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_88_S157_L001_R1_001.good.fq2,186,267303,865,328100.0%139.0 bases150 bases94.1%
errorsPputida_HGL_88_S157_L001_R2_001.good.fq2,186,267303,865,328100.0%139.0 bases150 bases92.3%
total4,372,534607,730,656100.0%139.0 bases150 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92991.13.3100.0%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≤ 10000088590
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 ≤ 50001765
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.088

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.74859

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 input03:00:38 22 Aug 201903:01:41 22 Aug 20191 minute 3 seconds
Read alignment to reference genome03:01:41 22 Aug 201903:11:50 22 Aug 201910 minutes 9 seconds
Preprocessing alignments for candidate junction identification03:11:50 22 Aug 201903:12:55 22 Aug 20191 minute 5 seconds
Preliminary analysis of coverage distribution03:12:55 22 Aug 201903:15:00 22 Aug 20192 minutes 5 seconds
Identifying junction candidates03:15:00 22 Aug 201903:49:32 22 Aug 201934 minutes 32 seconds
Re-alignment to junction candidates03:49:32 22 Aug 201903:52:34 22 Aug 20193 minutes 2 seconds
Resolving best read alignments03:52:34 22 Aug 201903:54:18 22 Aug 20191 minute 44 seconds
Creating BAM files03:54:18 22 Aug 201903:56:11 22 Aug 20191 minute 53 seconds
Tabulating error counts03:56:11 22 Aug 201903:56:55 22 Aug 201944 seconds
Re-calibrating base error rates03:56:55 22 Aug 201903:56:57 22 Aug 20192 seconds
Examining read alignment evidence03:56:57 22 Aug 201904:05:37 22 Aug 20198 minutes 40 seconds
Polymorphism statistics04:05:37 22 Aug 201904:05:38 22 Aug 20191 second
Output04:05:38 22 Aug 201904:06:33 22 Aug 201955 seconds
Total 1 hour 5 minutes 55 seconds