breseq  version 0.30.0  revision f53f5bf51c1f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-Atp-I-to-C-KO-16-65_S20_L001_R2_001709,016190,849,594100.0%269.2 bases301 bases96.5%
errorsqtrim-Atp-I-to-C-KO-16-65_S20_L001_R1_001709,035191,702,806100.0%270.4 bases301 bases99.0%
total1,418,051382,552,400100.0%269.8 bases301 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,638,90283.74.4100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,638,902100.0%

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≤ 1000002362
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 ≤ 5000163
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88858

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

Software Versions

programversion
bowtie22.2.6
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input23:55:53 24 Apr 201723:56:25 24 Apr 201732 seconds
Read alignment to reference genome23:56:26 24 Apr 201723:58:36 24 Apr 20172 minutes 10 seconds
Preprocessing alignments for candidate junction identification23:58:36 24 Apr 201723:59:28 24 Apr 201752 seconds
Preliminary analysis of coverage distribution23:59:28 24 Apr 201700:00:52 25 Apr 20171 minute 24 seconds
Identifying junction candidates00:00:52 25 Apr 201700:00:57 25 Apr 20175 seconds
Re-alignment to junction candidates00:00:57 25 Apr 201700:01:16 25 Apr 201719 seconds
Resolving alignments with junction candidates00:01:16 25 Apr 201700:02:49 25 Apr 20171 minute 33 seconds
Creating BAM files00:02:49 25 Apr 201700:03:35 25 Apr 201746 seconds
Tabulating error counts00:03:35 25 Apr 201700:05:16 25 Apr 20171 minute 41 seconds
Re-calibrating base error rates00:05:16 25 Apr 201700:05:17 25 Apr 20171 second
Examining read alignment evidence00:05:17 25 Apr 201700:19:09 25 Apr 201713 minutes 52 seconds
Polymorphism statistics00:19:09 25 Apr 201700:19:09 25 Apr 20170 seconds
Output00:19:09 25 Apr 201700:19:23 25 Apr 201714 seconds
Total 23 minutes 29 seconds