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_PALE__HGL_Pputida_164_S152_L001_R1_001.good.fq5,630,858835,221,782100.0%148.3 bases150 bases97.0%
errorsPputida_PALE__HGL_Pputida_164_S152_L001_R2_001.good.fq5,630,858835,221,782100.0%148.3 bases150 bases96.3%
total11,261,7161,670,443,564100.0%148.3 bases150 bases96.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,878260.64.0100.0%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≤ 100000100016
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 ≤ 50001162
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.058

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.55253

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input06:41:19 05 Apr 202006:44:14 05 Apr 20202 minutes 55 seconds
Read alignment to reference genome06:44:14 05 Apr 202007:08:15 05 Apr 202024 minutes 1 second
Preprocessing alignments for candidate junction identification07:08:15 05 Apr 202007:10:57 05 Apr 20202 minutes 42 seconds
Preliminary analysis of coverage distribution07:10:57 05 Apr 202007:16:08 05 Apr 20205 minutes 11 seconds
Identifying junction candidates07:16:08 05 Apr 202007:28:37 05 Apr 202012 minutes 29 seconds
Re-alignment to junction candidates07:28:37 05 Apr 202007:35:18 05 Apr 20206 minutes 41 seconds
Resolving best read alignments07:35:18 05 Apr 202007:40:30 05 Apr 20205 minutes 12 seconds
Creating BAM files07:40:30 05 Apr 202007:45:00 05 Apr 20204 minutes 30 seconds
Tabulating error counts07:45:00 05 Apr 202007:47:26 05 Apr 20202 minutes 26 seconds
Re-calibrating base error rates07:47:26 05 Apr 202007:47:28 05 Apr 20202 seconds
Examining read alignment evidence07:47:28 05 Apr 202009:18:02 05 Apr 20201 hour 30 minutes 34 seconds
Polymorphism statistics09:18:02 05 Apr 202009:18:17 05 Apr 202015 seconds
Output09:18:17 05 Apr 202009:22:24 05 Apr 20204 minutes 7 seconds
Total 2 hours 41 minutes 5 seconds