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_4_S333_L002_R1_001.good.fq1,269,030171,193,365100.0%134.9 bases150 bases92.3%
errorsPputida_HGL_4_S333_L002_R2_001.good.fq1,269,030171,193,365100.0%134.9 bases150 bases90.4%
total2,538,060342,386,730100.0%134.9 bases150 bases91.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92950.43.1100.0%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≤ 10000061081
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 ≤ 50001025
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.051

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.84141

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 input22:11:59 06 Apr 202022:12:42 06 Apr 202043 seconds
Read alignment to reference genome22:12:42 06 Apr 202022:19:09 06 Apr 20206 minutes 27 seconds
Preprocessing alignments for candidate junction identification22:19:09 06 Apr 202022:19:45 06 Apr 202036 seconds
Preliminary analysis of coverage distribution22:19:45 06 Apr 202022:21:07 06 Apr 20201 minute 22 seconds
Identifying junction candidates22:21:07 06 Apr 202022:31:43 06 Apr 202010 minutes 36 seconds
Re-alignment to junction candidates22:31:43 06 Apr 202022:33:27 06 Apr 20201 minute 44 seconds
Resolving best read alignments22:33:27 06 Apr 202022:34:28 06 Apr 20201 minute 1 second
Creating BAM files22:34:28 06 Apr 202022:35:43 06 Apr 20201 minute 15 seconds
Tabulating error counts22:35:43 06 Apr 202022:36:08 06 Apr 202025 seconds
Re-calibrating base error rates22:36:08 06 Apr 202022:36:10 06 Apr 20202 seconds
Examining read alignment evidence22:36:10 06 Apr 202022:41:23 06 Apr 20205 minutes 13 seconds
Polymorphism statistics22:41:23 06 Apr 202022:41:24 06 Apr 20201 second
Output22:41:24 06 Apr 202022:41:58 06 Apr 202034 seconds
Total 29 minutes 59 seconds