breseq  version 0.33.2  revision caddc01d3be9
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 input10:13:08 21 Aug 201910:14:02 21 Aug 201954 seconds
Read alignment to reference genome10:14:03 21 Aug 201910:21:49 21 Aug 20197 minutes 46 seconds
Preprocessing alignments for candidate junction identification10:21:49 21 Aug 201910:22:34 21 Aug 201945 seconds
Preliminary analysis of coverage distribution10:22:34 21 Aug 201910:23:52 21 Aug 20191 minute 18 seconds
Identifying junction candidates10:23:52 21 Aug 201910:41:30 21 Aug 201917 minutes 38 seconds
Re-alignment to junction candidates10:41:30 21 Aug 201910:43:38 21 Aug 20192 minutes 8 seconds
Resolving best read alignments10:43:38 21 Aug 201910:44:45 21 Aug 20191 minute 7 seconds
Creating BAM files10:44:45 21 Aug 201910:46:04 21 Aug 20191 minute 19 seconds
Tabulating error counts10:46:04 21 Aug 201910:46:43 21 Aug 201939 seconds
Re-calibrating base error rates10:46:43 21 Aug 201910:46:45 21 Aug 20192 seconds
Examining read alignment evidence10:46:45 21 Aug 201910:54:59 21 Aug 20198 minutes 14 seconds
Polymorphism statistics10:54:59 21 Aug 201910:55:00 21 Aug 20191 second
Output10:55:00 21 Aug 201910:55:36 21 Aug 201936 seconds
Total 42 minutes 27 seconds