breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR10752704_R1.good.fq7,898,431975,544,200100.0%123.5 bases125 bases99.9%
total7,898,431975,544,200100.0%123.5 bases125 bases99.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,873160.75.0100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,873100.0%

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≤ 1000001006
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 ≤ 500076
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.54997

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≤ 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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input08:52:15 27 Jan 202008:55:26 27 Jan 20203 minutes 11 seconds
Read alignment to reference genome08:55:27 27 Jan 202009:08:37 27 Jan 202013 minutes 10 seconds
Preprocessing alignments for candidate junction identification09:08:37 27 Jan 202009:11:45 27 Jan 20203 minutes 8 seconds
Preliminary analysis of coverage distribution09:11:45 27 Jan 202009:15:28 27 Jan 20203 minutes 43 seconds
Identifying junction candidates09:15:28 27 Jan 202009:15:28 27 Jan 20200 seconds
Re-alignment to junction candidates09:15:28 27 Jan 202009:19:19 27 Jan 20203 minutes 51 seconds
Resolving best read alignments09:19:19 27 Jan 202009:25:01 27 Jan 20205 minutes 42 seconds
Creating BAM files09:25:01 27 Jan 202009:28:16 27 Jan 20203 minutes 15 seconds
Tabulating error counts09:28:16 27 Jan 202009:30:41 27 Jan 20202 minutes 25 seconds
Re-calibrating base error rates09:30:41 27 Jan 202009:30:43 27 Jan 20202 seconds
Examining read alignment evidence09:30:43 27 Jan 202009:51:52 27 Jan 202021 minutes 9 seconds
Polymorphism statistics09:51:52 27 Jan 202009:51:52 27 Jan 20200 seconds
Output09:51:52 27 Jan 202009:53:02 27 Jan 20201 minute 10 seconds
Total 1 hour 46 seconds