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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_sub_A4_F36_I1_R1_001.good.fq837,118111,483,027100.0%133.2 bases136 bases97.0%
errorsPputida_sub_A4_F36_I1_R2_001.good.fq837,118111,483,027100.0%133.2 bases136 bases82.9%
total1,674,236222,966,054100.0%133.2 bases136 bases89.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,85835.74.4100.0%na
total6,183,858100.0%

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≤ 1000003350
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 ≤ 500089
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.91554

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 input04:05:03 03 Feb 202104:06:30 03 Feb 20211 minute 27 seconds
Read alignment to reference genome04:06:31 03 Feb 202104:18:45 03 Feb 202112 minutes 14 seconds
Preprocessing alignments for candidate junction identification04:18:45 03 Feb 202104:19:48 03 Feb 20211 minute 3 seconds
Preliminary analysis of coverage distribution04:19:48 03 Feb 202104:22:37 03 Feb 20212 minutes 49 seconds
Identifying junction candidates04:22:37 03 Feb 202104:22:39 03 Feb 20212 seconds
Re-alignment to junction candidates04:22:39 03 Feb 202104:25:36 03 Feb 20212 minutes 57 seconds
Resolving best read alignments04:25:36 03 Feb 202104:27:01 03 Feb 20211 minute 25 seconds
Creating BAM files04:27:01 03 Feb 202104:29:29 03 Feb 20212 minutes 28 seconds
Tabulating error counts04:29:29 03 Feb 202104:30:21 03 Feb 202152 seconds
Re-calibrating base error rates04:30:21 03 Feb 202104:30:24 03 Feb 20213 seconds
Examining read alignment evidence04:30:24 03 Feb 202104:42:11 03 Feb 202111 minutes 47 seconds
Polymorphism statistics04:42:11 03 Feb 202104:42:12 03 Feb 20211 second
Output04:42:12 03 Feb 202104:44:12 03 Feb 20212 minutes 0 seconds
Total 39 minutes 8 seconds