=@,DD8D8@8,@E=,@,,@F,@?,C+AFD6AD++=FF5:+99?FF>56FFFAAAC6EEE085>AC@EEF?:DBF446<:AE@=EC??<***9(6>@=@E<9?FFDF################################# NM:i:13 AS:i:492 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.3 83 NC_001422.1 344 60 31=1X211=1X56=1X = 239 -406 TACTATCTGAGTCCGATGCTGTTCAACCACTTATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTAGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTAN <<>:09BFF?2A???FBA742<<4.*.,2AFFA:=A9)6@:F@6B6=FBD@:=GGFF8**3C7CFCFFCD7EGGGEGGGGGGC=E6CGGGCGGGGFCFB?GECB8B,CCEGEBC8FGGGGGED>CC@GGGGFGGGGGF:C@FC>8DF=FGGGFCGGDF?FGDGGGGFDFFGGFADCF>=CCDC6+GFFGGGF@F=CE@CGDGFGGEDGGFCF@GFGF9FB:FFF<@C6@FFFGGGFCF;>DGGGFD+DGFFF?9DDC?FFFFF;ADFDF<7A8A=5):CAFFF@E@8@9AA@DFCCAEBEEE@######### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.4 99 NC_001422.1 3491 60 1X300= = 3616 426 NACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFFGFGGFGFGFFFFFFFFFFF1A@FFFF?5@EC?,(2/67;BFFFFFB???DFBFBFFF<2:>BF0 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.4 147 NC_001422.1 3616 60 300=1X = 3491 -426 TGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATN ####CEEFE<<;93E@311C;3CD@82>?D@=7E?>8FEEFFEFFFFFFFFFEAEFFEFEFEEFFB=BCAEFFFFFFFFFFFFFFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.5 99 NC_001422.1 2494 60 1X236=1X63= = 2606 413 NCACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGGATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGGGGGAGFGFFGFDABDFFFFFFFFFFFFEEFEEFFD:+-05871>F4:A(6444FB?:<31:2DAB?67<6A?FB>B;>8<::9AABFFFB:816B??FFBFFFFFFFFFFD?EEFFFFFFFFFFFFFFF0.044:6B0>BF>003>>:(:<>B9;914.))81.,,,4-(2466))6>>60?B?>>>24(422)C67FFFFFFF5:85B:ADEFGGGGGFGGGGC7GGGFGGGGFC?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.7 163 NC_001422.1 141 60 1X299=1X = 256 416 NTTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTT #8AF6BFFCFFF4AA>A4A4>:E>7?-55>;(>?E38*878CB6@EC7C;6C>C<)6FFF@E>2)(4179:BB?FB#### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.8 83 NC_001422.1 1254 60 124=1X132=1X42=1X = 1179 -376 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCATGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGCCTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGAN #################################?<9<464:AC;CFAF;AFFA77AFAGFGFACB73DC4CD64GGGGCGEC=>+FGGFEFGE8GGGGCE=EC7GEFEFF5>A@FFE=<)1*-..:@29@29@0:1;3=6@=(544?4)9;C>5))7).474CB)99?###### NM:i:5 AS:i:572 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.9 83 NC_001422.1 4731 60 300=1X = 4650 -382 TGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAN ?BFF?<:?FCF@FFF?EFFF@EFEFFFFEEEB?FD<<)8083:?>FFDFFECC49FFD?3<@FFFFEDEC?3E?C?0EFFFFFFF>@5FECFFGGGFGD:FGGCDGFGGGGGG>GGGGGGGDGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.11 99 NC_001422.1 5117 60 1X268=32S = 5220 270 NAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCGGAGTTTTATCGCTTCCATGACGCAGAAGTTA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGDGGGGF8FFGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGCFGGGGGGGGGGEE5EGGGGGGGGGFGGGGFDGEGDGGDGGGE7FFGGG>*?*:<>9BDECDFGF<*9@F?*7B?;F;F;B:AFFFFFF7*(03:0:AAAFFF:18?BA:82><9B>4<2BAA2A<<:?:4,.(B?C?.37;)EE<;)C?6(((;FFFFFEE?7)?9/);FDFB>A=FDAFFFFFFFDEDDCCFAGFFGGGGGGF:GGGFGGGGGFGGGGFGCGGEECDEFCCGGFGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:0 AS:i:344 na:i:2 al:i:1 ga:i:1 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.12 99 NC_001422.1 1 60 57S238=1X5= = 28 328 NAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGATGTGGC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGDCGGGGGGGGGGFGGGGGGGFGFGGFGFGFFFFFFFFFFFAFFFFFFFFFFFA3.1.48?A<:?FFFFFFBDFFFF?1GGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.13 99 NC_001422.1 5006 60 1X300= = 5049 344 NTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCFGGFGFGFFFFFFFFFFFDFFFFB:>FFFFF2.1.4::?FFFFF?BAAFFFFFFDFF>>9>9? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.13 147 NC_001422.1 5049 60 300=1X = 5006 -344 GCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGN #FFFFBFFFBD>A<::64>AAFFFB><?FFBABBAFFFFFFBAFFFFFFFFFFFFFE;@F@FFFFFFFD@FE?FFFFFFFFFFFFFEBFFFFFFFFGFFGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCC8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.14 99 NC_001422.1 66 60 1X300= = 156 391 NTCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT #8@CCGGGGGGFFGGGGGGGGGGGGGFGGGGGGGGGGGGGFGGEEFGGGGGGGGGGGGGFGDCFEFGGGGGFGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGGGGGGGGGDFGGGGGGGFGGEGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGDGGGGGGGGDGGGGGGGFEGGGGGGGFGGFFGFGGGGGGGGGFGGGFG7FGGFGDGGGGGFFCGGGGGGGGGGGGGFGFGGC>FGCF=A@FFFFFFFFFFEFFFFFFE<=/04(34:501:AB>4 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.14 147 NC_001422.1 156 60 300=1X = 66 -391 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGN ############?>BFAAA45FFFFB:7/(9>9;B@=63?FFED>52FE?>5*>852BCEEFFAA@A>8@8C>=7EFCFFEAFFFF:FAFFFFFFFFD?9*DDGGGGGDGGGGGGFGFGGFFCFFGDGFGGGGGFGFEF?GGFCGGGGGGGGGGGGFEEGFFGGFE9GGGFFGFAGGGGGGGGFAGGGFGFFFGGGGGGGEFAFFCFGGGF@GF@AE@FFCEF73?FFFFFFF3-048:BDFFAFFFFFF06>BFF######### NM:i:1 AS:i:372 na:i:1 al:i:2 ga:i:1 X0:i:1 mr:i:1 RG:Z:1 -SRR1377138.15 147 NC_001422.1 1907 60 80S186=35S = 1907 186 TTTTGTTTTCTCTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACCCTCTTTCCCTACACGACGCTCTTCCGATCTCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACAAGAACGGAAAACATCCTTCATAGAAATTTCACGN ########################A?0<6FFFB>676?:1(??BBB?FA4733(FF@@8@513?;;@>FEFEF@BEFFFFFFFFFFFFFFGCFCGFFDDGGGGGGGGGDGGGGDGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:0 AS:i:372 na:i:1 al:i:2 ga:i:1 X0:i:1 mr:i:1 RG:Z:1 -SRR1377138.16 83 NC_001422.1 2072 60 27=1X20=1X83=1X50=1X116=1X = 2012 -361 TATGTTTCTCCTGCTTATCACCTTCTTTAAGGCTTCCCATTCATTCAGCAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGAAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGTCCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGN ############################################################################################################GC;D>,5E>B*,,;98F>FE,9E4,@F@7,;CF>3,,BF7=@,3CF>,E,,F@83++3>@3++CBC,5B+68+FB,7=>=F=F,8CE@F?9E=FF;,,=,33D==@E8DG,@3DG8=2A0==96D?8=8D=D######################################################################################################## NM:i:17 AS:i:452 na:i:1 al:i:1 ga:i:1 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.17 83 NC_001422.1 820 60 13=1X286=1X = 767 -354 AAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAN ##############AB<92A<6-.1),FD>=9A??>F??45EFFFBEEFEED:GFGGFGFGDGGGGGGGGGGDCGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGFGGGGGGGGGGGGGGFGFFFFBFCGGGGGGGGGGGGFAB<:>AA-669)46:AFFFFF>B9>>>F;3?::BA216??<4 NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.18 83 NC_001422.1 1781 60 300=1X = 1681 -401 TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTN B?:::>B;960<7FA2FA:4A>9<4..4./.,::.)0>FFFF?F?<9)@@7)>65?C@7?=FGGGGGGFC95GGGGGGGE78CEEGGGGGGGGGGEDGCEGGGGCGE99GGGGGGGGGFFGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGDFFGGGGGEGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.18 163 NC_001422.1 1681 60 1X299=1X = 1781 401 NTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGG #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGFFFGGCGGGGGGGGGGGGGGGGGGGGGGGGGFFGFFFFF?DEFF>FFCF>CFFFEECFEFFFFFFFFFFFEFFFFAEFAFEFFEFCFCFDFFFFFFFF;@9;9>>0:?94::?BFF(:?22>4FFFFFFFFFGGFGFGGDGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.19 163 NC_001422.1 1100 60 1X126=1X36=1X19=1X6=1X27=1X51=1X10=1X15=1X2= = 1156 357 NCTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCCCGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAGGGTGTTAATGCCACTCCTCCCCCGACGGTTAACACTACTGGTTATATTGACCATCCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTGGTTTCAGGGTAATTTGAATATCTATACCA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC95EFGDEFFD?AFF+++4A:AFF8E,CEFDE=EFDDEFCCF9>==,D8EC,,@8=>EGGADFGGGC7CFCC+@C*;C9*;@DGGGGFA*98A;F/=A1B++4=*8))48((7@D;?E3<)634;2;2@4>F15:1)6A2?::BAD########################################### NM:i:9 AS:i:532 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.20 99 NC_001422.1 1974 60 1X300= = 2102 429 NGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGFFGFFFGF=AFFAFFFFFFFF=CCFF9>BFFFA2::2 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.20 147 NC_001422.1 2102 60 300=1X = 1974 -429 GGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCN 4B?:(0BA44<>54A960:4(0??BA?AFFFB97(64E@EFFFFFEEFEFFFEDFFFFFFFFFFFFFFFAFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.21 83 NC_001422.1 3579 60 1X30=1X268=1X = 3494 -386 CCCAATCTTTCCAAGCAACAGCAGGTTTCCGCGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTN #FFFF?FFFFFFFFFF?AFFFFF@@>;:62(+6FFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGGFGGGGGGGGGGGCGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.21 163 NC_001422.1 3494 60 1X300= = 3579 386 NAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACT #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGCCGGFFGFFFFFFFFFFFFFFFACFFFFEFFFFFFF=FFFFFFFFCFF@EFFDBFFFF@F8EEFFFFFFFF@=>;>@64>9AFF>?:AAB9<><6AFFFB??822<0(4-9A<:?:6<4.-0.*>FFFFF?FFFFF;AA6A6D>DFFFGACFGGFGFGFCGDD5DGGFFGGFB<:CDFGGDEDGFE;CGGGGGGGFAFFGGGGGGGFGGGGFGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGFGFFGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGFEFFFGGGEGFGGGGGGFGGGGGGGGGGGFFGGGGGGGGGGGEFGGGGGGGGGGGGGGGGDGGGGGGGFAGGGGGGDGGGGGGGGGGGFEGGGGGCAA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.22 163 NC_001422.1 4301 60 1X300= = 4354 354 NCTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGAC #8ABCGGCFFGFFGGFGGAFGGAFFFGGGGG7:FFFEGGGGCGDGGGCGFGF@EEFGGGGGGEGGDCFG8C>FFFGGFGCGFEFFFFCGGGFGFDDFG,@EGGG7DFGGGCEGGGGGCFFFEFGFFGGGGGGGGGGFGCFGFFCFAEFFFA5?F685A)09FEFF)9CF;389>9)))4>FEFF2AECEFEFFF?@EFFFFCE@FEFFFCCFFFFDFFF@;@AFFF######### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.24 99 NC_001422.1 4756 60 1X300= = 4832 377 NTGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFA>FFFFBBB0-1.44?FFB<=0@@>22=FBEDBA:-FCFFFFEFAFFFAEADFFFFA5FDFGG?DC>GD=?FGFGGGGDGGFGGGFGEGFGGGGFE>DEGGGFDFGGGGGGFGGGGGGGGGGGFC>GGGGGGGGGGFFFGGGGGGGGGGGGGEGGGGGGGGGCGGGGGGGGGGGGGGGGGGFGGGGGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC@A6# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.25 99 NC_001422.1 3666 60 1X300= = 3787 422 NACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATC #8ACCGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGDFF@CCGGGFFGFGFFGFGFFFA+;FBFFF>D@FFA;=CB3FFE?:/:/(/3@E@?35)75?@EFFE);).:8EF## NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.25 147 NC_001422.1 3787 60 23=1X276=1X = 3666 -422 TCGTCACTGATGCTGCTTCTGGTTTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTN ###########################?3357(DFFFFEC<@@9)?<7:->84A6=EA4FFFFFFEB9AFFEA>FD?DFAFFFFFFFFGFFDGGDCCFGGGGGGDGGFD2FFDGFA9CGGGGGGGEDD=FFGEGEGEEFDFEF>CGGGGGGGFGGGGGEGGGGGGFCGFFEB?AFBFFA7FFDFDFA9:4.1.,A>FFFDFBAFFF?FFFFFFFFB@;CFGFGGFFFGGGGGGGGGGGGGGGCGFFFGGFGGGGGGGGGGGGGGGFCGFDGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.26 163 NC_001422.1 1584 60 1X300= = 1642 359 NTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTAC #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFGFGGGGGG8DFGGFFGGGGGGGGGGCGGGFGFG=DFGFFFFFFFFFFFFFFFF56CFFFEECC@CFFFFFFEFFFF=A@FFFEFEFFFFEFFE3BFFF@FF;CEEFFFFF>CC)/39;;7=EC;@803<7??#### NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.27 83 NC_001422.1 4289 60 31=1X268=1X = 4187 -403 TGTGCTCCCCCAACTTGATATTAATAACACTTTAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTN 0FFF>>96BBAE9FFFF@FFFDFFFFGFGFGGDGFGGDGGGGGGGGGFGGGGEGGGGGGGGGGGGGGGGEGDFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGGGGGGGGGGF?GGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.27 163 NC_001422.1 4187 60 1X300= = 4289 403 NGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAG #8AA@DAFGGGGGGGGFEFEGGGGGGGGGGGGGGGGGGGFGEGGGGGFGGGGGGGGGGGGGGGFDFGGGGGGFGGGGGGGGGGGGGGGGFGGGGGGBFGGGGGGGFEFGDGGGGGGGGGGGGGGGGGFGEFFGGGFC=FGGGGGGGGGGGGGGGBEEEGGG+DFGGFFGGGGFG9AFFGECDEFFGGDGGGGGGGDGGFFFGF>BBEFFF4;B6AEAF=A3A@@BFD89CEFFFF@EFFFFB9(1);56))9((FFFFEAFFFEAFDDFFFFEEFAFFFFFCDGGGGGGGFDDFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.29 99 NC_001422.1 155 60 1X300= = 250 396 NGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAG #8BCCGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGGFGGGGGGGDGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGEGGGGGFGFGGFGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFACFGGFGEFGGGGFEGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGGGGG6C<>=4A:AEDFFFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGFCGEGGGGGGGGGGD9FGGGGGGGGGFGFFGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGFCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.30 81 NC_001422.1 1 60 97S203=1X = 5176 5386 TTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACN FFFBFF?4(>7,.6FF?;96FFFB>??450.3:FFFFFBB,>EGFGGGGFGCEGCFEEEGDEGGGFGGGCF4CFGGGGC3*85CFF4:3?@FF6*.9*96<4:>?F24><?FB9AAFBFF2796;??BFFF99:A96-)))46?F>(:0<>4>5<2))-5>BFBFBFFFAF?FF9B? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.31 147 NC_001422.1 4401 60 300=1X = 4320 -382 GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATN ################AA4)19>B913<96.))6<6<976;6B>9EGGGGGGGGGFGFEF9GEGGGGGGGGGDGGGFGGGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.32 99 NC_001422.1 1433 60 1X268=1X31= = 1487 355 NCCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGCCCTTTACTTGTCATGCGCTCTAATCTCTGGG #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFFFFFFFFFF*.:6=;CFFFFFEFFEF9;(3:AFFB)66>?: NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.32 147 NC_001422.1 1487 60 300=1X = 1433 -355 TGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTN 186?FFFFAAE@;E@DFBFFB@@FFFFF@FFEC=EF@6:DEEFFF@A@=FFFFFBBA:**=ECFFFFFFEFEFFFFFFFFFFFFFFFFGFCGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.33 99 NC_001422.1 3817 60 1X268=1X31= = 3887 371 NTATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTCCTCAATCCCCAATGCTTGGCTTCCATAAGCA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGFGGFGGGGGGFFFGGFGFGFFFAFFFFFFBDFEFFEFFFFFFC,)217@EFFFDF<@EFFFF?FFFDE####### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.33 147 NC_001422.1 3887 60 1X299=1X = 3817 -371 GGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAAN #?:25FFFA<-42FABAFFF?9FFFFFFEE>A>4FFFFFFFFFFFFFFFEFGFFGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.34 83 NC_001422.1 812 60 21=1X9=1X268=1X = 774 -339 CGTGCGTCAAAAATTACGTGCAGAAGGAGTGGTGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCN 3>>BBD?>FFFFFBF?:BFBFFFFF?87:8.,AFFFFFFFBBBFFFFFFFFFFFFFFFGFGGFGDGGGGGGGGGGGGGGGGGGEDGGGGGGGGFFGGGGGGGFFCGGGGFFGGGGGGGDGGGFGGGE?GGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGDGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.34 163 NC_001422.1 774 60 1X58=1X215=1X25= = 812 339 NCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCTATCTTGGCTTCCTTGCTGGTCAGAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGG8FGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGG?FCGEEGGGGDFFGGGGFGGFGGGGGGGGGGGGG>EE@EGGFFC@FFFGFCG9EGGFGGGGGGGGGGGGGGGGGGDFFGFFFFEDFEFFFFFFFFEFFF<<A;>B:0203>DFFF))62<<42?B??F2<6:>4?7A#### NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.35 83 NC_001422.1 4037 60 300=1X = 3960 -378 TATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAN 2?FFB::0FFFFFA)466<74)<4)FFFA:9>6<0AABABFFFFB?AFBFFBA:.);*B5FEBFFGFFGGGGGDGGGGGGGGGFCDFFGFFGGGGGGGGGGGGGGGGGGEGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:0 AS:i:538 na:i:1 al:i:1 ga:i:1 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.37 83 NC_001422.1 793 60 31=1X8=1X259=1X = 702 -392 TTACTGACGCAGAAGAAAACGTGCGTCAAAAGTTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATN >FFFFFFFBBFFDAFF?FFB9FFFB<6..1.13FFFFFFFFFFFBFFF?FFFFFFFFFGFGGFGFGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.37 163 NC_001422.1 702 60 1X130=1X97=1X27=1X43= = 793 392 NAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCACGTCTTTGGTATGTAGGTGGTCAACAAATTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTAT #8ACCGGGGGGGGGGGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGEEGGGGGGGGGFGGGGGGGGGGFGAFGGGCFFGGGGGGGG8DFE7CFGGGGGGGGGGGFGG,@FGDFFGGDFFGGGGGFFAFGGA9BCFCFGGGFGGGEGGDGDEGDGGGFFCGDGGGGGG5DFDD5AFGFFFFFFF9=FFFFFF5:<(06?F######################################################################## NM:i:4 AS:i:582 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.38 83 NC_001422.1 4940 60 20=1X8=1X1=1X268=1X = 4838 -403 TTGGTTGTGGCCTGTTGATGGTAAAGGTGGGGCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAN ######BF??6FF?8.()44)D<80<42-).1444@C?FFFFEFFFFFFFFFFFFFF::FGCFGFGFGC84F6GFFGGCFCGGGGGF5DF:DGGGGGGGGGGGGGFCGGGFGFFGGFFFGGAGGE>EF9GGGGGDGGGCGGGGGGGFGFFFGGGGGGGGGF>GGGGGGGGGGCEGGGGGGFFGGFGFGGGGGGFGGGGGEGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGCGGFF46@BFFFF9B<06AEFE8C>=383>6>=E=B4>@F;3113;<;(,681<33@F######################################## NM:i:7 AS:i:532 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.39 83 NC_001422.1 1791 60 300=1X = 1688 -404 GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCN :FFFFAFFFFFFAFAFFFFFFFFFFF9440-2?FBFFB@FFFFFFFFFFFFFFFFFGFGFGGFGFGGFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.39 163 NC_001422.1 1688 60 1X15=1X284= = 1791 404 NACGCTGACAACCGTCATTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCEGG8FEGGGGGGGGGGGGGGGGGGGGGCFADFFFFAFFFFFFFFFFFFFFFFFF25A@FFFE=(7>EFF?@??*8BFFFAA:??9AFFFBF??A))491;03>9>63AF9A NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.40 83 NC_001422.1 3017 60 116=1X183=1X = 2955 -363 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -SRR1377138.40 163 NC_001422.1 2955 60 1X177=1X122= = 3017 363 NTTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGT #8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))EGGGGG8#GGGGGFAFEFFFFB=6>EEEGGGGBGGGGGGG;<;7EF;@EEC9CEFF??6?EF<@EDFFF### na:i:0 al:i:0 ga:i:0 X0:i:0 mr:i:0 RG:Z:1 -rescuable.42 83 NC_001422.1 3017 60 116=1X183=1X = 2956 -362 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -rescuable.42 163 NC_001422.1 2956 60 1X6=1X6=1X6=1X6=1X6=1X6=1X6=1X13=1X6=1X6=1X6=1X6=1X6=1X6=1X13=1X6=1X6=1X13=1X6=1X6=1X13=1X20=1X6=1X6=90S = 3017 362 CTGCTTCGGCTCTTCCTGGTGCCGCCATATCTAAAGTGTTTGTAGGCGGCCAAAAAGCCGCCTTCGGTGGGATTCAAAGTGATGCGCTTGCAACCGATTACAATATTGTAGGCATGGGTAATGCTGCTATTAAGTCTGCCATTCAAGCCTCTAAAGTTCCTCACCCTGATGAGGCTGCCCCTAGTTTTGTTTCTGGCGCTATGACTAAAGGTGGTAAGGGACTTCTTGAAGATACGTTACAGGCTCGCACTTCTGCCGTCTCTGATAAGTTGCGTGATTTGGTTGGAGTTGGTGACAAGT 8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8 NM:i:25 AS:i:120 na:i:0 al:i:0 ga:i:0 X0:i:1 mr:i:1 RG:Z:1 -rescuable.43 163 NC_001422.1 2955 60 1X177=1X122= = 3137 362 NTTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGT #8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -not.rescuable 165 NC_001422.1 3017 0 * = 3017 0 GGTTTCGCAGCACCTGCACGGCGCCGTTTCTAGGACGTACATACCGGACAAGAGTATATCCGCGATGGACGGGTGATCCATGTAGGAAGTCTAGT GGGGGFFFFFFFFEEB@F29?3>EGGGGG8#GGGGGFAFEFFFFB=6>EEEGGGGBGGGGGGG;<;7EF;@EEC9CEFF??6?EF<@EDFFF### na:i:0 al:i:0 ga:i:0 X0:i:1 mr:i:0 RG:Z:1 -empty 77 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 mr:i:0 RG:Z:1 -empty 141 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 mr:i:0 RG:Z:1 +SRR1377138.1 99 NC_001422.1 4043 60 1X300= = 4151 409 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.1 147 NC_001422.1 4151 60 300=1X = 4043 -409 TCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAN #####FFB?B:?<>??<9>>>BFFFFFFFF?A4BFA?:>FFFFDFFFFBFFFF?BAFFFFFB@FFFFECFFBAFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.2 83 NC_001422.1 1723 60 300=1X = 1568 -456 TAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCN 2BB=FG,4,,9=@,DD8D8@8,@E=,@,,@F,@?,C+AFD6AD++=FF5:+99?FF>56FFFAAAC6EEE085>AC@EEF?:DBF446<:AE@=EC??<***9(6>@=@E<9?FFDF################################# NM:i:13 AS:i:492 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.3 83 NC_001422.1 344 60 31=1X211=1X56=1X = 239 -406 TACTATCTGAGTCCGATGCTGTTCAACCACTTATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTAGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTAN <<>:09BFF?2A???FBA742<<4.*.,2AFFA:=A9)6@:F@6B6=FBD@:=GGFF8**3C7CFCFFCD7EGGGEGGGGGGC=E6CGGGCGGGGFCFB?GECB8B,CCEGEBC8FGGGGGED>CC@GGGGFGGGGGF:C@FC>8DF=FGGGFCGGDF?FGDGGGGFDFFGGFADCF>=CCDC6+GFFGGGF@F=CE@CGDGFGGEDGGFCF@GFGF9FB:FFF<@C6@FFFGGGFCF;>DGGGFD+DGFFF?9DDC?FFFFF;ADFDF<7A8A=5):CAFFF@E@8@9AA@DFCCAEBEEE@######### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.4 99 NC_001422.1 3491 60 1X300= = 3616 426 NACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGG8FFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFFGFGGFGFGFFFFFFFFFFF1A@FFFF?5@EC?,(2/67;BFFFFFB???DFBFBFFF<2:>BF0 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.4 147 NC_001422.1 3616 60 300=1X = 3491 -426 TGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATN ####CEEFE<<;93E@311C;3CD@82>?D@=7E?>8FEEFFEFFFFFFFFFEAEFFEFEFEEFFB=BCAEFFFFFFFFFFFFFFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.5 99 NC_001422.1 2494 60 1X236=1X63= = 2606 413 NCACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGGATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGGGGGAGFGFFGFDABDFFFFFFFFFFFFEEFEEFFD:+-05871>F4:A(6444FB?:<31:2DAB?67<6A?FB>B;>8<::9AABFFFB:816B??FFBFFFFFFFFFFD?EEFFFFFFFFFFFFFFF0.044:6B0>BF>003>>:(:<>B9;914.))81.,,,4-(2466))6>>60?B?>>>24(422)C67FFFFFFF5:85B:ADEFGGGGGFGGGGC7GGGFGGGGFC?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.7 163 NC_001422.1 141 60 1X299=1X = 256 416 NTTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTT #8AF6BFFCFFF4AA>A4A4>:E>7?-55>;(>?E38*878CB6@EC7C;6C>C<)6FFF@E>2)(4179:BB?FB#### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.8 83 NC_001422.1 1254 60 124=1X132=1X42=1X = 1179 -376 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCATGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGCCTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGAN #################################?<9<464:AC;CFAF;AFFA77AFAGFGFACB73DC4CD64GGGGCGEC=>+FGGFEFGE8GGGGCE=EC7GEFEFF5>A@FFE=<)1*-..:@29@29@0:1;3=6@=(544?4)9;C>5))7).474CB)99?###### NM:i:5 AS:i:572 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.9 83 NC_001422.1 4731 60 300=1X = 4650 -382 TGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAN ?BFF?<:?FCF@FFF?EFFF@EFEFFFFEEEB?FD<<)8083:?>FFDFFECC49FFD?3<@FFFFEDEC?3E?C?0EFFFFFFF>@5FECFFGGGFGD:FGGCDGFGGGGGG>GGGGGGGDGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.11 99 NC_001422.1 5117 60 1X268=32S = 5220 270 NAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCGGAGTTTTATCGCTTCCATGACGCAGAAGTTA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGDGGGGF8FFGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGCFGGGGGGGGGGEE5EGGGGGGGGGFGGGGFDGEGDGGDGGGE7FFGGG>*?*:<>9BDECDFGF<*9@F?*7B?;F;F;B:AFFFFFF7*(03:0:AAAFFF:18?BA:82><9B>4<2BAA2A<<:?:4,.(B?C?.37;)EE<;)C?6(((;FFFFFEE?7)?9/);FDFB>A=FDAFFFFFFFDEDDCCFAGFFGGGGGGF:GGGFGGGGGFGGGGFGCGGEECDEFCCGGFGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:0 AS:i:344 na:i:2 al:i:1 ga:i:1 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.12 99 NC_001422.1 1 60 57S238=1X5= = 28 328 NAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGATGTGGC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGDCGGGGGGGGGGFGGGGGGGFGFGGFGFGFFFFFFFFFFFAFFFFFFFFFFFA3.1.48?A<:?FFFFFFBDFFFF?1GGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.13 99 NC_001422.1 5006 60 1X300= = 5049 344 NTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCFGGFGFGFFFFFFFFFFFDFFFFB:>FFFFF2.1.4::?FFFFF?BAAFFFFFFDFF>>9>9? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.13 147 NC_001422.1 5049 60 300=1X = 5006 -344 GCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGN #FFFFBFFFBD>A<::64>AAFFFB><?FFBABBAFFFFFFBAFFFFFFFFFFFFFE;@F@FFFFFFFD@FE?FFFFFFFFFFFFFEBFFFFFFFFGFFGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCC8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.14 99 NC_001422.1 66 60 1X300= = 156 391 NTCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT #8@CCGGGGGGFFGGGGGGGGGGGGGFGGGGGGGGGGGGGFGGEEFGGGGGGGGGGGGGFGDCFEFGGGGGFGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGGGGGGGGGDFGGGGGGGFGGEGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGDGGGGGGGGDGGGGGGGFEGGGGGGGFGGFFGFGGGGGGGGGFGGGFG7FGGFGDGGGGGFFCGGGGGGGGGGGGGFGFGGC>FGCF=A@FFFFFFFFFFEFFFFFFE<=/04(34:501:AB>4 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.14 147 NC_001422.1 156 60 300=1X = 66 -391 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGN ############?>BFAAA45FFFFB:7/(9>9;B@=63?FFED>52FE?>5*>852BCEEFFAA@A>8@8C>=7EFCFFEAFFFF:FAFFFFFFFFD?9*DDGGGGGDGGGGGGFGFGGFFCFFGDGFGGGGGFGFEF?GGFCGGGGGGGGGGGGFEEGFFGGFE9GGGFFGFAGGGGGGGGFAGGGFGFFFGGGGGGGEFAFFCFGGGF@GF@AE@FFCEF73?FFFFFFF3-048:BDFFAFFFFFF06>BFF######### NM:i:1 AS:i:372 na:i:1 al:i:2 ga:i:1 X0:i:1 du:i:0 mr:i:1 RG:Z:1 +SRR1377138.15 147 NC_001422.1 1907 60 80S186=35S = 1907 186 TTTTGTTTTCTCTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACCCTCTTTCCCTACACGACGCTCTTCCGATCTCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACAAGAACGGAAAACATCCTTCATAGAAATTTCACGN ########################A?0<6FFFB>676?:1(??BBB?FA4733(FF@@8@513?;;@>FEFEF@BEFFFFFFFFFFFFFFGCFCGFFDDGGGGGGGGGDGGGGDGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:0 AS:i:372 na:i:1 al:i:2 ga:i:1 X0:i:1 du:i:0 mr:i:1 RG:Z:1 +SRR1377138.16 83 NC_001422.1 2072 60 27=1X20=1X83=1X50=1X116=1X = 2012 -361 TATGTTTCTCCTGCTTATCACCTTCTTTAAGGCTTCCCATTCATTCAGCAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGAAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGTCCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGN ############################################################################################################GC;D>,5E>B*,,;98F>FE,9E4,@F@7,;CF>3,,BF7=@,3CF>,E,,F@83++3>@3++CBC,5B+68+FB,7=>=F=F,8CE@F?9E=FF;,,=,33D==@E8DG,@3DG8=2A0==96D?8=8D=D######################################################################################################## NM:i:17 AS:i:452 na:i:1 al:i:1 ga:i:1 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.17 83 NC_001422.1 820 60 13=1X286=1X = 767 -354 AAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAN ##############AB<92A<6-.1),FD>=9A??>F??45EFFFBEEFEED:GFGGFGFGDGGGGGGGGGGDCGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGFGGGGGGGGGGGGGGFGFFFFBFCGGGGGGGGGGGGFAB<:>AA-669)46:AFFFFF>B9>>>F;3?::BA216??<4 NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.18 83 NC_001422.1 1781 60 300=1X = 1681 -401 TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTN B?:::>B;960<7FA2FA:4A>9<4..4./.,::.)0>FFFF?F?<9)@@7)>65?C@7?=FGGGGGGFC95GGGGGGGE78CEEGGGGGGGGGGEDGCEGGGGCGE99GGGGGGGGGFFGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGDFFGGGGGEGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.18 163 NC_001422.1 1681 60 1X299=1X = 1781 401 NTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGG #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGFFFGGCGGGGGGGGGGGGGGGGGGGGGGGGGFFGFFFFF?DEFF>FFCF>CFFFEECFEFFFFFFFFFFFEFFFFAEFAFEFFEFCFCFDFFFFFFFF;@9;9>>0:?94::?BFF(:?22>4FFFFFFFFFGGFGFGGDGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.19 163 NC_001422.1 1100 60 1X126=1X36=1X19=1X6=1X27=1X51=1X10=1X15=1X2= = 1156 357 NCTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCCCGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAGGGTGTTAATGCCACTCCTCCCCCGACGGTTAACACTACTGGTTATATTGACCATCCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTGGTTTCAGGGTAATTTGAATATCTATACCA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC95EFGDEFFD?AFF+++4A:AFF8E,CEFDE=EFDDEFCCF9>==,D8EC,,@8=>EGGADFGGGC7CFCC+@C*;C9*;@DGGGGFA*98A;F/=A1B++4=*8))48((7@D;?E3<)634;2;2@4>F15:1)6A2?::BAD########################################### NM:i:9 AS:i:532 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.20 99 NC_001422.1 1974 60 1X300= = 2102 429 NGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGFFGFFFGF=AFFAFFFFFFFF=CCFF9>BFFFA2::2 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.20 147 NC_001422.1 2102 60 300=1X = 1974 -429 GGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCN 4B?:(0BA44<>54A960:4(0??BA?AFFFB97(64E@EFFFFFEEFEFFFEDFFFFFFFFFFFFFFFAFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.21 83 NC_001422.1 3579 60 1X30=1X268=1X = 3494 -386 CCCAATCTTTCCAAGCAACAGCAGGTTTCCGCGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTN #FFFF?FFFFFFFFFF?AFFFFF@@>;:62(+6FFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGGFGGGGGGGGGGGCGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.21 163 NC_001422.1 3494 60 1X300= = 3579 386 NAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACT #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGCCGGFFGFFFFFFFFFFFFFFFACFFFFEFFFFFFF=FFFFFFFFCFF@EFFDBFFFF@F8EEFFFFFFFF@=>;>@64>9AFF>?:AAB9<><6AFFFB??822<0(4-9A<:?:6<4.-0.*>FFFFF?FFFFF;AA6A6D>DFFFGACFGGFGFGFCGDD5DGGFFGGFB<:CDFGGDEDGFE;CGGGGGGGFAFFGGGGGGGFGGGGFGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGFGFFGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGFEFFFGGGEGFGGGGGGFGGGGGGGGGGGFFGGGGGGGGGGGEFGGGGGGGGGGGGGGGGDGGGGGGGFAGGGGGGDGGGGGGGGGGGFEGGGGGCAA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.22 163 NC_001422.1 4301 60 1X300= = 4354 354 NCTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGAC #8ABCGGCFFGFFGGFGGAFGGAFFFGGGGG7:FFFEGGGGCGDGGGCGFGF@EEFGGGGGGEGGDCFG8C>FFFGGFGCGFEFFFFCGGGFGFDDFG,@EGGG7DFGGGCEGGGGGCFFFEFGFFGGGGGGGGGGFGCFGFFCFAEFFFA5?F685A)09FEFF)9CF;389>9)))4>FEFF2AECEFEFFF?@EFFFFCE@FEFFFCCFFFFDFFF@;@AFFF######### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.24 99 NC_001422.1 4756 60 1X300= = 4832 377 NTGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFA>FFFFBBB0-1.44?FFB<=0@@>22=FBEDBA:-FCFFFFEFAFFFAEADFFFFA5FDFGG?DC>GD=?FGFGGGGDGGFGGGFGEGFGGGGFE>DEGGGFDFGGGGGGFGGGGGGGGGGGFC>GGGGGGGGGGFFFGGGGGGGGGGGGGEGGGGGGGGGCGGGGGGGGGGGGGGGGGGFGGGGGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC@A6# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.25 99 NC_001422.1 3666 60 1X300= = 3787 422 NACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATC #8ACCGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGDFF@CCGGGFFGFGFFGFGFFFA+;FBFFF>D@FFA;=CB3FFE?:/:/(/3@E@?35)75?@EFFE);).:8EF## NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.25 147 NC_001422.1 3787 60 23=1X276=1X = 3666 -422 TCGTCACTGATGCTGCTTCTGGTTTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTN ###########################?3357(DFFFFEC<@@9)?<7:->84A6=EA4FFFFFFEB9AFFEA>FD?DFAFFFFFFFFGFFDGGDCCFGGGGGGDGGFD2FFDGFA9CGGGGGGGEDD=FFGEGEGEEFDFEF>CGGGGGGGFGGGGGEGGGGGGFCGFFEB?AFBFFA7FFDFDFA9:4.1.,A>FFFDFBAFFF?FFFFFFFFB@;CFGFGGFFFGGGGGGGGGGGGGGGCGFFFGGFGGGGGGGGGGGGGGGFCGFDGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.26 163 NC_001422.1 1584 60 1X300= = 1642 359 NTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTAC #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFGFGGGGGG8DFGGFFGGGGGGGGGGCGGGFGFG=DFGFFFFFFFFFFFFFFFF56CFFFEECC@CFFFFFFEFFFF=A@FFFEFEFFFFEFFE3BFFF@FF;CEEFFFFF>CC)/39;;7=EC;@803<7??#### NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.27 83 NC_001422.1 4289 60 31=1X268=1X = 4187 -403 TGTGCTCCCCCAACTTGATATTAATAACACTTTAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTN 0FFF>>96BBAE9FFFF@FFFDFFFFGFGFGGDGFGGDGGGGGGGGGFGGGGEGGGGGGGGGGGGGGGGEGDFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGGGGGGGGGGF?GGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.27 163 NC_001422.1 4187 60 1X300= = 4289 403 NGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAG #8AA@DAFGGGGGGGGFEFEGGGGGGGGGGGGGGGGGGGFGEGGGGGFGGGGGGGGGGGGGGGFDFGGGGGGFGGGGGGGGGGGGGGGGFGGGGGGBFGGGGGGGFEFGDGGGGGGGGGGGGGGGGGFGEFFGGGFC=FGGGGGGGGGGGGGGGBEEEGGG+DFGGFFGGGGFG9AFFGECDEFFGGDGGGGGGGDGGFFFGF>BBEFFF4;B6AEAF=A3A@@BFD89CEFFFF@EFFFFB9(1);56))9((FFFFEAFFFEAFDDFFFFEEFAFFFFFCDGGGGGGGFDDFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.29 99 NC_001422.1 155 60 1X300= = 250 396 NGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAG #8BCCGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGGFGGGGGGGDGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGEGGGGGFGFGGFGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFACFGGFGEFGGGGFEGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGGGGG6C<>=4A:AEDFFFFFFFFFFFFFGFFGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGFCGEGGGGGGGGGGD9FGGGGGGGGGFGFFGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGFCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.30 81 NC_001422.1 1 60 97S203=1X = 5176 5386 TTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACN FFFBFF?4(>7,.6FF?;96FFFB>??450.3:FFFFFBB,>EGFGGGGFGCEGCFEEEGDEGGGFGGGCF4CFGGGGC3*85CFF4:3?@FF6*.9*96<4:>?F24><?FB9AAFBFF2796;??BFFF99:A96-)))46?F>(:0<>4>5<2))-5>BFBFBFFFAF?FF9B? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.31 147 NC_001422.1 4401 60 300=1X = 4320 -382 GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATN ################AA4)19>B913<96.))6<6<976;6B>9EGGGGGGGGGFGFEF9GEGGGGGGGGGDGGGFGGGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.32 99 NC_001422.1 1433 60 1X268=1X31= = 1487 355 NCCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGCCCTTTACTTGTCATGCGCTCTAATCTCTGGG #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFFFFFFFFFF*.:6=;CFFFFFEFFEF9;(3:AFFB)66>?: NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.32 147 NC_001422.1 1487 60 300=1X = 1433 -355 TGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTN 186?FFFFAAE@;E@DFBFFB@@FFFFF@FFEC=EF@6:DEEFFF@A@=FFFFFBBA:**=ECFFFFFFEFEFFFFFFFFFFFFFFFFGFCGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.33 99 NC_001422.1 3817 60 1X268=1X31= = 3887 371 NTATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTCCTCAATCCCCAATGCTTGGCTTCCATAAGCA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGFGGFGGGGGGFFFGGFGFGFFFAFFFFFFBDFEFFEFFFFFFC,)217@EFFFDF<@EFFFF?FFFDE####### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.33 147 NC_001422.1 3887 60 1X299=1X = 3817 -371 GGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAAN #?:25FFFA<-42FABAFFF?9FFFFFFEE>A>4FFFFFFFFFFFFFFFEFGFFGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.34 83 NC_001422.1 812 60 21=1X9=1X268=1X = 774 -339 CGTGCGTCAAAAATTACGTGCAGAAGGAGTGGTGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCN 3>>BBD?>FFFFFBF?:BFBFFFFF?87:8.,AFFFFFFFBBBFFFFFFFFFFFFFFFGFGGFGDGGGGGGGGGGGGGGGGGGEDGGGGGGGGFFGGGGGGGFFCGGGGFFGGGGGGGDGGGFGGGE?GGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGDGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.34 163 NC_001422.1 774 60 1X58=1X215=1X25= = 812 339 NCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCTATCTTGGCTTCCTTGCTGGTCAGAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGG8FGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGG?FCGEEGGGGDFFGGGGFGGFGGGGGGGGGGGGG>EE@EGGFFC@FFFGFCG9EGGFGGGGGGGGGGGGGGGGGGDFFGFFFFEDFEFFFFFFFFEFFF<<A;>B:0203>DFFF))62<<42?B??F2<6:>4?7A#### NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.35 83 NC_001422.1 4037 60 300=1X = 3960 -378 TATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAN 2?FFB::0FFFFFA)466<74)<4)FFFA:9>6<0AABABFFFFB?AFBFFBA:.);*B5FEBFFGFFGGGGGDGGGGGGGGGFCDFFGFFGGGGGGGGGGGGGGGGGGEGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:0 AS:i:538 na:i:1 al:i:1 ga:i:1 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.37 83 NC_001422.1 793 60 31=1X8=1X259=1X = 702 -392 TTACTGACGCAGAAGAAAACGTGCGTCAAAAGTTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATN >FFFFFFFBBFFDAFF?FFB9FFFB<6..1.13FFFFFFFFFFFBFFF?FFFFFFFFFGFGGFGFGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.37 163 NC_001422.1 702 60 1X130=1X97=1X27=1X43= = 793 392 NAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCACGTCTTTGGTATGTAGGTGGTCAACAAATTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTAT #8ACCGGGGGGGGGGGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGEEGGGGGGGGGFGGGGGGGGGGFGAFGGGCFFGGGGGGGG8DFE7CFGGGGGGGGGGGFGG,@FGDFFGGDFFGGGGGFFAFGGA9BCFCFGGGFGGGEGGDGDEGDGGGFFCGDGGGGGG5DFDD5AFGFFFFFFF9=FFFFFF5:<(06?F######################################################################## NM:i:4 AS:i:582 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.38 83 NC_001422.1 4940 60 20=1X8=1X1=1X268=1X = 4838 -403 TTGGTTGTGGCCTGTTGATGGTAAAGGTGGGGCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAN ######BF??6FF?8.()44)D<80<42-).1444@C?FFFFEFFFFFFFFFFFFFF::FGCFGFGFGC84F6GFFGGCFCGGGGGF5DF:DGGGGGGGGGGGGGFCGGGFGFFGGFFFGGAGGE>EF9GGGGGDGGGCGGGGGGGFGFFFGGGGGGGGGF>GGGGGGGGGGCEGGGGGGFFGGFGFGGGGGGFGGGGGEGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGCGGFF46@BFFFF9B<06AEFE8C>=383>6>=E=B4>@F;3113;<;(,681<33@F######################################## NM:i:7 AS:i:532 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.39 83 NC_001422.1 1791 60 300=1X = 1688 -404 GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCN :FFFFAFFFFFFAFAFFFFFFFFFFF9440-2?FBFFB@FFFFFFFFFFFFFFFFFGFGFGGFGFGGFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.39 163 NC_001422.1 1688 60 1X15=1X284= = 1791 404 NACGCTGACAACCGTCATTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCEGG8FEGGGGGGGGGGGGGGGGGGGGGCFADFFFFAFFFFFFFFFFFFFFFFFF25A@FFFE=(7>EFF?@??*8BFFFAA:??9AFFFBF??A))491;03>9>63AF9A NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.40 83 NC_001422.1 3017 60 116=1X183=1X = 2955 -363 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +SRR1377138.40 163 NC_001422.1 2955 60 1X177=1X122= = 3017 363 NTTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGT #8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))EGGGGG8#GGGGGFAFEFFFFB=6>EEEGGGGBGGGGGGG;<;7EF;@EEC9CEFF??6?EF<@EDFFF### na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 mr:i:0 RG:Z:1 +rescuable.42 83 NC_001422.1 3017 60 116=1X183=1X = 2956 -362 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +rescuable.42 163 NC_001422.1 2956 60 1X6=1X6=1X6=1X6=1X6=1X6=1X6=1X13=1X6=1X6=1X6=1X6=1X6=1X6=1X13=1X6=1X6=1X13=1X6=1X6=1X13=1X20=1X6=1X6=90S = 3017 362 CTGCTTCGGCTCTTCCTGGTGCCGCCATATCTAAAGTGTTTGTAGGCGGCCAAAAAGCCGCCTTCGGTGGGATTCAAAGTGATGCGCTTGCAACCGATTACAATATTGTAGGCATGGGTAATGCTGCTATTAAGTCTGCCATTCAAGCCTCTAAAGTTCCTCACCCTGATGAGGCTGCCCCTAGTTTTGTTTCTGGCGCTATGACTAAAGGTGGTAAGGGACTTCTTGAAGATACGTTACAGGCTCGCACTTCTGCCGTCTCTGATAAGTTGCGTGATTTGGTTGGAGTTGGTGACAAGT 8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8 NM:i:25 AS:i:120 na:i:0 al:i:0 ga:i:0 X0:i:1 du:i:0 mr:i:1 RG:Z:1 +rescuable.43 163 NC_001422.1 2955 60 1X177=1X122= = 3137 362 NTTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGT #8BCCGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEFGGGCFGGGGFGGGGGGGGGGGGGGGGFGGGFFCGGGFGGGGGGGGGGGGGGGFGGDEG>C9:FCFFDFGCFGGGGGGFFGFFFFF4AAFFFFFFFFFFFFFBEFFFFFE=@@8C@3>BF=4=>;?6?@F@;E:BFF?F6?F?)))?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +not.rescuable 165 NC_001422.1 3017 0 * = 3017 0 GGTTTCGCAGCACCTGCACGGCGCCGTTTCTAGGACGTACATACCGGACAAGAGTATATCCGCGATGGACGGGTGATCCATGTAGGAAGTCTAGT GGGGGFFFFFFFFEEB@F29?3>EGGGGG8#GGGGGFAFEFFFFB=6>EEEGGGGBGGGGGGG;<;7EF;@EEC9CEFF??6?EF<@EDFFF### na:i:0 al:i:0 ga:i:0 X0:i:1 du:i:0 mr:i:0 RG:Z:1 +empty 77 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 mr:i:0 RG:Z:1 +empty 141 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 mr:i:0 RG:Z:1 diff --git a/tests/phix.se.sam b/tests/phix.se.sam index a78c8796..f091aab6 100644 --- a/tests/phix.se.sam +++ b/tests/phix.se.sam @@ -1,48 +1,48 @@ @HD VN:1.6 SO:unsorted @SQ SN:NC_001422.1 LN:5386 @RG ID:1 SM:sample LB:library -SRR1377138.1 0 NC_001422.1 4043 60 1X300= * 0 0 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.2 16 NC_001422.1 1723 60 300=1X * 0 0 TAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCN 2B<<>:09BFF?2A???FBA742<<4.*.,2AFFA:=A9)6@:F@6B6=FBD@:=GGFF8**3C7CFCFFCD7EGGGEGGGGGGC=E6CGGGCGGGGFCFB?GECB8B,CCEGEBC8FGGGGGED>CC@GGGGFGGGGGF:C@FC>8DF=FGGGFCGGDF?FGDGGGGFDFFGGFADCF>=CCDC6+GFFGGGF@F=CE@CGDGFGGEDGGFCF@GFGF9FB:FFF<@C6@FFFGGGFCF;BF0 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.5 0 NC_001422.1 2494 60 1X236=1X63= * 0 0 NCACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGGATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGGGGGAGFGFFGFDABDFFFFFFFFFFFFEEFEEFFD:+-05871>F4:A(6444EEFFFFFFFFFFFFFFF0.044:6B0>BF>003>>:(:<>B?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.8 16 NC_001422.1 1254 60 124=1X132=1X42=1X * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCATGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGCCTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGAN #################################?<9<464:AC;CFAF;AFFA77AFAGFGFACB73DC4CD64GGGGCGEC=>+FGGFEFGE8GGGGCE=EC7GEF*?*:<>9BDECDFGF<*9@F?*7B?;F;F;B:AFFFFFF7*(03:0:AAAFFF:18?BA:FFFFF2.1.4::?FFFFF?BAAFFFFFFDFF>>9>9? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.14 0 NC_001422.1 66 60 1X300= * 0 0 NTCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT #8@CCGGGGGGFFGGGGGGGGGGGGGFGGGGGGGGGGGGGFGGEEFGGGGGGGGGGGGGFGDCFEFGGGGGFGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGGGGGGGGGDFGGGGGGGFGGEGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGDGGGGGGGGDGGGGGGGFEGGGGGGGFGGFFGFGGGGGGGGGFGGGFG7FGGFGDGGGGGFFCGGGGGGGGGGGGGFGFGGC>FGCF=A@FFFFFFFFFFEFFFFFFE<=/04(34:501:AB>4 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.15 0 NC_001422.1 1907 60 1X185=115S * 0 0 NTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACAAGAACGGAAAACATCCTTCATAGAAATTTCACGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAGATA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFGFFFFFFFFFFFFF>73?FFFFFFF3-048:BDFFAFFFFFF06>BFF######### NM:i:1 AS:i:372 na:i:1 al:i:1 ga:i:1 X0:i:0 RG:Z:1 -SRR1377138.16 16 NC_001422.1 2072 60 27=1X20=1X83=1X50=1X116=1X * 0 0 TATGTTTCTCCTGCTTATCACCTTCTTTAAGGCTTCCCATTCATTCAGCAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGAAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGTCCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGN ############################################################################################################GC;D>,5E>B*,,;98F>FE,9E4,@F@7,;CF>3,,BF7=@,3CF>,E,,F@83++3>@3++CBC,5B+68+FB,7=>=F=F,B<92A<6-.1),FD>=9A??>F??45EFFFBEEFEED:GFGGFGFGDGGGGGGGGGGDCGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGFGGGGGGGGGGGGGGFGFFFFBFCGGGGGGGGGGGGFB;960<7FA2FA:4A>9<4..4./.,::.)0>FFFF?F?<9)@@7)>65?C@7?=FGGGGGGFC95GGGGGGGE78CEEGGGGGGGGGGEDGCEGGGGCGE99GGGGGGGGGFFGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGDFFGGGGGEGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.19 16 NC_001422.1 1156 60 300=1X * 0 0 TTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTN ##############BFFFDDCC3;?55;/31<755A<9FEC8A;EFFFF=>FFFFFFFFFGGFGFGGDGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.20 0 NC_001422.1 1974 60 1X300= * 0 0 NGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGFFGFFFGF=AFFAFFFFFFFF=CCFF9>BFFFA2::2 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.21 16 NC_001422.1 3579 60 1X30=1X268=1X * 0 0 CCCAATCTTTCCAAGCAACAGCAGGTTTCCGCGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTN #FFFF?FFFFFFFFFF?AFFFFF@@>;:62(+6FFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGGFGGGGGGGGGGGCGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.22 16 NC_001422.1 4354 60 31=1X268=1X * 0 0 TTTTAGAGAACGAGAAGACGGTTACGCAGTTGTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCN <2>AFFFB??822<0(4-9A<:?:6<4.-0.*>FFFFF?FFFFF;AA6A6D>DFFFGACFGGFGFGFCGDD5DGGFFGGFB<:CDFGGDEDGFE;CGGGGGGGFAFFGGGGGGGFGGGGFGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGFGFFGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGFEFFFGGGEGFGGGGGGFGGGGGGGGGGGFFGGGGGGGGGGGEFGGGGGGGGGGGGGGGGDGGGGGGGFAGGGGGGDGGGGGGGGGGGFEGGGGGCAA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.23 16 NC_001422.1 3170 60 300=1X * 0 0 TAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAN 4FFBAA9FFFFFFFFF?FFFFFFFFD=36218CFFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGDDGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.24 0 NC_001422.1 4756 60 1X300= * 0 0 NTGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFA>FFFFBBB0-1.44?FFBFF@CCGGGFFGFGFFGFGFFFA+;FBFFF>D@FFA;=CB3FFE?:/:/(/3@E@?35)75?@EFFE);).:8EF## NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.26 16 NC_001422.1 1642 60 300=1X * 0 0 GCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATN #FFFFBDF>B?AFBFFA7FFDFDFA9:4.1.,A>FFFDFBAFFF?FFFFFFFFB@;CFGFGGFFFGGGGGGGGGGGGGGGCGFFFGGFGGGGGGGGGGGGGGGFCGFDGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.27 16 NC_001422.1 4289 60 31=1X268=1X * 0 0 TGTGCTCCCCCAACTTGATATTAATAACACTTTAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTN 0FFF>>96BBAE9FFFF@FFFDFFFFGFGFGGDGFGGDGGGGGGGGGFGGGGEGGGGGGGGGGGGGGGGEGDFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGGGGGGGGGGF?GGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.28 0 NC_001422.1 3016 60 1X116=1X183= * 0 0 NCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGFGGFGGGGGDFGGFGGGGGFGFGGFGFGFFFFFFFFFFF:FEF@@F@=FEF@8/;?9))9CCEFFFFEFFEFF<7,.6FF?;96FFFB>??450.3:FFFFFBBFBFFFAF?FF9B? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.32 0 NC_001422.1 1433 60 1X268=1X31= * 0 0 NCCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGCCCTTTACTTGTCATGCGCTCTAATCTCTGGG #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFFFFFFFFFF*.:6=;CFFFFFEFFEF9;(3:AFFB)66>?: NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.33 0 NC_001422.1 3817 60 1X268=1X31= * 0 0 NTATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTCCTCAATCCCCAATGCTTGGCTTCCATAAGCA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGFGGFGGGGGGFFFGGFGFGFFFAFFFFFFBDFEFFEFFFFFFC,)217@EFFFDF<@EFFFF?FFFDE####### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.34 16 NC_001422.1 812 60 21=1X9=1X268=1X * 0 0 CGTGCGTCAAAAATTACGTGCAGAAGGAGTGGTGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCN 3>>BBD?>FFFFFBF?:BFBFFFFF?87:8.,AFFFFFFFBBBFFFFFFFFFFFFFFFGFGGFGDGGGGGGGGGGGGGGGGGGEDGGGGGGGGFFGGGGGGGFFCGGGGFFGGGGGGGDGGGFGGGE?GGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGDGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.35 16 NC_001422.1 4037 60 300=1X * 0 0 TATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAN 2?FFB::0FFFFFAFFFFFFFBBFFDAFF?FFB9FFFB<6..1.13FFFFFFFFFFFBFFF?FFFFFFFFFGFGGFGFGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -SRR1377138.38 16 NC_001422.1 4940 60 20=1X8=1X1=1X268=1X * 0 0 TTGGTTGTGGCCTGTTGATGGTAAAGGTGGGGCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAN ######BF??6FF?8.()44)D<80<42-).1444@C?FFFFEFFFFFFFFFFFFFF::FGCFGFGFGC84F6GFFGGCFCGGGGGF5DF:DGGGGGGGGGGGGGFCGGGFGFFGGFFFGGAGGE>EF9GGGGGDGGGCGGGGGGGFGFFFGGGGGGGGGF>GGGGGGGGGGCEGGGGGGFFGGFGFGGGGGGFGGGGGEGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGCGGF?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -unmappable.41 4 * 0 0 * * 0 0 TGCATGCAGTACGTGCTCGCCGTAGGTTGTGGCTCATTCCTGCAACACGTTCCCGAAACGCCCAATAGCACCCCGTCGGTATAGAGCATACCCGA GGGGG3GGCGG?GGGG4GGGGGG8#GGGGGGGGGBGGGGGGGGGGGGGGGFGGGGGGGGGGGG@GGGGGGGGFGGGGGG7GDGGGGGGGGGG### na:i:0 al:i:0 ga:i:0 X0:i:0 RG:Z:1 -rescuable.42 16 NC_001422.1 3017 60 116=1X183=1X * 0 0 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -rescuable.43 4 * 0 0 * * 0 0 ATAAGATCAGAAAATACAGCAGCAAAATAAACACGAGTATACTTTACTTTATCAGAGGCAAACTTACCACAAAGTACAACAAAATAAAGCAACTTATCAGAAACGACAGAAGTGCAAGCCAGCAAAGTACATTCAAGAAGACCTTAACCAACTTTAGCCAAAGCAACAGAAACAAAACTAAGGACAGCCTAATCAAGGTTAGGAAAATTAAAGCCATGAAAGGCAAATTTAATACAAGCAACACCAATGCATACAATATTATTATAGGTAACAAGAACATAACCTAGAATACCACAGGAG 8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGFGGGGGGGGGGGGGGD7?>DFGGGGFGFGGFGFGFFFFFFFFFFFFFEFCEFFFFEF;+,26CEFDF;@<@EFFFFBFFFBF?BFFFFF6 na:i:0 al:i:0 ga:i:0 X0:i:0 RG:Z:1 -not.rescuable 16 NC_001422.1 3017 60 116=1X183=1X * 0 0 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 RG:Z:1 -empty 4 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 RG:Z:1 +SRR1377138.1 0 NC_001422.1 4043 60 1X300= * 0 0 NGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGAC #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFDBFFFFFFF?:CEF<1397@EFEEEFFFFF@FFF@FFFFFF>FFF# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.2 16 NC_001422.1 1723 60 300=1X * 0 0 TAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCN 2B<<>:09BFF?2A???FBA742<<4.*.,2AFFA:=A9)6@:F@6B6=FBD@:=GGFF8**3C7CFCFFCD7EGGGEGGGGGGC=E6CGGGCGGGGFCFB?GECB8B,CCEGEBC8FGGGGGED>CC@GGGGFGGGGGF:C@FC>8DF=FGGGFCGGDF?FGDGGGGFDFFGGFADCF>=CCDC6+GFFGGGF@F=CE@CGDGFGGEDGGFCF@GFGF9FB:FFF<@C6@FFFGGGFCF;BF0 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.5 0 NC_001422.1 2494 60 1X236=1X63= * 0 0 NCACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGGATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCC #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGGGGGAGFGFFGFDABDFFFFFFFFFFFFEEFEEFFD:+-05871>F4:A(6444EEFFFFFFFFFFFFFFF0.044:6B0>BF>003>>:(:<>B?FFFA>:5)9FFFFDAAB<4<60.,AB>FFFFDFFEFA6FFFFFFA8=FGFCFCGFGFF7CGGGGFGGGGFECCGGGGGGGGGGGGGGGGGGGEGGGGGGGFFFGGGGGFEFGGCGGGGGGGGFGEAFGGGFGGGGGGGGGGFCGFFGEGGGGGGGGFGGGGGGGGGDFCFFF<9GGGGGGGGGGGGGGGFFF=8GFGGGGGGGGGGGGGGGGGGEGGGEFFEFGGGGGGGGGGGEFGFFEFGGEFDFCFGGFCCGGDFGGGGGFCGGGGGEGEFGEDEGGGEGGGGGGBCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.8 16 NC_001422.1 1254 60 124=1X132=1X42=1X * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCATGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGCCTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGAN #################################?<9<464:AC;CFAF;AFFA77AFAGFGFACB73DC4CD64GGGGCGEC=>+FGGFEFGE8GGGGCE=EC7GEF*?*:<>9BDECDFGF<*9@F?*7B?;F;F;B:AFFFFFF7*(03:0:AAAFFF:18?BA:FFFFF2.1.4::?FFFFF?BAAFFFFFFDFF>>9>9? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.14 0 NC_001422.1 66 60 1X300= * 0 0 NTCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT #8@CCGGGGGGFFGGGGGGGGGGGGGFGGGGGGGGGGGGGFGGEEFGGGGGGGGGGGGGFGDCFEFGGGGGFGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGGGGGGGGGDFGGGGGGGFGGEGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGDGGGGGGGGDGGGGGGGFEGGGGGGGFGGFFGFGGGGGGGGGFGGGFG7FGGFGDGGGGGFFCGGGGGGGGGGGGGFGFGGC>FGCF=A@FFFFFFFFFFEFFFFFFE<=/04(34:501:AB>4 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.15 0 NC_001422.1 1907 60 1X185=115S * 0 0 NTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACAAGAACGGAAAACATCCTTCATAGAAATTTCACGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAGATA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFGFFFFFFFFFFFFF>73?FFFFFFF3-048:BDFFAFFFFFF06>BFF######### NM:i:1 AS:i:372 na:i:1 al:i:1 ga:i:1 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.16 16 NC_001422.1 2072 60 27=1X20=1X83=1X50=1X116=1X * 0 0 TATGTTTCTCCTGCTTATCACCTTCTTTAAGGCTTCCCATTCATTCAGCAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGAAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGTCCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGN ############################################################################################################GC;D>,5E>B*,,;98F>FE,9E4,@F@7,;CF>3,,BF7=@,3CF>,E,,F@83++3>@3++CBC,5B+68+FB,7=>=F=F,B<92A<6-.1),FD>=9A??>F??45EFFFBEEFEED:GFGGFGFGDGGGGGGGGGGDCGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGFGGGGGGGGGGGGGGFGFFFFBFCGGGGGGGGGGGGFB;960<7FA2FA:4A>9<4..4./.,::.)0>FFFF?F?<9)@@7)>65?C@7?=FGGGGGGFC95GGGGGGGE78CEEGGGGGGGGGGEDGCEGGGGCGE99GGGGGGGGGFFGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGDFFGGGGGEGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.19 16 NC_001422.1 1156 60 300=1X * 0 0 TTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTN ##############BFFFDDCC3;?55;/31<755A<9FEC8A;EFFFF=>FFFFFFFFFGGFGFGGDGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.20 0 NC_001422.1 1974 60 1X300= * 0 0 NGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFGFFGFFFGF=AFFAFFFFFFFF=CCFF9>BFFFA2::2 NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.21 16 NC_001422.1 3579 60 1X30=1X268=1X * 0 0 CCCAATCTTTCCAAGCAACAGCAGGTTTCCGCGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTN #FFFF?FFFFFFFFFF?AFFFFF@@>;:62(+6FFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGGFGGGGGGGGGGGCGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.22 16 NC_001422.1 4354 60 31=1X268=1X * 0 0 TTTTAGAGAACGAGAAGACGGTTACGCAGTTGTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCN <2>AFFFB??822<0(4-9A<:?:6<4.-0.*>FFFFF?FFFFF;AA6A6D>DFFFGACFGGFGFGFCGDD5DGGFFGGFB<:CDFGGDEDGFE;CGGGGGGGFAFFGGGGGGGFGGGGFGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGFGFFGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGFEFFFGGGEGFGGGGGGFGGGGGGGGGGGFFGGGGGGGGGGGEFGGGGGGGGGGGGGGGGDGGGGGGGFAGGGGGGDGGGGGGGGGGGFEGGGGGCAA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.23 16 NC_001422.1 3170 60 300=1X * 0 0 TAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAN 4FFBAA9FFFFFFFFF?FFFFFFFFD=36218CFFFFFFFFFFFFFFFFFFFFFFFGFGFGGFGFGGGGGGDDGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.24 0 NC_001422.1 4756 60 1X300= * 0 0 NTGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA #8CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFA>FFFFBBB0-1.44?FFBFF@CCGGGFFGFGFFGFGFFFA+;FBFFF>D@FFA;=CB3FFE?:/:/(/3@E@?35)75?@EFFE);).:8EF## NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.26 16 NC_001422.1 1642 60 300=1X * 0 0 GCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATN #FFFFBDF>B?AFBFFA7FFDFDFA9:4.1.,A>FFFDFBAFFF?FFFFFFFFB@;CFGFGGFFFGGGGGGGGGGGGGGGCGFFFGGFGGGGGGGGGGGGGGGFCGFDGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGCCA8# NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.27 16 NC_001422.1 4289 60 31=1X268=1X * 0 0 TGTGCTCCCCCAACTTGATATTAATAACACTTTAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTN 0FFF>>96BBAE9FFFF@FFFDFFFFGFGFGGDGFGGDGGGGGGGGGFGGGGEGGGGGGGGGGGGGGGGEGDFDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGGGGGGGGGGF?GGGGGGGGGGGGCCA8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.28 0 NC_001422.1 3016 60 1X116=1X183= * 0 0 NCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAA #8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGFGGFGGGGGDFGGFGGGGGFGFGGFGFGFFFFFFFFFFF:FEF@@F@=FEF@8/;?9))9CCEFFFFEFFEFF<7,.6FF?;96FFFB>??450.3:FFFFFBBFBFFFAF?FF9B? NM:i:1 AS:i:612 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.32 0 NC_001422.1 1433 60 1X268=1X31= * 0 0 NCCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGCCCTTTACTTGTCATGCGCTCTAATCTCTGGG #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGFGFGFFFFFFFFFFFFFFFFFFFFFFFF*.:6=;CFFFFFEFFEF9;(3:AFFB)66>?: NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.33 0 NC_001422.1 3817 60 1X268=1X31= * 0 0 NTATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTCCTCAATCCCCAATGCTTGGCTTCCATAAGCA #8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGFGGFGGGGGGFFFGGFGFGFFFAFFFFFFBDFEFFEFFFFFFC,)217@EFFFDF<@EFFFF?FFFDE####### NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.34 16 NC_001422.1 812 60 21=1X9=1X268=1X * 0 0 CGTGCGTCAAAAATTACGTGCAGAAGGAGTGGTGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCN 3>>BBD?>FFFFFBF?:BFBFFFFF?87:8.,AFFFFFFFBBBFFFFFFFFFFFFFFFGFGGFGDGGGGGGGGGGGGGGGGGGEDGGGGGGGGFFGGGGGGGFFCGGGGFFGGGGGGGDGGGFGGGE?GGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGDGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.35 16 NC_001422.1 4037 60 300=1X * 0 0 TATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAN 2?FFB::0FFFFFAFFFFFFFBBFFDAFF?FFB9FFFB<6..1.13FFFFFFFFFFFBFFF?FFFFFFFFFGFGGFGFGGGGGGFCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:3 AS:i:592 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +SRR1377138.38 16 NC_001422.1 4940 60 20=1X8=1X1=1X268=1X * 0 0 TTGGTTGTGGCCTGTTGATGGTAAAGGTGGGGCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAN ######BF??6FF?8.()44)D<80<42-).1444@C?FFFFEFFFFFFFFFFFFFF::FGCFGFGFGC84F6GFFGGCFCGGGGGF5DF:DGGGGGGGGGGGGGFCGGGFGFFGGFFFGGAGGE>EF9GGGGGDGGGCGGGGGGGFGFFFGGGGGGGGGF>GGGGGGGGGGCEGGGGGGFFGGFGFGGGGGGFGGGGGEGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGCGGF?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +unmappable.41 4 * 0 0 * * 0 0 TGCATGCAGTACGTGCTCGCCGTAGGTTGTGGCTCATTCCTGCAACACGTTCCCGAAACGCCCAATAGCACCCCGTCGGTATAGAGCATACCCGA GGGGG3GGCGG?GGGG4GGGGGG8#GGGGGGGGGBGGGGGGGGGGGGGGGFGGGGGGGGGGGG@GGGGGGGGFGGGGGG7GDGGGGGGGGGG### na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +rescuable.42 16 NC_001422.1 3017 60 116=1X183=1X * 0 0 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +rescuable.43 4 * 0 0 * * 0 0 ATAAGATCAGAAAATACAGCAGCAAAATAAACACGAGTATACTTTACTTTATCAGAGGCAAACTTACCACAAAGTACAACAAAATAAAGCAACTTATCAGAAACGACAGAAGTGCAAGCCAGCAAAGTACATTCAAGAAGACCTTAACCAACTTTAGCCAAAGCAACAGAAACAAAACTAAGGACAGCCTAATCAAGGTTAGGAAAATTAAAGCCATGAAAGGCAAATTTAATACAAGCAACACCAATGCATACAATATTATTATAGGTAACAAGAACATAACCTAGAATACCACAGGAG 8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGFGGGGGGGGGGGGGGD7?>DFGGGGFGFGGFGFGFFFFFFFFFFFFFEFCEFFFFEF;+,26CEFDF;@<@EFFFFBFFFBF?BFFFFF6 na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +not.rescuable 16 NC_001422.1 3017 60 116=1X183=1X * 0 0 CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGTCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAAN 6FFFFFB?FBFFFBFFFFE@<@;FDFEC62,+;FEFFFFECFEFFFFFFFFFFFFFGFGFGGFGFGGGGFD>?7DGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCB8# NM:i:2 AS:i:602 na:i:1 al:i:1 ga:i:0 X0:i:0 du:i:0 RG:Z:1 +empty 4 * 0 0 * * 0 0 * * na:i:0 al:i:0 ga:i:0 X0:i:0 du:i:0 RG:Z:1 diff --git a/tests/test.rs b/tests/test.rs index c1af67d5..18d37f92 100644 --- a/tests/test.rs +++ b/tests/test.rs @@ -164,3 +164,21 @@ fn fail_when_create_index_is_used_without_read_length() { .assert() .failure(); } + +/// Reads carrying tandem duplications output a primary plus supplementary +/// records with SA:Z tags +#[test] +fn duplication_sam() { + let expected = String::from_utf8(read("tests/phix.dup.sam").unwrap()).unwrap(); + let mut cmd = cmd(); + let p = cmd.args([ + "--no-PG", + "--eqx", + "--details", + "--dl=50", + "tests/phix.fasta", + "tests/phix.dup.fastq", + ]); + let a = p.assert(); + a.success().stdout(predicate::str::diff(expected)); +}