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-IL40_S48_L001_R1_0012,286,300344,191,52299.9%150.5 bases151 bases99.7%
errorsALE-IL40_S48_L001_R2_0012,280,481343,297,43699.7%150.5 bases151 bases98.3%
errorsALE-IL40_S48_L002_R1_0012,272,391342,119,68499.9%150.6 bases151 bases99.7%
errorsALE-IL40_S48_L002_R2_0012,266,483341,209,56699.7%150.5 bases151 bases98.3%
errorsALE-IL40_S48_L003_R1_0012,305,722347,139,511100.0%150.6 bases151 bases99.7%
errorsALE-IL40_S48_L003_R2_0012,301,405346,448,51599.8%150.5 bases151 bases98.0%
errorsALE-IL40_S48_L004_R1_0012,303,881346,885,007100.0%150.6 bases151 bases99.6%
errorsALE-IL40_S48_L004_R2_0012,298,993346,121,84199.8%150.6 bases151 bases98.5%
total18,315,6562,757,413,08299.8%150.5 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707585.84.598.1%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≤ 10000026154
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 ≤ 5000252
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.017

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.25809

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 input22:20:37 18 Oct 201622:36:19 18 Oct 201615 minutes 42 seconds
Read alignment to reference genome22:36:33 18 Oct 201601:03:19 19 Oct 20162 hours 26 minutes 46 seconds
Preprocessing alignments for candidate junction identification01:03:19 19 Oct 201601:29:37 19 Oct 201626 minutes 18 seconds
Preliminary analysis of coverage distribution01:29:37 19 Oct 201602:14:52 19 Oct 201645 minutes 15 seconds
Identifying junction candidates02:14:52 19 Oct 201602:15:21 19 Oct 201629 seconds
Re-alignment to junction candidates02:15:21 19 Oct 201602:54:02 19 Oct 201638 minutes 41 seconds
Resolving alignments with junction candidates02:54:02 19 Oct 201604:13:51 19 Oct 20161 hour 19 minutes 49 seconds
Creating BAM files04:13:51 19 Oct 201604:35:02 19 Oct 201621 minutes 11 seconds
Tabulating error counts04:35:02 19 Oct 201605:03:06 19 Oct 201628 minutes 4 seconds
Re-calibrating base error rates05:03:06 19 Oct 201605:03:12 19 Oct 20166 seconds
Examining read alignment evidence05:03:12 19 Oct 201607:37:49 19 Oct 20162 hours 34 minutes 37 seconds
Polymorphism statistics07:37:49 19 Oct 201607:37:50 19 Oct 20161 second
Output07:37:50 19 Oct 201607:39:43 19 Oct 20161 minute 53 seconds
Total 9 hours 18 minutes 52 seconds