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_A5_F2_I1_R1_001.good.fq8,703,0331,273,114,011100.0%146.3 bases150 bases95.2%
errorsPputida_sub_A5_F2_I1_R2_001.good.fq8,703,0331,273,114,011100.0%146.3 bases150 bases94.6%
total17,406,0662,546,228,022100.0%146.3 bases150 bases94.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,878387.36.4100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,186,878100.0%

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≤ 100000100000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000698
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.035

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.43619

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 input08:32:03 05 Mar 202108:37:00 05 Mar 20214 minutes 57 seconds
Read alignment to reference genome08:37:01 05 Mar 202109:19:16 05 Mar 202142 minutes 15 seconds
Preprocessing alignments for candidate junction identification09:19:16 05 Mar 202109:23:31 05 Mar 20214 minutes 15 seconds
Preliminary analysis of coverage distribution09:23:31 05 Mar 202109:31:35 05 Mar 20218 minutes 4 seconds
Identifying junction candidates09:31:35 05 Mar 202109:34:40 05 Mar 20213 minutes 5 seconds
Re-alignment to junction candidates09:34:40 05 Mar 202109:46:03 05 Mar 202111 minutes 23 seconds
Resolving best read alignments09:46:03 05 Mar 202109:51:51 05 Mar 20215 minutes 48 seconds
Creating BAM files09:51:51 05 Mar 202109:59:13 05 Mar 20217 minutes 22 seconds
Tabulating error counts09:59:13 05 Mar 202110:02:53 05 Mar 20213 minutes 40 seconds
Re-calibrating base error rates10:02:53 05 Mar 202110:02:54 05 Mar 20211 second
Examining read alignment evidence10:02:54 05 Mar 202110:45:15 05 Mar 202142 minutes 21 seconds
Polymorphism statistics10:45:15 05 Mar 202110:45:34 05 Mar 202119 seconds
Output10:45:34 05 Mar 202110:46:23 05 Mar 202149 seconds
Total 2 hours 14 minutes 19 seconds