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-F1_S88_R1_001.good.fq5,698,161339,264,235100.0%59.5 bases71 bases66.1%
total5,698,161339,264,235100.0%59.5 bases71 bases66.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionExported2,987,94275.38.3100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total2,987,942100.0%

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≤ 10000042236
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 ≤ 50001243
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.062

Junction Skew Score Calculation

reference sequencepr(no read start)
Exported0.67043

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 input09:51:13 28 Jun 201909:52:09 28 Jun 201956 seconds
Read alignment to reference genome09:52:10 28 Jun 201910:35:06 28 Jun 201942 minutes 56 seconds
Preprocessing alignments for candidate junction identification10:35:06 28 Jun 201910:36:04 28 Jun 201958 seconds
Preliminary analysis of coverage distribution10:36:04 28 Jun 201910:37:12 28 Jun 20191 minute 8 seconds
Identifying junction candidates10:37:12 28 Jun 201910:37:53 28 Jun 201941 seconds
Re-alignment to junction candidates10:37:53 28 Jun 201910:40:20 28 Jun 20192 minutes 27 seconds
Resolving best read alignments10:40:20 28 Jun 201910:41:46 28 Jun 20191 minute 26 seconds
Creating BAM files10:41:46 28 Jun 201910:42:48 28 Jun 20191 minute 2 seconds
Tabulating error counts10:42:48 28 Jun 201910:43:08 28 Jun 201920 seconds
Re-calibrating base error rates10:43:08 28 Jun 201910:43:08 28 Jun 20190 seconds
Examining read alignment evidence10:43:08 28 Jun 201910:49:03 28 Jun 20195 minutes 55 seconds
Polymorphism statistics10:49:03 28 Jun 201910:49:06 28 Jun 20193 seconds
Output10:49:06 28 Jun 201910:51:47 28 Jun 20192 minutes 41 seconds
Total 1 hour 33 seconds