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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_91_S286_L002_R1_001.good.fq1,398,047187,543,336100.0%134.1 bases150 bases94.6%
errorsPputida_HGL_91_S286_L002_R2_001.good.fq1,398,047187,543,336100.0%134.1 bases150 bases92.9%
total2,796,094375,086,672100.0%134.1 bases150 bases93.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92956.62.7100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,929100.0%

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≤ 10000046810
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 ≤ 5000767
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.039

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.82371

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 input06:33:14 22 Aug 201906:33:52 22 Aug 201938 seconds
Read alignment to reference genome06:33:52 22 Aug 201906:39:55 22 Aug 20196 minutes 3 seconds
Preprocessing alignments for candidate junction identification06:39:55 22 Aug 201906:40:38 22 Aug 201943 seconds
Preliminary analysis of coverage distribution06:40:38 22 Aug 201906:42:09 22 Aug 20191 minute 31 seconds
Identifying junction candidates06:42:09 22 Aug 201906:49:52 22 Aug 20197 minutes 43 seconds
Re-alignment to junction candidates06:49:53 22 Aug 201906:51:24 22 Aug 20191 minute 31 seconds
Resolving best read alignments06:51:24 22 Aug 201906:52:27 22 Aug 20191 minute 3 seconds
Creating BAM files06:52:27 22 Aug 201906:53:43 22 Aug 20191 minute 16 seconds
Tabulating error counts06:53:43 22 Aug 201906:54:10 22 Aug 201927 seconds
Re-calibrating base error rates06:54:10 22 Aug 201906:54:11 22 Aug 20191 second
Examining read alignment evidence06:54:11 22 Aug 201906:59:31 22 Aug 20195 minutes 20 seconds
Polymorphism statistics06:59:31 22 Aug 201906:59:32 22 Aug 20191 second
Output06:59:32 22 Aug 201906:59:54 22 Aug 201922 seconds
Total 26 minutes 39 seconds