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_557_CCGTTATT-GACCGCCA.R1.good.fq1,508,324168,750,808100.0%111.9 bases139 bases94.6%
errorsT1000_557_CCGTTATT-GACCGCCA.R2.good.fq1,508,324168,750,808100.0%111.9 bases139 bases94.5%
total3,016,648337,501,616100.0%111.9 bases139 bases94.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65265.34.6100.0%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≤ 1000002012
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 ≤ 5000308
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.019

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79752

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 input00:59:36 20 Jul 201801:00:08 20 Jul 201832 seconds
Read alignment to reference genome01:00:09 20 Jul 201801:01:48 20 Jul 20181 minute 39 seconds
Preprocessing alignments for candidate junction identification01:01:48 20 Jul 201801:02:27 20 Jul 201839 seconds
Preliminary analysis of coverage distribution01:02:27 20 Jul 201801:03:34 20 Jul 20181 minute 7 seconds
Identifying junction candidates01:03:34 20 Jul 201801:03:35 20 Jul 20181 second
Re-alignment to junction candidates01:03:35 20 Jul 201801:03:55 20 Jul 201820 seconds
Resolving best read alignments01:03:55 20 Jul 201801:05:00 20 Jul 20181 minute 5 seconds
Creating BAM files01:05:00 20 Jul 201801:05:58 20 Jul 201858 seconds
Tabulating error counts01:05:58 20 Jul 201801:06:25 20 Jul 201827 seconds
Re-calibrating base error rates01:06:25 20 Jul 201801:06:25 20 Jul 20180 seconds
Examining read alignment evidence01:06:25 20 Jul 201801:11:29 20 Jul 20185 minutes 4 seconds
Polymorphism statistics01:11:29 20 Jul 201801:11:30 20 Jul 20181 second
Output01:11:30 20 Jul 201801:11:43 20 Jul 201813 seconds
Total 12 minutes 6 seconds