breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJBI_KHP_HGL_027_S387_L001_R1_001.good.fq9,102,9701,356,132,447100.0%149.0 bases149 bases96.4%
errorsJBI_KHP_HGL_027_S387_L001_R2_001.good.fq9,102,9701,356,132,447100.0%149.0 bases149 bases96.1%
total18,205,9402,712,264,894100.0%149.0 bases149 bases96.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,878426.88.3100.0%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≤ 100000100006
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000731
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.036

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.37935

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 input09:22:26 05 Apr 202009:27:07 05 Apr 20204 minutes 41 seconds
Read alignment to reference genome09:27:07 05 Apr 202010:06:16 05 Apr 202039 minutes 9 seconds
Preprocessing alignments for candidate junction identification10:06:16 05 Apr 202010:10:37 05 Apr 20204 minutes 21 seconds
Preliminary analysis of coverage distribution10:10:37 05 Apr 202010:18:54 05 Apr 20208 minutes 17 seconds
Identifying junction candidates10:18:54 05 Apr 202010:20:40 05 Apr 20201 minute 46 seconds
Re-alignment to junction candidates10:20:40 05 Apr 202010:30:46 05 Apr 202010 minutes 6 seconds
Resolving best read alignments10:30:46 05 Apr 202010:39:10 05 Apr 20208 minutes 24 seconds
Creating BAM files10:39:10 05 Apr 202010:46:28 05 Apr 20207 minutes 18 seconds
Tabulating error counts10:46:28 05 Apr 202010:50:40 05 Apr 20204 minutes 12 seconds
Re-calibrating base error rates10:50:40 05 Apr 202010:50:41 05 Apr 20201 second
Examining read alignment evidence10:50:41 05 Apr 202011:29:45 05 Apr 202039 minutes 4 seconds
Polymorphism statistics11:29:45 05 Apr 202011:30:02 05 Apr 202017 seconds
Output11:30:02 05 Apr 202011:31:29 05 Apr 20201 minute 27 seconds
Total 2 hours 9 minutes 3 seconds