breseq  version 0.28.1  revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL37_S45_L001_R1_0011,936,947291,593,72799.8%150.5 bases151 bases99.6%
errorsALE-IL37_S45_L001_R2_0011,935,097291,298,72299.7%150.5 bases151 bases98.2%
errorsALE-IL37_S45_L002_R1_0011,920,972289,203,72999.8%150.6 bases151 bases99.5%
errorsALE-IL37_S45_L002_R2_0011,918,791288,854,78699.7%150.5 bases151 bases98.3%
errorsALE-IL37_S45_L003_R1_0011,955,150294,356,68999.9%150.6 bases151 bases99.5%
errorsALE-IL37_S45_L003_R2_0011,953,048294,008,38999.8%150.5 bases151 bases98.0%
errorsALE-IL37_S45_L004_R1_0011,938,674291,890,01399.9%150.6 bases151 bases99.5%
errorsALE-IL37_S45_L004_R2_0011,936,524291,540,22199.8%150.5 bases151 bases98.5%
total15,495,2032,332,746,27699.8%150.5 bases151 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707501.54.198.2%Escherichia coli DH1, complete genome.
total4,630,707100.0%

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≤ 10000017401
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 ≤ 5000179
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.30423

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input22:20:01 18 Oct 201622:34:36 18 Oct 201614 minutes 35 seconds
Read alignment to reference genome22:34:44 18 Oct 201600:45:03 19 Oct 20162 hours 10 minutes 19 seconds
Preprocessing alignments for candidate junction identification00:45:05 19 Oct 201601:16:17 19 Oct 201631 minutes 12 seconds
Preliminary analysis of coverage distribution01:16:17 19 Oct 201601:52:23 19 Oct 201636 minutes 6 seconds
Identifying junction candidates01:52:23 19 Oct 201601:52:47 19 Oct 201624 seconds
Re-alignment to junction candidates01:52:47 19 Oct 201602:28:00 19 Oct 201635 minutes 13 seconds
Resolving alignments with junction candidates02:28:00 19 Oct 201603:40:13 19 Oct 20161 hour 12 minutes 13 seconds
Creating BAM files03:40:13 19 Oct 201604:03:07 19 Oct 201622 minutes 54 seconds
Tabulating error counts04:03:07 19 Oct 201604:21:57 19 Oct 201618 minutes 50 seconds
Re-calibrating base error rates04:21:57 19 Oct 201604:22:01 19 Oct 20164 seconds
Examining read alignment evidence04:22:01 19 Oct 201606:58:10 19 Oct 20162 hours 36 minutes 9 seconds
Polymorphism statistics06:58:10 19 Oct 201606:58:12 19 Oct 20162 seconds
Output06:58:12 19 Oct 201607:00:44 19 Oct 20162 minutes 32 seconds
Total 8 hours 40 minutes 33 seconds