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_50_S241_L002_R1_001.good.fq1,427,630191,287,876100.0%134.0 bases150 bases93.8%
errorsPputida_HGL_50_S241_L002_R2_001.good.fq1,427,630191,287,876100.0%134.0 bases150 bases91.9%
total2,855,260382,575,752100.0%134.0 bases150 bases92.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92957.42.5100.0%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≤ 10000056029
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 ≤ 50001085
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.054

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.82262

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 input03:14:35 30 Mar 202003:15:22 30 Mar 202047 seconds
Read alignment to reference genome03:15:22 30 Mar 202003:22:15 30 Mar 20206 minutes 53 seconds
Preprocessing alignments for candidate junction identification03:22:15 30 Mar 202003:22:53 30 Mar 202038 seconds
Preliminary analysis of coverage distribution03:22:53 30 Mar 202003:24:22 30 Mar 20201 minute 29 seconds
Identifying junction candidates03:24:22 30 Mar 202003:43:27 30 Mar 202019 minutes 5 seconds
Re-alignment to junction candidates03:43:27 30 Mar 202003:45:19 30 Mar 20201 minute 52 seconds
Resolving best read alignments03:45:19 30 Mar 202003:46:27 30 Mar 20201 minute 8 seconds
Creating BAM files03:46:27 30 Mar 202003:47:54 30 Mar 20201 minute 27 seconds
Tabulating error counts03:47:54 30 Mar 202003:48:23 30 Mar 202029 seconds
Re-calibrating base error rates03:48:23 30 Mar 202003:48:25 30 Mar 20202 seconds
Examining read alignment evidence03:48:25 30 Mar 202004:06:07 30 Mar 202017 minutes 42 seconds
Polymorphism statistics04:06:07 30 Mar 202004:06:09 30 Mar 20202 seconds
Output04:06:09 30 Mar 202004:10:10 30 Mar 20204 minutes 1 second
Total 55 minutes 35 seconds