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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR7212220_R1.good.fq4,906,308606,849,893100.0%123.7 bases125 bases99.9%
errorsSRR7212220_R2.good.fq4,906,308592,365,421100.0%120.7 bases125 bases99.7%
total9,812,6161,199,215,314100.0%122.2 bases125 bases99.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,873186.23.5100.0%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≤ 1000001641
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 ≤ 500096
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.47959

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 input13:21:09 27 Jan 202013:25:19 27 Jan 20204 minutes 10 seconds
Read alignment to reference genome13:25:19 27 Jan 202013:41:23 27 Jan 202016 minutes 4 seconds
Preprocessing alignments for candidate junction identification13:41:23 27 Jan 202013:45:14 27 Jan 20203 minutes 51 seconds
Preliminary analysis of coverage distribution13:45:14 27 Jan 202013:50:02 27 Jan 20204 minutes 48 seconds
Identifying junction candidates13:50:02 27 Jan 202013:50:04 27 Jan 20202 seconds
Re-alignment to junction candidates13:50:04 27 Jan 202013:54:50 27 Jan 20204 minutes 46 seconds
Resolving best read alignments13:54:50 27 Jan 202014:02:24 27 Jan 20207 minutes 34 seconds
Creating BAM files14:02:24 27 Jan 202014:06:35 27 Jan 20204 minutes 11 seconds
Tabulating error counts14:06:35 27 Jan 202014:09:34 27 Jan 20202 minutes 59 seconds
Re-calibrating base error rates14:09:35 27 Jan 202014:09:37 27 Jan 20202 seconds
Examining read alignment evidence14:09:37 27 Jan 202014:35:30 27 Jan 202025 minutes 53 seconds
Polymorphism statistics14:35:30 27 Jan 202014:35:31 27 Jan 20201 second
Output14:35:31 27 Jan 202014:36:38 27 Jan 20201 minute 7 seconds
Total 1 hour 15 minutes 28 seconds