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-IL36_S44_L001_R1_0011,377,213207,310,24099.6%150.5 bases151 bases99.4%
errorsALE-IL36_S44_L001_R2_0011,377,546207,358,25499.7%150.5 bases151 bases97.9%
errorsALE-IL36_S44_L002_R1_0011,365,852205,614,03899.7%150.5 bases151 bases99.4%
errorsALE-IL36_S44_L002_R2_0011,365,637205,573,22699.7%150.5 bases151 bases98.0%
errorsALE-IL36_S44_L003_R1_0011,389,161209,129,00399.8%150.5 bases151 bases99.2%
errorsALE-IL36_S44_L003_R2_0011,388,565209,017,46999.8%150.5 bases151 bases97.6%
errorsALE-IL36_S44_L004_R1_0011,380,476207,834,26599.8%150.6 bases151 bases99.3%
errorsALE-IL36_S44_L004_R2_0011,379,664207,695,28799.8%150.5 bases151 bases98.1%
total11,024,1141,659,531,78299.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707359.14.398.2%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≤ 1000008355
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 ≤ 5000118
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.40661

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 input22:19:50 18 Oct 201622:30:43 18 Oct 201610 minutes 53 seconds
Read alignment to reference genome22:30:48 18 Oct 201623:43:51 18 Oct 20161 hour 13 minutes 3 seconds
Preprocessing alignments for candidate junction identification23:43:51 18 Oct 201623:51:31 18 Oct 20167 minutes 40 seconds
Preliminary analysis of coverage distribution23:51:31 18 Oct 201600:08:28 19 Oct 201616 minutes 57 seconds
Identifying junction candidates00:08:28 19 Oct 201600:08:40 19 Oct 201612 seconds
Re-alignment to junction candidates00:08:40 19 Oct 201600:41:00 19 Oct 201632 minutes 20 seconds
Resolving alignments with junction candidates00:41:01 19 Oct 201602:07:22 19 Oct 20161 hour 26 minutes 21 seconds
Creating BAM files02:07:22 19 Oct 201602:33:54 19 Oct 201626 minutes 32 seconds
Tabulating error counts02:33:54 19 Oct 201602:43:26 19 Oct 20169 minutes 32 seconds
Re-calibrating base error rates02:43:27 19 Oct 201602:43:29 19 Oct 20162 seconds
Examining read alignment evidence02:43:29 19 Oct 201603:46:50 19 Oct 20161 hour 3 minutes 21 seconds
Polymorphism statistics03:46:50 19 Oct 201603:46:54 19 Oct 20164 seconds
Output03:46:54 19 Oct 201603:49:43 19 Oct 20162 minutes 49 seconds
Total 5 hours 29 minutes 46 seconds