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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR4111264_R1.good.fq338,28499,578,370100.0%294.4 bases298 bases95.7%
errorsSRR4111264_R2.good.fq338,28499,578,370100.0%294.4 bases298 bases41.9%
total676,568199,156,740100.0%294.4 bases298 bases68.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0065844,835,60127.72.1100.0%Escherichia coli LY180, complete genome.
total4,835,601100.0%

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≤ 10000013678
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000228
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.028

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0065840.95829

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 input01:48:49 10 Apr 202001:49:07 10 Apr 202018 seconds
Read alignment to reference genome01:49:07 10 Apr 202001:54:36 10 Apr 20205 minutes 29 seconds
Preprocessing alignments for candidate junction identification01:54:36 10 Apr 202001:54:48 10 Apr 202012 seconds
Preliminary analysis of coverage distribution01:54:48 10 Apr 202001:55:16 10 Apr 202028 seconds
Identifying junction candidates01:55:16 10 Apr 202001:55:28 10 Apr 202012 seconds
Re-alignment to junction candidates01:55:28 10 Apr 202001:56:17 10 Apr 202049 seconds
Resolving best read alignments01:56:17 10 Apr 202001:56:38 10 Apr 202021 seconds
Creating BAM files01:56:38 10 Apr 202001:57:01 10 Apr 202023 seconds
Tabulating error counts01:57:01 10 Apr 202001:57:14 10 Apr 202013 seconds
Re-calibrating base error rates01:57:14 10 Apr 202001:57:14 10 Apr 20200 seconds
Examining read alignment evidence01:57:14 10 Apr 202001:59:53 10 Apr 20202 minutes 39 seconds
Polymorphism statistics01:59:53 10 Apr 202001:59:53 10 Apr 20200 seconds
Output01:59:53 10 Apr 202002:00:14 10 Apr 202021 seconds
Total 11 minutes 25 seconds