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-IL17_S25_L001_R1_0011,907,142287,088,16199.8%150.5 bases151 bases99.4%
errorsALE-IL17_S25_L001_R2_0011,903,395286,511,40199.6%150.5 bases151 bases97.7%
errorsALE-IL17_S25_L002_R1_0011,899,788285,992,55399.8%150.5 bases151 bases99.4%
errorsALE-IL17_S25_L002_R2_0011,896,415285,472,17799.6%150.5 bases151 bases97.7%
errorsALE-IL17_S25_L003_R1_0011,925,690289,900,18499.9%150.5 bases151 bases99.3%
errorsALE-IL17_S25_L003_R2_0011,922,390289,371,45299.7%150.5 bases151 bases97.4%
errorsALE-IL17_S25_L004_R1_0011,947,261293,162,99299.9%150.6 bases151 bases99.3%
errorsALE-IL17_S25_L004_R2_0011,943,094292,513,15499.7%150.5 bases151 bases97.9%
total15,345,1752,310,012,07499.8%150.5 bases151 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707490.43.898.2%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≤ 10000015647
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 ≤ 5000223
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.30222

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 input15:17:02 18 Oct 201615:26:26 18 Oct 20169 minutes 24 seconds
Read alignment to reference genome15:26:29 18 Oct 201616:49:19 18 Oct 20161 hour 22 minutes 50 seconds
Preprocessing alignments for candidate junction identification16:49:19 18 Oct 201617:22:56 18 Oct 201633 minutes 37 seconds
Preliminary analysis of coverage distribution17:22:56 18 Oct 201618:05:25 18 Oct 201642 minutes 29 seconds
Identifying junction candidates18:05:25 18 Oct 201618:05:51 18 Oct 201626 seconds
Re-alignment to junction candidates18:05:51 18 Oct 201618:30:26 18 Oct 201624 minutes 35 seconds
Resolving alignments with junction candidates18:30:26 18 Oct 201619:25:17 18 Oct 201654 minutes 51 seconds
Creating BAM files19:25:18 18 Oct 201619:46:24 18 Oct 201621 minutes 6 seconds
Tabulating error counts19:46:24 18 Oct 201620:06:25 18 Oct 201620 minutes 1 second
Re-calibrating base error rates20:06:25 18 Oct 201620:06:28 18 Oct 20163 seconds
Examining read alignment evidence20:06:28 18 Oct 201622:07:32 18 Oct 20162 hours 1 minute 4 seconds
Polymorphism statistics22:07:32 18 Oct 201622:07:36 18 Oct 20164 seconds
Output22:07:36 18 Oct 201622:09:32 18 Oct 20161 minute 56 seconds
Total 6 hours 52 minutes 26 seconds