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_46_S295_L002_R1_001.good.fq3,844,479513,514,827100.0%133.6 bases150 bases95.9%
errorsPputida_HGL_46_S295_L002_R2_001.good.fq3,844,479513,514,827100.0%133.6 bases150 bases94.3%
total7,688,9581,027,029,654100.0%133.6 bases150 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,929157.94.2100.0%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≤ 10000086949
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 ≤ 50001722
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.086

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.60773

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 input17:12:18 20 Aug 201917:15:25 20 Aug 20193 minutes 7 seconds
Read alignment to reference genome17:15:25 20 Aug 201917:42:11 20 Aug 201926 minutes 46 seconds
Preprocessing alignments for candidate junction identification17:42:11 20 Aug 201917:44:56 20 Aug 20192 minutes 45 seconds
Preliminary analysis of coverage distribution17:44:56 20 Aug 201917:50:26 20 Aug 20195 minutes 30 seconds
Identifying junction candidates17:50:26 20 Aug 201920:06:07 20 Aug 20192 hours 15 minutes 41 seconds
Re-alignment to junction candidates20:06:07 20 Aug 201920:15:35 20 Aug 20199 minutes 28 seconds
Resolving best read alignments20:15:35 20 Aug 201920:19:47 20 Aug 20194 minutes 12 seconds
Creating BAM files20:19:47 20 Aug 201920:24:37 20 Aug 20194 minutes 50 seconds
Tabulating error counts20:24:37 20 Aug 201920:27:17 20 Aug 20192 minutes 40 seconds
Re-calibrating base error rates20:27:17 20 Aug 201920:27:18 20 Aug 20191 second
Examining read alignment evidence20:27:18 20 Aug 201921:03:39 20 Aug 201936 minutes 21 seconds
Polymorphism statistics21:03:39 20 Aug 201921:03:41 20 Aug 20192 seconds
Output21:03:41 20 Aug 201921:05:35 20 Aug 20191 minute 54 seconds
Total 3 hours 53 minutes 17 seconds