breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsBOP1000_sucB_S2198_L006_R1_001.good.fq2,284,624341,741,371100.0%149.6 bases150 bases96.8%
errorsBOP1000_sucB_S2198_L006_R2_001.good.fq2,284,624341,741,371100.0%149.6 bases150 bases95.2%
errorsBOP1000_sucB_S2198_L008_R1_001.good.fq981,454146,765,520100.0%149.5 bases150 bases96.7%
errorsBOP1000_sucB_S2198_L008_R2_001.good.fq981,454146,765,520100.0%149.5 bases150 bases93.2%
total6,532,156977,013,782100.0%149.6 bases150 bases95.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652200.82.7100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 100000100000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000340
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.022

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.60710

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input05:57:12 11 Sep 202005:58:52 11 Sep 20201 minute 40 seconds
Read alignment to reference genome05:58:52 11 Sep 202006:12:23 11 Sep 202013 minutes 31 seconds
Preprocessing alignments for candidate junction identification06:12:23 11 Sep 202006:14:06 11 Sep 20201 minute 43 seconds
Preliminary analysis of coverage distribution06:14:06 11 Sep 202006:17:34 11 Sep 20203 minutes 28 seconds
Identifying junction candidates06:17:34 11 Sep 202006:19:15 11 Sep 20201 minute 41 seconds
Re-alignment to junction candidates06:19:15 11 Sep 202006:23:25 11 Sep 20204 minutes 10 seconds
Resolving best read alignments06:23:25 11 Sep 202006:26:05 11 Sep 20202 minutes 40 seconds
Creating BAM files06:26:05 11 Sep 202006:29:14 11 Sep 20203 minutes 9 seconds
Tabulating error counts06:29:14 11 Sep 202006:30:28 11 Sep 20201 minute 14 seconds
Re-calibrating base error rates06:30:28 11 Sep 202006:30:29 11 Sep 20201 second
Examining read alignment evidence06:30:29 11 Sep 202006:45:28 11 Sep 202014 minutes 59 seconds
Polymorphism statistics06:45:28 11 Sep 202006:45:29 11 Sep 20201 second
Output06:45:29 11 Sep 202006:46:05 11 Sep 202036 seconds
Total 48 minutes 53 seconds