breseq  version 0.33.2  revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_53_S174_L001_R1_001.good.fq718,398103,147,636100.0%143.6 bases150 bases95.0%
errorsPputida_HGL_53_S174_L001_R2_001.good.fq718,398103,147,636100.0%143.6 bases150 bases92.3%
total1,436,796206,295,272100.0%143.6 bases150 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92931.42.0100.0%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≤ 10000017670
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 ≤ 5000225
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.90394

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 input16:17:03 21 Aug 201916:17:41 21 Aug 201938 seconds
Read alignment to reference genome16:17:41 21 Aug 201916:23:15 21 Aug 20195 minutes 34 seconds
Preprocessing alignments for candidate junction identification16:23:15 21 Aug 201916:23:46 21 Aug 201931 seconds
Preliminary analysis of coverage distribution16:23:46 21 Aug 201916:24:44 21 Aug 201958 seconds
Identifying junction candidates16:24:44 21 Aug 201916:25:59 21 Aug 20191 minute 15 seconds
Re-alignment to junction candidates16:25:59 21 Aug 201916:27:19 21 Aug 20191 minute 20 seconds
Resolving best read alignments16:27:19 21 Aug 201916:28:06 21 Aug 201947 seconds
Creating BAM files16:28:06 21 Aug 201916:28:56 21 Aug 201950 seconds
Tabulating error counts16:28:56 21 Aug 201916:29:25 21 Aug 201929 seconds
Re-calibrating base error rates16:29:25 21 Aug 201916:29:26 21 Aug 20191 second
Examining read alignment evidence16:29:26 21 Aug 201916:36:09 21 Aug 20196 minutes 43 seconds
Polymorphism statistics16:36:09 21 Aug 201916:36:09 21 Aug 20190 seconds
Output16:36:09 21 Aug 201916:36:30 21 Aug 201921 seconds
Total 19 minutes 27 seconds