breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_89_S218_L002_R1_001.good.fq1,499,791197,406,360100.0%131.6 bases150 bases93.2%
errorsPputida_HGL_89_S218_L002_R2_001.good.fq1,499,791197,406,360100.0%131.6 bases150 bases91.4%
total2,999,582394,812,720100.0%131.6 bases150 bases92.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92958.42.5100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,929100.0%

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≤ 10000087791
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 ≤ 50001546
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.077

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.81565

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
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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input10:58:19 22 Aug 201910:59:00 22 Aug 201941 seconds
Read alignment to reference genome10:59:00 22 Aug 201911:05:48 22 Aug 20196 minutes 48 seconds
Preprocessing alignments for candidate junction identification11:05:48 22 Aug 201911:06:33 22 Aug 201945 seconds
Preliminary analysis of coverage distribution11:06:33 22 Aug 201911:07:58 22 Aug 20191 minute 25 seconds
Identifying junction candidates11:07:58 22 Aug 201911:27:58 22 Aug 201920 minutes 0 seconds
Re-alignment to junction candidates11:27:58 22 Aug 201911:30:00 22 Aug 20192 minutes 2 seconds
Resolving best read alignments11:30:00 22 Aug 201911:31:12 22 Aug 20191 minute 12 seconds
Creating BAM files11:31:12 22 Aug 201911:32:30 22 Aug 20191 minute 18 seconds
Tabulating error counts11:32:30 22 Aug 201911:32:58 22 Aug 201928 seconds
Re-calibrating base error rates11:32:58 22 Aug 201911:32:59 22 Aug 20191 second
Examining read alignment evidence11:32:59 22 Aug 201911:38:30 22 Aug 20195 minutes 31 seconds
Polymorphism statistics11:38:30 22 Aug 201911:38:31 22 Aug 20191 second
Output11:38:31 22 Aug 201911:39:15 22 Aug 201944 seconds
Total 40 minutes 56 seconds