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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR14920191_R1.good.fq5,213,578720,532,020100.0%138.2 bases140 bases99.2%
errorsSRR14920191_R2.good.fq5,213,578720,532,020100.0%138.2 bases140 bases94.9%
total10,427,1561,441,064,040100.0%138.2 bases140 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_CP0252684,643,559316.713.1100.0%Escherichia coli str. K-12 substr. MG1655 strain K-12 chromosome,
total4,643,559100.0%

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≤ 10000017296
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 ≤ 5000858
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.054

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_CP0252680.66486

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≤ 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 input23:00:53 05 Mar 202323:03:25 05 Mar 20232 minutes 32 seconds
Read alignment to reference genome23:03:26 05 Mar 202323:26:03 05 Mar 202322 minutes 37 seconds
Preprocessing alignments for candidate junction identification23:26:03 05 Mar 202323:28:23 05 Mar 20232 minutes 20 seconds
Preliminary analysis of coverage distribution23:28:23 05 Mar 202323:33:49 05 Mar 20235 minutes 26 seconds
Identifying junction candidates23:33:49 05 Mar 202323:34:20 05 Mar 202331 seconds
Re-alignment to junction candidates23:34:20 05 Mar 202323:41:25 05 Mar 20237 minutes 5 seconds
Resolving best read alignments23:41:25 05 Mar 202323:44:57 05 Mar 20233 minutes 32 seconds
Creating BAM files23:44:57 05 Mar 202323:49:55 05 Mar 20234 minutes 58 seconds
Tabulating error counts23:49:55 05 Mar 202323:51:56 05 Mar 20232 minutes 1 second
Re-calibrating base error rates23:51:56 05 Mar 202323:51:57 05 Mar 20231 second
Examining read alignment evidence23:51:57 05 Mar 202300:18:13 06 Mar 202326 minutes 16 seconds
Polymorphism statistics00:18:13 06 Mar 202300:18:14 06 Mar 20231 second
Output00:18:14 06 Mar 202300:19:48 06 Mar 20231 minute 34 seconds
Total 1 hour 18 minutes 54 seconds