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-IL43_S51_L001_R1_0011,960,262295,100,32899.0%150.5 bases151 bases98.8%
errorsALE-IL43_S51_L001_R2_0011,972,390296,914,38499.6%150.5 bases151 bases96.3%
errorsALE-IL43_S51_L002_R1_0011,951,520293,800,77899.0%150.5 bases151 bases98.8%
errorsALE-IL43_S51_L002_R2_0011,962,911295,506,86999.6%150.5 bases151 bases96.4%
errorsALE-IL43_S51_L003_R1_0011,992,066299,913,40099.4%150.6 bases151 bases98.3%
errorsALE-IL43_S51_L003_R2_0011,997,376300,677,72499.7%150.5 bases151 bases96.0%
errorsALE-IL43_S51_L004_R1_0011,977,207297,694,41999.5%150.6 bases151 bases98.7%
errorsALE-IL43_S51_L004_R2_0011,980,674298,189,83399.7%150.5 bases151 bases97.0%
total15,794,4062,377,797,73599.4%150.5 bases151 bases97.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707510.221.298.1%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≤ 10000023299
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 ≤ 5000808
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.055

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.31028

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 input22:21:16 18 Oct 201622:36:18 18 Oct 201615 minutes 2 seconds
Read alignment to reference genome22:36:27 18 Oct 201600:52:18 19 Oct 20162 hours 15 minutes 51 seconds
Preprocessing alignments for candidate junction identification00:52:18 19 Oct 201601:18:40 19 Oct 201626 minutes 22 seconds
Preliminary analysis of coverage distribution01:18:40 19 Oct 201601:54:12 19 Oct 201635 minutes 32 seconds
Identifying junction candidates01:54:12 19 Oct 201602:01:58 19 Oct 20167 minutes 46 seconds
Re-alignment to junction candidates02:01:59 19 Oct 201602:39:58 19 Oct 201637 minutes 59 seconds
Resolving alignments with junction candidates02:39:58 19 Oct 201603:54:46 19 Oct 20161 hour 14 minutes 48 seconds
Creating BAM files03:54:46 19 Oct 201604:19:53 19 Oct 201625 minutes 7 seconds
Tabulating error counts04:19:53 19 Oct 201604:42:55 19 Oct 201623 minutes 2 seconds
Re-calibrating base error rates04:42:55 19 Oct 201604:43:00 19 Oct 20165 seconds
Examining read alignment evidence04:43:00 19 Oct 201607:12:45 19 Oct 20162 hours 29 minutes 45 seconds
Polymorphism statistics07:12:45 19 Oct 201607:12:47 19 Oct 20162 seconds
Output07:12:47 19 Oct 201607:15:01 19 Oct 20162 minutes 14 seconds
Total 8 hours 53 minutes 35 seconds