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-IL45_S53_L001_R1_0012,066,449311,098,55399.6%150.5 bases151 bases99.3%
errorsALE-IL45_S53_L001_R2_0012,068,978311,462,31199.7%150.5 bases151 bases97.6%
errorsALE-IL45_S53_L002_R1_0012,056,716309,651,55999.6%150.6 bases151 bases99.3%
errorsALE-IL45_S53_L002_R2_0012,059,249310,012,54299.7%150.5 bases151 bases97.7%
errorsALE-IL45_S53_L003_R1_0012,091,681314,927,09299.8%150.6 bases151 bases99.1%
errorsALE-IL45_S53_L003_R2_0012,091,850314,909,17199.8%150.5 bases151 bases97.3%
errorsALE-IL45_S53_L004_R1_0012,078,219312,913,56899.8%150.6 bases151 bases99.2%
errorsALE-IL45_S53_L004_R2_0012,077,741312,813,21399.8%150.6 bases151 bases98.0%
total16,590,8832,497,788,00999.7%150.6 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707529.84.298.2%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≤ 10000020887
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 ≤ 5000171
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.28120

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 input22:21:42 18 Oct 201622:36:19 18 Oct 201614 minutes 37 seconds
Read alignment to reference genome22:36:29 18 Oct 201601:02:15 19 Oct 20162 hours 25 minutes 46 seconds
Preprocessing alignments for candidate junction identification01:02:15 19 Oct 201601:45:07 19 Oct 201642 minutes 52 seconds
Preliminary analysis of coverage distribution01:45:07 19 Oct 201602:39:35 19 Oct 201654 minutes 28 seconds
Identifying junction candidates02:39:35 19 Oct 201602:40:22 19 Oct 201647 seconds
Re-alignment to junction candidates02:40:23 19 Oct 201603:18:51 19 Oct 201638 minutes 28 seconds
Resolving alignments with junction candidates03:18:51 19 Oct 201604:22:50 19 Oct 20161 hour 3 minutes 59 seconds
Creating BAM files04:22:50 19 Oct 201604:40:47 19 Oct 201617 minutes 57 seconds
Tabulating error counts04:40:47 19 Oct 201605:05:53 19 Oct 201625 minutes 6 seconds
Re-calibrating base error rates05:05:53 19 Oct 201605:05:58 19 Oct 20165 seconds
Examining read alignment evidence05:05:58 19 Oct 201607:30:30 19 Oct 20162 hours 24 minutes 32 seconds
Polymorphism statistics07:30:30 19 Oct 201607:30:31 19 Oct 20161 second
Output07:30:31 19 Oct 201607:32:15 19 Oct 20161 minute 44 seconds
Total 9 hours 10 minutes 22 seconds