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-IL35_S43_L001_R1_0012,051,201308,781,76699.7%150.5 bases151 bases99.5%
errorsALE-IL35_S43_L001_R2_0012,050,890308,720,22999.7%150.5 bases151 bases98.1%
errorsALE-IL35_S43_L002_R1_0012,036,999306,656,90999.7%150.5 bases151 bases99.5%
errorsALE-IL35_S43_L002_R2_0012,035,712306,444,13399.7%150.5 bases151 bases98.2%
errorsALE-IL35_S43_L003_R1_0012,070,547311,712,43999.8%150.5 bases151 bases99.3%
errorsALE-IL35_S43_L003_R2_0012,069,521311,522,17099.8%150.5 bases151 bases97.8%
errorsALE-IL35_S43_L004_R1_0012,060,204310,168,93699.8%150.6 bases151 bases99.4%
errorsALE-IL35_S43_L004_R2_0012,058,725309,918,54999.8%150.5 bases151 bases98.3%
total16,433,7992,473,925,13199.8%150.5 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707529.73.998.2%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≤ 10000020067
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 ≤ 5000157
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.28672

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 input22:19:29 18 Oct 201622:32:49 18 Oct 201613 minutes 20 seconds
Read alignment to reference genome22:33:03 18 Oct 201600:57:49 19 Oct 20162 hours 24 minutes 46 seconds
Preprocessing alignments for candidate junction identification00:57:52 19 Oct 201601:22:44 19 Oct 201624 minutes 52 seconds
Preliminary analysis of coverage distribution01:22:44 19 Oct 201602:02:10 19 Oct 201639 minutes 26 seconds
Identifying junction candidates02:02:10 19 Oct 201602:02:41 19 Oct 201631 seconds
Re-alignment to junction candidates02:02:41 19 Oct 201602:37:55 19 Oct 201635 minutes 14 seconds
Resolving alignments with junction candidates02:37:55 19 Oct 201603:58:18 19 Oct 20161 hour 20 minutes 23 seconds
Creating BAM files03:58:18 19 Oct 201604:24:06 19 Oct 201625 minutes 48 seconds
Tabulating error counts04:24:06 19 Oct 201604:48:35 19 Oct 201624 minutes 29 seconds
Re-calibrating base error rates04:48:35 19 Oct 201604:48:39 19 Oct 20164 seconds
Examining read alignment evidence04:48:39 19 Oct 201607:20:01 19 Oct 20162 hours 31 minutes 22 seconds
Polymorphism statistics07:20:01 19 Oct 201607:20:03 19 Oct 20162 seconds
Output07:20:03 19 Oct 201607:21:50 19 Oct 20161 minute 47 seconds
Total 9 hours 2 minutes 4 seconds