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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ0-E2_S87_R1_001.good.fq7,939,938476,842,436100.0%60.1 bases71 bases96.9%
total7,939,938476,842,436100.0%60.1 bases71 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAP0090484,646,33299.610.1100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total4,646,332100.0%

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≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000489
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
AP0090480.57958

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input12:49:15 01 Jul 201912:50:59 01 Jul 20191 minute 44 seconds
Read alignment to reference genome12:51:00 01 Jul 201913:01:44 01 Jul 201910 minutes 44 seconds
Preprocessing alignments for candidate junction identification13:01:44 01 Jul 201913:03:19 01 Jul 20191 minute 35 seconds
Preliminary analysis of coverage distribution13:03:19 01 Jul 201913:05:46 01 Jul 20192 minutes 27 seconds
Identifying junction candidates13:05:46 01 Jul 201913:07:47 01 Jul 20192 minutes 1 second
Re-alignment to junction candidates13:07:47 01 Jul 201913:10:32 01 Jul 20192 minutes 45 seconds
Resolving best read alignments13:10:32 01 Jul 201913:12:47 01 Jul 20192 minutes 15 seconds
Creating BAM files13:12:47 01 Jul 201913:15:05 01 Jul 20192 minutes 18 seconds
Tabulating error counts13:15:05 01 Jul 201913:15:48 01 Jul 201943 seconds
Re-calibrating base error rates13:15:48 01 Jul 201913:15:49 01 Jul 20191 second
Examining read alignment evidence13:15:49 01 Jul 201913:29:59 01 Jul 201914 minutes 10 seconds
Polymorphism statistics13:29:59 01 Jul 201913:30:01 01 Jul 20192 seconds
Output13:30:01 01 Jul 201913:31:06 01 Jul 20191 minute 5 seconds
Total 41 minutes 50 seconds