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-14-63_S18_L001_R1_0011,438,839411,386,749100.0%285.9 bases301 bases99.4%
errorsqtrim-Atp-I-to-C-KO-14-63_S18_L001_R2_0011,438,792408,118,975100.0%283.7 bases301 bases94.4%
total2,877,631819,505,724100.0%284.8 bases301 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,638,902176.64.5100.0%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≤ 1000002109
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 ≤ 5000204
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.027

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81312

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 input21:53:26 24 Apr 201721:54:33 24 Apr 20171 minute 7 seconds
Read alignment to reference genome21:54:34 24 Apr 201721:59:39 24 Apr 20175 minutes 5 seconds
Preprocessing alignments for candidate junction identification21:59:39 24 Apr 201722:01:34 24 Apr 20171 minute 55 seconds
Preliminary analysis of coverage distribution22:01:34 24 Apr 201722:04:33 24 Apr 20172 minutes 59 seconds
Identifying junction candidates22:04:33 24 Apr 201722:04:38 24 Apr 20175 seconds
Re-alignment to junction candidates22:04:38 24 Apr 201722:05:20 24 Apr 201742 seconds
Resolving alignments with junction candidates22:05:20 24 Apr 201722:08:42 24 Apr 20173 minutes 22 seconds
Creating BAM files22:08:42 24 Apr 201722:10:18 24 Apr 20171 minute 36 seconds
Tabulating error counts22:10:18 24 Apr 201722:13:52 24 Apr 20173 minutes 34 seconds
Re-calibrating base error rates22:13:52 24 Apr 201722:13:53 24 Apr 20171 second
Examining read alignment evidence22:13:53 24 Apr 201722:42:34 24 Apr 201728 minutes 41 seconds
Polymorphism statistics22:42:34 24 Apr 201722:42:34 24 Apr 20170 seconds
Output22:42:34 24 Apr 201722:42:57 24 Apr 201723 seconds
Total 49 minutes 30 seconds