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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-76_S76_L001_R1_001.good.fq318,35945,771,029100.0%143.8 bases149 bases91.6%
errorsALE-76_S76_L001_R2_001.good.fq318,35945,495,632100.0%142.9 bases149 bases92.9%
errorsALE-76_S76_L002_R1_001.good.fq305,64443,876,720100.0%143.6 bases149 bases93.3%
errorsALE-76_S76_L002_R2_001.good.fq305,64443,641,762100.0%142.8 bases149 bases93.7%
errorsALE-76_S76_L003_R1_001.good.fq324,36046,546,685100.0%143.5 bases149 bases93.1%
errorsALE-76_S76_L003_R2_001.good.fq324,36046,282,816100.0%142.7 bases149 bases94.1%
errorsALE-76_S76_L004_R1_001.good.fq292,86242,008,085100.0%143.4 bases149 bases93.2%
errorsALE-76_S76_L004_R2_001.good.fq292,86241,782,586100.0%142.7 bases149 bases93.3%
total2,482,450355,405,315100.0%143.2 bases149 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,87353.82.1100.0%Pseudomonas putida KT2440 chromosome, complete genome.

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

Number of alignment pairs examined for constructing junction candidates≤ 10000062042
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 ≤ 5000532
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.026

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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


Execution Times

Read and reference sequence file input05:35:03 19 Feb 202005:35:40 19 Feb 202037 seconds
Read alignment to reference genome05:35:41 19 Feb 202005:41:11 19 Feb 20205 minutes 30 seconds
Preprocessing alignments for candidate junction identification05:41:11 19 Feb 202005:41:45 19 Feb 202034 seconds
Preliminary analysis of coverage distribution05:41:45 19 Feb 202005:43:09 19 Feb 20201 minute 24 seconds
Identifying junction candidates05:43:09 19 Feb 202005:51:07 19 Feb 20207 minutes 58 seconds
Re-alignment to junction candidates05:51:07 19 Feb 202005:52:49 19 Feb 20201 minute 42 seconds
Resolving best read alignments05:52:49 19 Feb 202005:53:43 19 Feb 202054 seconds
Creating BAM files05:53:43 19 Feb 202005:55:00 19 Feb 20201 minute 17 seconds
Tabulating error counts05:55:00 19 Feb 202005:55:25 19 Feb 202025 seconds
Re-calibrating base error rates05:55:25 19 Feb 202005:55:28 19 Feb 20203 seconds
Examining read alignment evidence05:55:28 19 Feb 202006:00:29 19 Feb 20205 minutes 1 second
Polymorphism statistics06:00:29 19 Feb 202006:00:30 19 Feb 20201 second
Output06:00:30 19 Feb 202006:01:04 19 Feb 202034 seconds
Total 26 minutes 0 seconds