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_54_S212_L002_R1_001.good.fq1,053,719141,406,848100.0%134.2 bases150 bases93.8%
errorsPputida_HGL_54_S212_L002_R2_001.good.fq1,053,719141,406,848100.0%134.2 bases150 bases91.9%
total2,107,438282,813,696100.0%134.2 bases150 bases92.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92942.22.5100.0%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≤ 10000041757
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 ≤ 5000630
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.032

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.86355

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 input15:24:15 26 Mar 202015:24:49 26 Mar 202034 seconds
Read alignment to reference genome15:24:49 26 Mar 202015:29:25 26 Mar 20204 minutes 36 seconds
Preprocessing alignments for candidate junction identification15:29:25 26 Mar 202015:29:55 26 Mar 202030 seconds
Preliminary analysis of coverage distribution15:29:55 26 Mar 202015:30:56 26 Mar 20201 minute 1 second
Identifying junction candidates15:30:56 26 Mar 202015:38:24 26 Mar 20207 minutes 28 seconds
Re-alignment to junction candidates15:38:24 26 Mar 202015:39:32 26 Mar 20201 minute 8 seconds
Resolving best read alignments15:39:32 26 Mar 202015:40:24 26 Mar 202052 seconds
Creating BAM files15:40:24 26 Mar 202015:41:24 26 Mar 20201 minute 0 seconds
Tabulating error counts15:41:24 26 Mar 202015:41:44 26 Mar 202020 seconds
Re-calibrating base error rates15:41:44 26 Mar 202015:41:46 26 Mar 20202 seconds
Examining read alignment evidence15:41:46 26 Mar 202015:46:00 26 Mar 20204 minutes 14 seconds
Polymorphism statistics15:46:00 26 Mar 202015:46:00 26 Mar 20200 seconds
Output15:46:00 26 Mar 202015:46:24 26 Mar 202024 seconds
Total 22 minutes 9 seconds