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-IL14_S18_L001_R1_0011,546,367232,767,26498.5%150.5 bases151 bases98.0%
errorsALE-IL14_S18_L001_R2_0011,563,138235,290,00599.6%150.5 bases151 bases95.1%
errorsALE-IL14_S18_L002_R1_0011,543,437232,337,82498.7%150.5 bases151 bases97.9%
errorsALE-IL14_S18_L002_R2_0011,556,718234,337,69799.6%150.5 bases151 bases95.4%
errorsALE-IL14_S18_L003_R1_0011,575,136237,122,94599.2%150.5 bases151 bases97.2%
errorsALE-IL14_S18_L003_R2_0011,582,722238,241,66799.7%150.5 bases151 bases94.7%
errorsALE-IL14_S18_L004_R1_0011,565,693235,714,86199.2%150.5 bases151 bases97.8%
errorsALE-IL14_S18_L004_R2_0011,572,540236,728,30599.6%150.5 bases151 bases95.8%
total12,505,7511,882,540,56899.3%150.5 bases151 bases96.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707392.13.098.2%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≤ 1000006325
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 ≤ 5000321
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.022

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.36416

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 input15:16:22 18 Oct 201615:22:40 18 Oct 20166 minutes 18 seconds
Read alignment to reference genome15:22:41 18 Oct 201616:21:36 18 Oct 201658 minutes 55 seconds
Preprocessing alignments for candidate junction identification16:21:36 18 Oct 201616:29:48 18 Oct 20168 minutes 12 seconds
Preliminary analysis of coverage distribution16:29:48 18 Oct 201616:50:21 18 Oct 201620 minutes 33 seconds
Identifying junction candidates16:50:21 18 Oct 201616:50:47 18 Oct 201626 seconds
Re-alignment to junction candidates16:50:48 18 Oct 201617:15:44 18 Oct 201624 minutes 56 seconds
Resolving alignments with junction candidates17:15:44 18 Oct 201618:14:58 18 Oct 201659 minutes 14 seconds
Creating BAM files18:14:58 18 Oct 201618:34:51 18 Oct 201619 minutes 53 seconds
Tabulating error counts18:34:51 18 Oct 201618:46:05 18 Oct 201611 minutes 14 seconds
Re-calibrating base error rates18:46:05 18 Oct 201618:46:07 18 Oct 20162 seconds
Examining read alignment evidence18:46:07 18 Oct 201620:04:22 18 Oct 20161 hour 18 minutes 15 seconds
Polymorphism statistics20:04:22 18 Oct 201620:04:24 18 Oct 20162 seconds
Output20:04:24 18 Oct 201620:06:35 18 Oct 20162 minutes 11 seconds
Total 4 hours 50 minutes 11 seconds