breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR12717915_R1.good.fq1,571,734229,602,031100.0%146.1 bases149 bases97.6%
errorsSRR12717915_R2.good.fq1,571,734233,663,290100.0%148.7 bases149 bases97.2%
total3,143,468463,265,321100.0%147.4 bases149 bases97.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65295.42.7100.0%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≤ 10000038384
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 ≤ 5000447
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.029

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.73394

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 input19:59:36 01 Feb 202120:02:52 01 Feb 20213 minutes 16 seconds
Read alignment to reference genome20:02:53 01 Feb 202120:26:27 01 Feb 202123 minutes 34 seconds
Preprocessing alignments for candidate junction identification20:26:27 01 Feb 202120:28:48 01 Feb 20212 minutes 21 seconds
Preliminary analysis of coverage distribution20:28:48 01 Feb 202120:34:24 01 Feb 20215 minutes 36 seconds
Identifying junction candidates20:34:24 01 Feb 202120:34:35 01 Feb 202111 seconds
Re-alignment to junction candidates20:34:35 01 Feb 202120:40:57 01 Feb 20216 minutes 22 seconds
Resolving best read alignments20:40:57 01 Feb 202120:44:50 01 Feb 20213 minutes 53 seconds
Creating BAM files20:44:50 01 Feb 202120:49:55 01 Feb 20215 minutes 5 seconds
Tabulating error counts20:49:55 01 Feb 202120:52:06 01 Feb 20212 minutes 11 seconds
Re-calibrating base error rates20:52:06 01 Feb 202120:52:11 01 Feb 20215 seconds
Examining read alignment evidence20:52:11 01 Feb 202121:21:59 01 Feb 202129 minutes 48 seconds
Polymorphism statistics21:21:59 01 Feb 202121:22:00 01 Feb 20211 second
Output21:22:00 01 Feb 202121:22:38 01 Feb 202138 seconds
Total 1 hour 23 minutes 1 second