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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR13416474_R1.good.fq1,602,646399,052,848100.0%249.0 bases249 bases67.4%
errorsSRR13416474_R2.good.fq1,602,646399,052,848100.0%249.0 bases249 bases66.6%
total3,205,292798,105,696100.0%249.0 bases249 bases67.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0255333,316,624174.01.6100.0%Corynebacterium glutamicum strain ATCC 13032 chromosome, complete
total3,316,624100.0%

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≤ 1000007085
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 ≤ 500054
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0255330.74543

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 input12:53:47 13 Feb 202312:54:52 13 Feb 20231 minute 5 seconds
Read alignment to reference genome12:54:52 13 Feb 202313:03:45 13 Feb 20238 minutes 53 seconds
Preprocessing alignments for candidate junction identification13:03:45 13 Feb 202313:04:20 13 Feb 202335 seconds
Preliminary analysis of coverage distribution13:04:20 13 Feb 202313:06:21 13 Feb 20232 minutes 1 second
Identifying junction candidates13:06:21 13 Feb 202313:06:21 13 Feb 20230 seconds
Re-alignment to junction candidates13:06:21 13 Feb 202313:08:49 13 Feb 20232 minutes 28 seconds
Resolving best read alignments13:08:49 13 Feb 202313:09:56 13 Feb 20231 minute 7 seconds
Creating BAM files13:09:56 13 Feb 202313:11:42 13 Feb 20231 minute 46 seconds
Tabulating error counts13:11:42 13 Feb 202313:12:29 13 Feb 202347 seconds
Re-calibrating base error rates13:12:29 13 Feb 202313:12:30 13 Feb 20231 second
Examining read alignment evidence13:12:30 13 Feb 202313:21:56 13 Feb 20239 minutes 26 seconds
Polymorphism statistics13:21:56 13 Feb 202313:21:56 13 Feb 20230 seconds
Output13:21:56 13 Feb 202313:22:21 13 Feb 202325 seconds
Total 28 minutes 34 seconds