breseq  version 0.27.0b  revision f32c2f7f32bc
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsBOP27Reseq_S1_L001_R15,978,523980,052,088100.0%163.9 bases251 bases99.0%
errorsBOP27Reseq_S1_L001_R25,977,520980,235,110100.0%164.0 bases251 bases98.7%
total11,956,0431,960,287,198100.0%164.0 bases251 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652422.411.9100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 1000006265
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000763
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.084

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.62484

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input13:30:07 14 Feb 201613:33:14 14 Feb 20163 minutes 7 seconds
Read alignment to reference genome13:33:15 14 Feb 201613:41:33 14 Feb 20168 minutes 18 seconds
Preprocessing alignments for candidate junction identification13:41:33 14 Feb 201613:45:58 14 Feb 20164 minutes 25 seconds
Preliminary analysis of coverage distribution13:45:58 14 Feb 201613:58:11 14 Feb 201612 minutes 13 seconds
Identifying junction candidates13:58:11 14 Feb 201613:58:12 14 Feb 20161 second
Re-alignment to junction candidates13:58:12 14 Feb 201614:00:48 14 Feb 20162 minutes 36 seconds
Resolving alignments with junction candidates14:00:48 14 Feb 201614:11:04 14 Feb 201610 minutes 16 seconds
Creating BAM files14:11:04 14 Feb 201614:19:03 14 Feb 20167 minutes 59 seconds
Tabulating error counts14:19:03 14 Feb 201614:29:23 14 Feb 201610 minutes 20 seconds
Re-calibrating base error rates14:29:23 14 Feb 201614:29:24 14 Feb 20161 second
Examining read alignment evidence14:29:24 14 Feb 201615:37:50 14 Feb 20161 hour 8 minutes 26 seconds
Polymorphism statistics15:37:50 14 Feb 201615:38:10 14 Feb 201620 seconds
Output15:38:10 14 Feb 201615:39:47 14 Feb 20161 minute 37 seconds
Total 2 hours 9 minutes 39 seconds