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-IL42_S50_L001_R1_0011,831,492275,730,39999.4%150.5 bases151 bases99.3%
errorsALE-IL42_S50_L001_R2_0011,834,823276,221,77399.6%150.5 bases151 bases97.1%
errorsALE-IL42_S50_L002_R1_0011,822,359274,371,31799.4%150.6 bases151 bases99.4%
errorsALE-IL42_S50_L002_R2_0011,825,125274,771,87499.6%150.5 bases151 bases97.2%
errorsALE-IL42_S50_L003_R1_0011,854,362279,198,68499.6%150.6 bases151 bases99.1%
errorsALE-IL42_S50_L003_R2_0011,855,363279,311,84399.7%150.5 bases151 bases96.8%
errorsALE-IL42_S50_L004_R1_0011,845,715277,912,08399.7%150.6 bases151 bases99.3%
errorsALE-IL42_S50_L004_R2_0011,844,023277,635,58099.7%150.6 bases151 bases97.7%
total14,713,2622,215,153,55399.6%150.6 bases151 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707479.315.498.2%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≤ 10000010134
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 ≤ 5000172
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.32652

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 input22:21:04 18 Oct 201622:36:19 18 Oct 201615 minutes 15 seconds
Read alignment to reference genome22:36:33 18 Oct 201600:36:29 19 Oct 20161 hour 59 minutes 56 seconds
Preprocessing alignments for candidate junction identification00:36:32 19 Oct 201601:10:22 19 Oct 201633 minutes 50 seconds
Preliminary analysis of coverage distribution01:10:22 19 Oct 201601:46:43 19 Oct 201636 minutes 21 seconds
Identifying junction candidates01:46:43 19 Oct 201601:47:00 19 Oct 201617 seconds
Re-alignment to junction candidates01:47:00 19 Oct 201602:22:26 19 Oct 201635 minutes 26 seconds
Resolving alignments with junction candidates02:22:26 19 Oct 201603:34:42 19 Oct 20161 hour 12 minutes 16 seconds
Creating BAM files03:34:42 19 Oct 201603:57:51 19 Oct 201623 minutes 9 seconds
Tabulating error counts03:57:51 19 Oct 201604:15:06 19 Oct 201617 minutes 15 seconds
Re-calibrating base error rates04:15:06 19 Oct 201604:15:11 19 Oct 20165 seconds
Examining read alignment evidence04:15:11 19 Oct 201606:43:45 19 Oct 20162 hours 28 minutes 34 seconds
Polymorphism statistics06:43:45 19 Oct 201606:43:47 19 Oct 20162 seconds
Output06:43:47 19 Oct 201606:46:36 19 Oct 20162 minutes 49 seconds
Total 8 hours 25 minutes 15 seconds