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-IL15_S19_L001_R1_0011,662,473250,232,58099.4%150.5 bases151 bases98.8%
errorsALE-IL15_S19_L001_R2_0011,665,290250,655,96999.5%150.5 bases151 bases96.6%
errorsALE-IL15_S19_L002_R1_0011,659,001249,728,14999.5%150.5 bases151 bases98.8%
errorsALE-IL15_S19_L002_R2_0011,660,019249,878,56799.5%150.5 bases151 bases96.7%
errorsALE-IL15_S19_L003_R1_0011,684,680253,605,86499.7%150.5 bases151 bases98.5%
errorsALE-IL15_S19_L003_R2_0011,684,122253,499,84799.7%150.5 bases151 bases96.3%
errorsALE-IL15_S19_L004_R1_0011,682,357253,264,85199.7%150.5 bases151 bases98.7%
errorsALE-IL15_S19_L004_R2_0011,680,801253,020,72999.6%150.5 bases151 bases97.0%
total13,378,7432,013,886,55699.6%150.5 bases151 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707424.43.198.2%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≤ 1000006462
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 ≤ 5000195
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.33971

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 input15:16:37 18 Oct 201615:23:56 18 Oct 20167 minutes 19 seconds
Read alignment to reference genome15:23:58 18 Oct 201616:27:47 18 Oct 20161 hour 3 minutes 49 seconds
Preprocessing alignments for candidate junction identification16:27:47 18 Oct 201616:43:39 18 Oct 201615 minutes 52 seconds
Preliminary analysis of coverage distribution16:43:39 18 Oct 201617:31:30 18 Oct 201647 minutes 51 seconds
Identifying junction candidates17:31:30 18 Oct 201617:31:53 18 Oct 201623 seconds
Re-alignment to junction candidates17:31:53 18 Oct 201618:09:48 18 Oct 201637 minutes 55 seconds
Resolving alignments with junction candidates18:09:48 18 Oct 201618:55:04 18 Oct 201645 minutes 16 seconds
Creating BAM files18:55:04 18 Oct 201619:15:58 18 Oct 201620 minutes 54 seconds
Tabulating error counts19:15:58 18 Oct 201619:26:49 18 Oct 201610 minutes 51 seconds
Re-calibrating base error rates19:26:49 18 Oct 201619:26:52 18 Oct 20163 seconds
Examining read alignment evidence19:26:52 18 Oct 201621:12:02 18 Oct 20161 hour 45 minutes 10 seconds
Polymorphism statistics21:12:02 18 Oct 201621:12:05 18 Oct 20163 seconds
Output21:12:05 18 Oct 201621:14:07 18 Oct 20162 minutes 2 seconds
Total 5 hours 57 minutes 28 seconds