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-IL34_S42_L001_R1_0011,079,364162,487,63599.6%150.5 bases151 bases99.4%
errorsALE-IL34_S42_L001_R2_0011,078,908162,413,81699.5%150.5 bases151 bases97.3%
errorsALE-IL34_S42_L002_R1_0011,072,197161,417,84499.6%150.5 bases151 bases99.4%
errorsALE-IL34_S42_L002_R2_0011,071,442161,300,52699.6%150.5 bases151 bases97.4%
errorsALE-IL34_S42_L003_R1_0011,089,529164,029,04199.8%150.6 bases151 bases99.2%
errorsALE-IL34_S42_L003_R2_0011,088,438163,846,99299.7%150.5 bases151 bases97.0%
errorsALE-IL34_S42_L004_R1_0011,084,922163,346,37499.7%150.6 bases151 bases99.3%
errorsALE-IL34_S42_L004_R2_0011,083,504163,120,26599.6%150.5 bases151 bases97.6%
total8,648,3041,301,962,49399.6%150.5 bases151 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707280.83.898.2%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≤ 1000006094
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 ≤ 5000142
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.47893

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 input22:18:39 18 Oct 201622:23:48 18 Oct 20165 minutes 9 seconds
Read alignment to reference genome22:23:50 18 Oct 201623:24:03 18 Oct 20161 hour 13 seconds
Preprocessing alignments for candidate junction identification23:24:04 18 Oct 201623:30:52 18 Oct 20166 minutes 48 seconds
Preliminary analysis of coverage distribution23:30:53 18 Oct 201623:44:34 18 Oct 201613 minutes 41 seconds
Identifying junction candidates23:44:34 18 Oct 201623:44:44 18 Oct 201610 seconds
Re-alignment to junction candidates23:44:44 18 Oct 201600:04:12 19 Oct 201619 minutes 28 seconds
Resolving alignments with junction candidates00:04:12 19 Oct 201600:43:51 19 Oct 201639 minutes 39 seconds
Creating BAM files00:43:53 19 Oct 201601:23:13 19 Oct 201639 minutes 20 seconds
Tabulating error counts01:23:13 19 Oct 201601:30:08 19 Oct 20166 minutes 55 seconds
Re-calibrating base error rates01:30:08 19 Oct 201601:30:16 19 Oct 20168 seconds
Examining read alignment evidence01:30:16 19 Oct 201602:28:05 19 Oct 201657 minutes 49 seconds
Polymorphism statistics02:28:05 19 Oct 201602:28:07 19 Oct 20162 seconds
Output02:28:07 19 Oct 201602:32:44 19 Oct 20164 minutes 37 seconds
Total 4 hours 13 minutes 59 seconds