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_9_59_0_S2354_L001_R1_001.good.fq464,02565,377,013100.0%140.9 bases141 bases97.5%
errorsSNFR_9_59_0_S2354_L001_R2_001.good.fq464,02565,377,013100.0%140.9 bases141 bases92.9%
total928,050130,754,026100.0%140.9 bases141 bases95.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91542.91.7100.0%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≤ 1000001722
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 ≤ 500019
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.87764

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 input11:58:36 22 Jun 201811:59:12 22 Jun 201836 seconds
Read alignment to reference genome11:59:12 22 Jun 201812:01:04 22 Jun 20181 minute 52 seconds
Preprocessing alignments for candidate junction identification12:01:04 22 Jun 201812:01:28 22 Jun 201824 seconds
Preliminary analysis of coverage distribution12:01:28 22 Jun 201812:02:06 22 Jun 201838 seconds
Identifying junction candidates12:02:06 22 Jun 201812:02:06 22 Jun 20180 seconds
Re-alignment to junction candidates12:02:06 22 Jun 201812:02:34 22 Jun 201828 seconds
Resolving best read alignments12:02:34 22 Jun 201812:03:15 22 Jun 201841 seconds
Creating BAM files12:03:15 22 Jun 201812:03:45 22 Jun 201830 seconds
Tabulating error counts12:03:45 22 Jun 201812:03:59 22 Jun 201814 seconds
Re-calibrating base error rates12:03:59 22 Jun 201812:04:01 22 Jun 20182 seconds
Examining read alignment evidence12:04:01 22 Jun 201812:12:49 22 Jun 20188 minutes 48 seconds
Polymorphism statistics12:12:49 22 Jun 201812:12:51 22 Jun 20182 seconds
Output12:12:51 22 Jun 201812:12:56 22 Jun 20185 seconds
Total 14 minutes 20 seconds