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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR_1261337_R1.good.fq1,407,155306,213,730100.0%217.6 bases250 bases94.5%
errorsSRR_1261337_R2.good.fq1,407,155306,213,730100.0%217.6 bases250 bases91.0%
total2,814,310612,427,460100.0%217.6 bases250 bases92.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_007779_cfb4,646,332128.14.2100.0%Escherichia coli str. K-12 substr. W3110, complete genome.
total4,646,332100.0%

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≤ 10000039672
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 ≤ 500059
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.006

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_007779_cfb0.76815

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 input06:33:47 01 Apr 202006:34:37 01 Apr 202050 seconds
Read alignment to reference genome06:34:38 01 Apr 202006:46:11 01 Apr 202011 minutes 33 seconds
Preprocessing alignments for candidate junction identification06:46:11 01 Apr 202006:47:05 01 Apr 202054 seconds
Preliminary analysis of coverage distribution06:47:05 01 Apr 202006:49:43 01 Apr 20202 minutes 38 seconds
Identifying junction candidates06:49:43 01 Apr 202006:51:11 01 Apr 20201 minute 28 seconds
Re-alignment to junction candidates06:51:11 01 Apr 202006:54:14 01 Apr 20203 minutes 3 seconds
Resolving best read alignments06:54:14 01 Apr 202006:55:42 01 Apr 20201 minute 28 seconds
Creating BAM files06:55:42 01 Apr 202006:57:59 01 Apr 20202 minutes 17 seconds
Tabulating error counts06:57:59 01 Apr 202006:58:52 01 Apr 202053 seconds
Re-calibrating base error rates06:58:52 01 Apr 202006:58:53 01 Apr 20201 second
Examining read alignment evidence06:58:53 01 Apr 202007:08:19 01 Apr 20209 minutes 26 seconds
Polymorphism statistics07:08:19 01 Apr 202007:08:19 01 Apr 20200 seconds
Output07:08:19 01 Apr 202007:08:49 01 Apr 202030 seconds
Total 35 minutes 1 second