breseq  version 0.32.1  revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsT1000_564_CCGTTATT-CACGTCAG.R2.good.fq1,319,668149,530,025100.0%113.3 bases139 bases94.4%
errorsT1000_564_CCGTTATT-CACGTCAG.R1.good.fq1,319,668149,530,025100.0%113.3 bases139 bases94.5%
total2,639,336299,060,050100.0%113.3 bases139 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65259.94.1100.0%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≤ 1000002080
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 ≤ 5000297
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.018

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81313

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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input07:00:28 20 Jul 201807:00:56 20 Jul 201828 seconds
Read alignment to reference genome07:00:57 20 Jul 201807:02:25 20 Jul 20181 minute 28 seconds
Preprocessing alignments for candidate junction identification07:02:25 20 Jul 201807:03:00 20 Jul 201835 seconds
Preliminary analysis of coverage distribution07:03:00 20 Jul 201807:03:58 20 Jul 201858 seconds
Identifying junction candidates07:03:58 20 Jul 201807:03:59 20 Jul 20181 second
Re-alignment to junction candidates07:03:59 20 Jul 201807:04:18 20 Jul 201819 seconds
Resolving best read alignments07:04:18 20 Jul 201807:05:15 20 Jul 201857 seconds
Creating BAM files07:05:15 20 Jul 201807:06:06 20 Jul 201851 seconds
Tabulating error counts07:06:06 20 Jul 201807:06:29 20 Jul 201823 seconds
Re-calibrating base error rates07:06:29 20 Jul 201807:06:30 20 Jul 20181 second
Examining read alignment evidence07:06:30 20 Jul 201807:11:03 20 Jul 20184 minutes 33 seconds
Polymorphism statistics07:11:03 20 Jul 201807:11:03 20 Jul 20180 seconds
Output07:11:03 20 Jul 201807:11:15 20 Jul 201812 seconds
Total 10 minutes 46 seconds