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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR4111267_R1.good.fq657,738194,029,221100.0%295.0 bases299 bases96.8%
errorsSRR4111267_R2.good.fq657,738194,029,221100.0%295.0 bases299 bases56.7%
total1,315,476388,058,442100.0%295.0 bases299 bases76.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0065844,835,60160.84.1100.0%Escherichia coli LY180, complete genome.
total4,835,601100.0%

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≤ 10000028861
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 ≤ 5000345
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.043

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0065840.91364

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input22:52:23 09 Apr 202022:52:55 09 Apr 202032 seconds
Read alignment to reference genome22:52:55 09 Apr 202023:03:17 09 Apr 202010 minutes 22 seconds
Preprocessing alignments for candidate junction identification23:03:17 09 Apr 202023:03:41 09 Apr 202024 seconds
Preliminary analysis of coverage distribution23:03:41 09 Apr 202023:04:42 09 Apr 20201 minute 1 second
Identifying junction candidates23:04:42 09 Apr 202023:05:10 09 Apr 202028 seconds
Re-alignment to junction candidates23:05:10 09 Apr 202023:06:51 09 Apr 20201 minute 41 seconds
Resolving best read alignments23:06:51 09 Apr 202023:07:32 09 Apr 202041 seconds
Creating BAM files23:07:32 09 Apr 202023:08:22 09 Apr 202050 seconds
Tabulating error counts23:08:22 09 Apr 202023:08:51 09 Apr 202029 seconds
Re-calibrating base error rates23:08:51 09 Apr 202023:08:52 09 Apr 20201 second
Examining read alignment evidence23:08:52 09 Apr 202023:14:24 09 Apr 20205 minutes 32 seconds
Polymorphism statistics23:14:24 09 Apr 202023:14:24 09 Apr 20200 seconds
Output23:14:24 09 Apr 202023:14:52 09 Apr 202028 seconds
Total 22 minutes 29 seconds