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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR10918231_R1.good.fq5,239,269789,496,005100.0%150.7 bases151 bases98.1%
errorsSRR10918231_R2.good.fq5,239,269789,496,005100.0%150.7 bases151 bases95.6%
total10,478,5381,578,992,010100.0%150.7 bases151 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0099745,798,534265.12.2100.0%Pseudomonas putida S12, complete genome.
total5,798,534100.0%

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≤ 10000095262
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 6
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001638
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.089

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0099740.46541

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 input14:47:55 25 Jan 202314:50:48 25 Jan 20232 minutes 53 seconds
Read alignment to reference genome14:50:48 25 Jan 202315:13:29 25 Jan 202322 minutes 41 seconds
Preprocessing alignments for candidate junction identification15:13:29 25 Jan 202315:15:54 25 Jan 20232 minutes 25 seconds
Preliminary analysis of coverage distribution15:15:54 25 Jan 202315:21:54 25 Jan 20236 minutes 0 seconds
Identifying junction candidates15:21:54 25 Jan 202315:28:39 25 Jan 20236 minutes 45 seconds
Re-alignment to junction candidates15:28:39 25 Jan 202315:38:06 25 Jan 20239 minutes 27 seconds
Resolving best read alignments15:38:06 25 Jan 202315:42:04 25 Jan 20233 minutes 58 seconds
Creating BAM files15:42:04 25 Jan 202315:47:33 25 Jan 20235 minutes 29 seconds
Tabulating error counts15:47:33 25 Jan 202315:49:43 25 Jan 20232 minutes 10 seconds
Re-calibrating base error rates15:49:43 25 Jan 202315:49:44 25 Jan 20231 second
Examining read alignment evidence15:49:44 25 Jan 202316:17:16 25 Jan 202327 minutes 32 seconds
Polymorphism statistics16:17:16 25 Jan 202316:17:18 25 Jan 20232 seconds
Output16:17:18 25 Jan 202316:18:45 25 Jan 20231 minute 27 seconds
Total 1 hour 30 minutes 50 seconds