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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR12117907_R1.good.fq1,464,963218,597,187100.0%149.2 bases150 bases95.4%
errorsSRR12117907_R2.good.fq1,464,963218,606,447100.0%149.2 bases150 bases94.8%
total2,929,926437,203,634100.0%149.2 bases150 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,46978.71.6100.0%Escherichia coli BW25113, complete genome.
total4,631,469100.0%

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≤ 10000016591
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 ≤ 5000121
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.76427

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≤ 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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input15:43:48 21 Feb 202315:44:52 21 Feb 20231 minute 4 seconds
Read alignment to reference genome15:44:53 21 Feb 202315:53:03 21 Feb 20238 minutes 10 seconds
Preprocessing alignments for candidate junction identification15:53:03 21 Feb 202315:53:42 21 Feb 202339 seconds
Preliminary analysis of coverage distribution15:53:42 21 Feb 202315:55:26 21 Feb 20231 minute 44 seconds
Identifying junction candidates15:55:26 21 Feb 202315:55:28 21 Feb 20232 seconds
Re-alignment to junction candidates15:55:28 21 Feb 202315:56:55 21 Feb 20231 minute 27 seconds
Resolving best read alignments15:56:55 21 Feb 202315:57:49 21 Feb 202354 seconds
Creating BAM files15:57:49 21 Feb 202315:59:33 21 Feb 20231 minute 44 seconds
Tabulating error counts15:59:33 21 Feb 202316:00:10 21 Feb 202337 seconds
Re-calibrating base error rates16:00:10 21 Feb 202316:00:11 21 Feb 20231 second
Examining read alignment evidence16:00:11 21 Feb 202316:16:16 21 Feb 202316 minutes 5 seconds
Polymorphism statistics16:16:16 21 Feb 202316:16:18 21 Feb 20232 seconds
Output16:16:18 21 Feb 202316:16:43 21 Feb 202325 seconds
Total 32 minutes 54 seconds