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-IL18_S26_L001_R1_0011,910,392287,597,12099.7%150.5 bases151 bases99.4%
errorsALE-IL18_S26_L001_R2_0011,908,978287,376,08199.7%150.5 bases151 bases97.8%
errorsALE-IL18_S26_L002_R1_0011,899,936286,040,68399.8%150.6 bases151 bases99.3%
errorsALE-IL18_S26_L002_R2_0011,897,809285,709,83899.7%150.5 bases151 bases97.9%
errorsALE-IL18_S26_L003_R1_0011,926,531290,053,85499.9%150.6 bases151 bases99.2%
errorsALE-IL18_S26_L003_R2_0011,924,630289,731,85299.8%150.5 bases151 bases97.5%
errorsALE-IL18_S26_L004_R1_0011,935,097291,355,76999.9%150.6 bases151 bases99.3%
errorsALE-IL18_S26_L004_R2_0011,932,295290,911,78299.7%150.6 bases151 bases98.1%
total15,335,6682,308,776,97999.8%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707490.13.498.3%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≤ 10000013456
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 ≤ 5000217
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.30123

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 input15:17:28 18 Oct 201615:26:25 18 Oct 20168 minutes 57 seconds
Read alignment to reference genome15:26:26 18 Oct 201616:49:19 18 Oct 20161 hour 22 minutes 53 seconds
Preprocessing alignments for candidate junction identification16:49:19 18 Oct 201617:22:38 18 Oct 201633 minutes 19 seconds
Preliminary analysis of coverage distribution17:22:38 18 Oct 201618:03:36 18 Oct 201640 minutes 58 seconds
Identifying junction candidates18:03:36 18 Oct 201618:04:03 18 Oct 201627 seconds
Re-alignment to junction candidates18:04:03 18 Oct 201618:28:28 18 Oct 201624 minutes 25 seconds
Resolving alignments with junction candidates18:28:28 18 Oct 201619:23:24 18 Oct 201654 minutes 56 seconds
Creating BAM files19:23:24 18 Oct 201619:45:41 18 Oct 201622 minutes 17 seconds
Tabulating error counts19:45:41 18 Oct 201620:05:26 18 Oct 201619 minutes 45 seconds
Re-calibrating base error rates20:05:26 18 Oct 201620:05:29 18 Oct 20163 seconds
Examining read alignment evidence20:05:29 18 Oct 201622:06:53 18 Oct 20162 hours 1 minute 24 seconds
Polymorphism statistics22:06:53 18 Oct 201622:06:55 18 Oct 20162 seconds
Output22:06:55 18 Oct 201622:09:02 18 Oct 20162 minutes 7 seconds
Total 6 hours 51 minutes 33 seconds