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_TALE__HGL_Pputida_113_S101_L001_R1_001.good.fq8,639,3991,280,832,661100.0%148.3 bases150 bases95.7%
errorsPputida_TALE__HGL_Pputida_113_S101_L001_R2_001.good.fq8,639,3991,280,832,661100.0%148.3 bases150 bases95.1%
total17,278,7982,561,665,322100.0%148.3 bases150 bases95.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,929394.66.0100.0%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≤ 100000100021
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 ≤ 5000780
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.039

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.44967

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 input19:56:48 06 Apr 202020:01:20 06 Apr 20204 minutes 32 seconds
Read alignment to reference genome20:01:20 06 Apr 202020:42:13 06 Apr 202040 minutes 53 seconds
Preprocessing alignments for candidate junction identification20:42:13 06 Apr 202020:46:56 06 Apr 20204 minutes 43 seconds
Preliminary analysis of coverage distribution20:46:56 06 Apr 202020:55:22 06 Apr 20208 minutes 26 seconds
Identifying junction candidates20:55:22 06 Apr 202021:00:15 06 Apr 20204 minutes 53 seconds
Re-alignment to junction candidates21:00:16 06 Apr 202021:10:34 06 Apr 202010 minutes 18 seconds
Resolving best read alignments21:10:34 06 Apr 202021:19:54 06 Apr 20209 minutes 20 seconds
Creating BAM files21:19:54 06 Apr 202021:26:57 06 Apr 20207 minutes 3 seconds
Tabulating error counts21:26:57 06 Apr 202021:31:05 06 Apr 20204 minutes 8 seconds
Re-calibrating base error rates21:31:05 06 Apr 202021:31:07 06 Apr 20202 seconds
Examining read alignment evidence21:31:07 06 Apr 202022:10:11 06 Apr 202039 minutes 4 seconds
Polymorphism statistics22:10:11 06 Apr 202022:10:28 06 Apr 202017 seconds
Output22:10:28 06 Apr 202022:11:50 06 Apr 20201 minute 22 seconds
Total 2 hours 15 minutes 1 second