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_741_CACGAGTT-TCACGGTT.R1.good.fq1,693,130172,060,212100.0%101.6 bases139 bases90.7%
errorsT1000_741_CACGAGTT-TCACGGTT.R2.good.fq1,693,130172,060,212100.0%101.6 bases139 bases90.7%
total3,386,260344,120,424100.0%101.6 bases139 bases90.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65265.23.6100.0%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≤ 1000004253
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 ≤ 5000604
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.037

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.78037

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 input13:55:03 20 Jul 201813:55:38 20 Jul 201835 seconds
Read alignment to reference genome13:55:38 20 Jul 201813:57:17 20 Jul 20181 minute 39 seconds
Preprocessing alignments for candidate junction identification13:57:17 20 Jul 201813:57:59 20 Jul 201842 seconds
Preliminary analysis of coverage distribution13:57:59 20 Jul 201813:59:05 20 Jul 20181 minute 6 seconds
Identifying junction candidates13:59:05 20 Jul 201813:59:11 20 Jul 20186 seconds
Re-alignment to junction candidates13:59:11 20 Jul 201813:59:33 20 Jul 201822 seconds
Resolving best read alignments13:59:33 20 Jul 201814:00:44 20 Jul 20181 minute 11 seconds
Creating BAM files14:00:44 20 Jul 201814:01:42 20 Jul 201858 seconds
Tabulating error counts14:01:42 20 Jul 201814:02:07 20 Jul 201825 seconds
Re-calibrating base error rates14:02:07 20 Jul 201814:02:08 20 Jul 20181 second
Examining read alignment evidence14:02:08 20 Jul 201814:07:01 20 Jul 20184 minutes 53 seconds
Polymorphism statistics14:07:01 20 Jul 201814:07:01 20 Jul 20180 seconds
Output14:07:01 20 Jul 201814:08:04 20 Jul 20181 minute 3 seconds
Total 13 minutes 1 second