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_36_S274_L002_R1_001.good.fq1,464,305194,426,903100.0%132.8 bases150 bases94.9%
errorsPputida_HGL_36_S274_L002_R2_001.good.fq1,464,305194,426,903100.0%132.8 bases150 bases93.1%
total2,928,610388,853,806100.0%132.8 bases150 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92958.73.7100.0%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≤ 10000053713
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 ≤ 5000757
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.038

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.81607

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 input23:49:35 20 Aug 201923:50:15 20 Aug 201940 seconds
Read alignment to reference genome23:50:16 20 Aug 201923:56:24 20 Aug 20196 minutes 8 seconds
Preprocessing alignments for candidate junction identification23:56:24 20 Aug 201923:57:04 20 Aug 201940 seconds
Preliminary analysis of coverage distribution23:57:04 20 Aug 201923:58:28 20 Aug 20191 minute 24 seconds
Identifying junction candidates23:58:28 20 Aug 201900:08:52 21 Aug 201910 minutes 24 seconds
Re-alignment to junction candidates00:08:52 21 Aug 201900:10:24 21 Aug 20191 minute 32 seconds
Resolving best read alignments00:10:24 21 Aug 201900:11:26 21 Aug 20191 minute 2 seconds
Creating BAM files00:11:26 21 Aug 201900:12:45 21 Aug 20191 minute 19 seconds
Tabulating error counts00:12:45 21 Aug 201900:13:13 21 Aug 201928 seconds
Re-calibrating base error rates00:13:13 21 Aug 201900:13:14 21 Aug 20191 second
Examining read alignment evidence00:13:14 21 Aug 201900:19:08 21 Aug 20195 minutes 54 seconds
Polymorphism statistics00:19:08 21 Aug 201900:19:08 21 Aug 20190 seconds
Output00:19:08 21 Aug 201900:19:34 21 Aug 201926 seconds
Total 29 minutes 58 seconds