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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsAA288_S2056__R1_001.good.fq2,599,978392,596,678100.0%151.0 bases151 bases89.8%
errorsAA288_S2056__R2_001.good.fq2,599,950392,592,450100.0%151.0 bases151 bases88.0%
total5,199,928785,189,128100.0%151.0 bases151 bases88.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652144.92.2100.0%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≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001148
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.076

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.67287

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
bowtie22.3.4.1
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input14:37:54 28 Nov 201814:40:17 28 Nov 20182 minutes 23 seconds
Read alignment to reference genome14:40:18 28 Nov 201814:51:43 28 Nov 201811 minutes 25 seconds
Preprocessing alignments for candidate junction identification14:51:43 28 Nov 201814:53:31 28 Nov 20181 minute 48 seconds
Preliminary analysis of coverage distribution14:53:31 28 Nov 201814:56:23 28 Nov 20182 minutes 52 seconds
Identifying junction candidates14:56:23 28 Nov 201814:56:40 28 Nov 201817 seconds
Re-alignment to junction candidates14:56:40 28 Nov 201815:00:03 28 Nov 20183 minutes 23 seconds
Resolving best read alignments15:00:03 28 Nov 201815:02:52 28 Nov 20182 minutes 49 seconds
Creating BAM files15:02:52 28 Nov 201815:05:17 28 Nov 20182 minutes 25 seconds
Tabulating error counts15:05:17 28 Nov 201815:06:06 28 Nov 201849 seconds
Re-calibrating base error rates15:06:06 28 Nov 201815:06:07 28 Nov 20181 second
Examining read alignment evidence15:06:07 28 Nov 201815:12:28 28 Nov 20186 minutes 21 seconds
Polymorphism statistics15:12:28 28 Nov 201815:12:29 28 Nov 20181 second
Output15:12:29 28 Nov 201815:12:51 28 Nov 201822 seconds
Total 34 minutes 56 seconds