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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1711322_R1.good.fq1,091,120219,608,116100.0%201.3 bases236 bases96.0%
errorsERR1711322_R2.good.fq1,091,117178,403,711100.0%163.5 bases236 bases94.1%
total2,182,237398,011,827100.0%182.4 bases236 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAE0154516,181,87362.03.4100.0%Pseudomonas putida KT2440 complete genome.
total6,181,873100.0%

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≤ 10000013916
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 ≤ 50001176
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.091

Junction Skew Score Calculation

reference sequencepr(no read start)
AE0154510.87192

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 input16:13:31 24 Jan 202316:14:22 24 Jan 202351 seconds
Read alignment to reference genome16:14:23 24 Jan 202316:20:47 24 Jan 20236 minutes 24 seconds
Preprocessing alignments for candidate junction identification16:20:47 24 Jan 202316:21:16 24 Jan 202329 seconds
Preliminary analysis of coverage distribution16:21:16 24 Jan 202316:22:52 24 Jan 20231 minute 36 seconds
Identifying junction candidates16:22:52 24 Jan 202316:23:05 24 Jan 202313 seconds
Re-alignment to junction candidates16:23:05 24 Jan 202316:25:14 24 Jan 20232 minutes 9 seconds
Resolving best read alignments16:25:14 24 Jan 202316:25:58 24 Jan 202344 seconds
Creating BAM files16:25:58 24 Jan 202316:27:23 24 Jan 20231 minute 25 seconds
Tabulating error counts16:27:23 24 Jan 202316:28:00 24 Jan 202337 seconds
Re-calibrating base error rates16:28:00 24 Jan 202316:28:01 24 Jan 20231 second
Examining read alignment evidence16:28:01 24 Jan 202316:45:14 24 Jan 202317 minutes 13 seconds
Polymorphism statistics16:45:14 24 Jan 202316:45:15 24 Jan 20231 second
Output16:45:15 24 Jan 202316:46:20 24 Jan 20231 minute 5 seconds
Total 32 minutes 48 seconds