breseq  version 0.32.1  revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFR_23_20_0_S2409_L001_R1_001.good.fq840,608118,495,895100.0%141.0 bases141 bases94.8%
errorsSNFR_23_20_0_S2409_L001_R2_001.good.fq840,608118,495,895100.0%141.0 bases141 bases91.3%
total1,681,216236,991,790100.0%141.0 bases141 bases93.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91576.53.2100.0%Staphylococcus aureus subsp. aureus USA300_TCH1516, complete
total2,872,915100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000002229
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500073
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.80523

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.025
Polymorphism minimum variant coverage each strand2
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.5.0

Execution Times

stepstartendelapsed
Read and reference sequence file input14:13:59 22 Jun 201814:14:57 22 Jun 201858 seconds
Read alignment to reference genome14:14:57 22 Jun 201814:18:42 22 Jun 20183 minutes 45 seconds
Preprocessing alignments for candidate junction identification14:18:42 22 Jun 201814:19:28 22 Jun 201846 seconds
Preliminary analysis of coverage distribution14:19:28 22 Jun 201814:20:41 22 Jun 20181 minute 13 seconds
Identifying junction candidates14:20:41 22 Jun 201814:20:41 22 Jun 20180 seconds
Re-alignment to junction candidates14:20:41 22 Jun 201814:21:34 22 Jun 201853 seconds
Resolving best read alignments14:21:34 22 Jun 201814:22:51 22 Jun 20181 minute 17 seconds
Creating BAM files14:22:51 22 Jun 201814:23:50 22 Jun 201859 seconds
Tabulating error counts14:23:50 22 Jun 201814:24:15 22 Jun 201825 seconds
Re-calibrating base error rates14:24:15 22 Jun 201814:24:17 22 Jun 20182 seconds
Examining read alignment evidence14:24:17 22 Jun 201814:44:05 22 Jun 201819 minutes 48 seconds
Polymorphism statistics14:44:05 22 Jun 201814:44:07 22 Jun 20182 seconds
Output14:44:07 22 Jun 201814:44:18 22 Jun 201811 seconds
Total 30 minutes 19 seconds