breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR13214404_R1.good.fq4,713,563697,464,008100.0%148.0 bases148 bases91.9%
errorsSRR13214404_R2.good.fq4,713,563697,464,008100.0%148.0 bases148 bases90.2%
total9,427,1261,394,928,016100.0%148.0 bases148 bases91.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0435232,416,272530.95.3100.0%Lactococcus lactis subsp. lactis bv. diacetylactis strain SD96
total2,416,272100.0%

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≤ 10000086868
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000132
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.017

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0435230.24298

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input10:20:19 08 Feb 202310:22:45 08 Feb 20232 minutes 26 seconds
Read alignment to reference genome10:22:46 08 Feb 202310:41:45 08 Feb 202318 minutes 59 seconds
Preprocessing alignments for candidate junction identification10:41:45 08 Feb 202310:44:07 08 Feb 20232 minutes 22 seconds
Preliminary analysis of coverage distribution10:44:07 08 Feb 202310:48:59 08 Feb 20234 minutes 52 seconds
Identifying junction candidates10:48:59 08 Feb 202310:49:37 08 Feb 202338 seconds
Re-alignment to junction candidates10:49:37 08 Feb 202310:54:46 08 Feb 20235 minutes 9 seconds
Resolving best read alignments10:54:46 08 Feb 202310:58:38 08 Feb 20233 minutes 52 seconds
Creating BAM files10:58:38 08 Feb 202311:02:45 08 Feb 20234 minutes 7 seconds
Tabulating error counts11:02:45 08 Feb 202311:04:58 08 Feb 20232 minutes 13 seconds
Re-calibrating base error rates11:04:58 08 Feb 202311:04:59 08 Feb 20231 second
Examining read alignment evidence11:04:59 08 Feb 202311:27:03 08 Feb 202322 minutes 4 seconds
Polymorphism statistics11:27:03 08 Feb 202311:27:06 08 Feb 20233 seconds
Output11:27:06 08 Feb 202311:27:53 08 Feb 202347 seconds
Total 1 hour 7 minutes 33 seconds