breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL11_S15_L002_R1_0011,845,248277,795,50299.0%150.5 bases151 bases98.1%
errorsALE-IL11_S15_L002_R2_0011,854,904279,244,17599.5%150.5 bases151 bases95.8%
errorsALE-IL11_S15_L004_R1_0011,868,119281,259,51199.3%150.6 bases151 bases97.9%
errorsALE-IL11_S15_L001_R2_0011,862,290280,340,34899.5%150.5 bases151 bases95.7%
errorsALE-IL11_S15_L003_R1_0011,882,702283,443,63399.4%150.6 bases151 bases97.5%
errorsALE-IL11_S15_L004_R2_0011,872,126281,846,99399.6%150.5 bases151 bases96.2%
errorsALE-IL11_S15_L001_R1_0011,849,912278,476,46798.9%150.5 bases151 bases98.2%
errorsALE-IL11_S15_L003_R2_0011,887,103284,081,56199.7%150.5 bases151 bases95.3%
total14,922,4042,246,488,19099.4%150.5 bases151 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652469.03.0100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 1000004246
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 ≤ 5000151
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.31386

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 input21:46:47 20 Apr 201621:56:43 20 Apr 20169 minutes 56 seconds
Read alignment to reference genome21:56:45 20 Apr 201623:08:03 20 Apr 20161 hour 11 minutes 18 seconds
Preprocessing alignments for candidate junction identification23:08:03 20 Apr 201623:23:21 20 Apr 201615 minutes 18 seconds
Preliminary analysis of coverage distribution23:23:21 20 Apr 201623:46:11 20 Apr 201622 minutes 50 seconds
Identifying junction candidates23:46:11 20 Apr 201623:46:13 20 Apr 20162 seconds
Re-alignment to junction candidates23:46:13 20 Apr 201623:52:50 20 Apr 20166 minutes 37 seconds
Resolving alignments with junction candidates23:52:50 20 Apr 201600:36:07 21 Apr 201643 minutes 17 seconds
Creating BAM files00:36:07 21 Apr 201600:49:41 21 Apr 201613 minutes 34 seconds
Tabulating error counts00:49:41 21 Apr 201601:10:39 21 Apr 201620 minutes 58 seconds
Re-calibrating base error rates01:10:39 21 Apr 201601:10:43 21 Apr 20164 seconds
Examining read alignment evidence01:10:43 21 Apr 201603:09:25 21 Apr 20161 hour 58 minutes 42 seconds
Polymorphism statistics03:09:25 21 Apr 201603:09:28 21 Apr 20163 seconds
Output03:09:28 21 Apr 201603:11:17 21 Apr 20161 minute 49 seconds
Total 5 hours 24 minutes 28 seconds