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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsDRR075745_R1.good.fq2,740,253690,021,896100.0%251.8 bases289 bases99.3%
errorsDRR075745_R2.good.fq2,740,253690,978,213100.0%252.2 bases289 bases94.5%
total5,480,5061,381,000,109100.0%252.0 bases289 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0425833,977,116340.17.7100.0%Escherichia coli str. K-12 substr. MDS42 strain SynAC chromosome,
total3,977,116100.0%

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≤ 10000015574
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 ≤ 500092
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0425830.69712

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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input06:22:01 07 Mar 202006:23:40 07 Mar 20201 minute 39 seconds
Read alignment to reference genome06:23:41 07 Mar 202006:46:04 07 Mar 202022 minutes 23 seconds
Preprocessing alignments for candidate junction identification06:46:04 07 Mar 202006:47:49 07 Mar 20201 minute 45 seconds
Preliminary analysis of coverage distribution06:47:49 07 Mar 202006:51:44 07 Mar 20203 minutes 55 seconds
Identifying junction candidates06:51:44 07 Mar 202006:53:06 07 Mar 20201 minute 22 seconds
Re-alignment to junction candidates06:53:06 07 Mar 202006:57:17 07 Mar 20204 minutes 11 seconds
Resolving best read alignments06:57:17 07 Mar 202007:00:17 07 Mar 20203 minutes 0 seconds
Creating BAM files07:00:17 07 Mar 202007:03:32 07 Mar 20203 minutes 15 seconds
Tabulating error counts07:03:32 07 Mar 202007:05:47 07 Mar 20202 minutes 15 seconds
Re-calibrating base error rates07:05:47 07 Mar 202007:05:48 07 Mar 20201 second
Examining read alignment evidence07:05:48 07 Mar 202007:29:46 07 Mar 202023 minutes 58 seconds
Polymorphism statistics07:29:46 07 Mar 202007:29:56 07 Mar 202010 seconds
Output07:29:56 07 Mar 202007:44:00 07 Mar 202014 minutes 4 seconds
Total 1 hour 21 minutes 58 seconds