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_82_S219_L002_R1_001.good.fq1,622,353217,373,057100.0%134.0 bases150 bases94.3%
errorsPputida_HGL_82_S219_L002_R2_001.good.fq1,622,353217,373,057100.0%134.0 bases150 bases92.4%
total3,244,706434,746,114100.0%134.0 bases150 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92965.62.6100.0%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≤ 10000056509
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 ≤ 50001102
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.055

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.80109

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 input08:47:26 22 Aug 201908:48:10 22 Aug 201944 seconds
Read alignment to reference genome08:48:10 22 Aug 201908:55:20 22 Aug 20197 minutes 10 seconds
Preprocessing alignments for candidate junction identification08:55:20 22 Aug 201908:56:06 22 Aug 201946 seconds
Preliminary analysis of coverage distribution08:56:06 22 Aug 201908:57:41 22 Aug 20191 minute 35 seconds
Identifying junction candidates08:57:41 22 Aug 201909:14:20 22 Aug 201916 minutes 39 seconds
Re-alignment to junction candidates09:14:20 22 Aug 201909:16:12 22 Aug 20191 minute 52 seconds
Resolving best read alignments09:16:12 22 Aug 201909:17:27 22 Aug 20191 minute 15 seconds
Creating BAM files09:17:27 22 Aug 201909:18:57 22 Aug 20191 minute 30 seconds
Tabulating error counts09:18:57 22 Aug 201909:19:28 22 Aug 201931 seconds
Re-calibrating base error rates09:19:28 22 Aug 201909:19:29 22 Aug 20191 second
Examining read alignment evidence09:19:29 22 Aug 201909:25:45 22 Aug 20196 minutes 16 seconds
Polymorphism statistics09:25:45 22 Aug 201909:25:45 22 Aug 20190 seconds
Output09:25:45 22 Aug 201909:26:16 22 Aug 201931 seconds
Total 38 minutes 50 seconds