breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-5-160-3-1_S22_L001_R2_001419,463125,952,13499.9%300.3 bases301 bases74.9%
errorsSSW-KHP-SSW-5-160-3-1_S22_L001_R1_001419,957126,225,736100.0%300.6 bases301 bases77.6%
total839,420252,177,87099.9%300.4 bases301 bases76.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65241.11.7100.0%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≤ 1000001938
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 ≤ 5000211
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.028

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.94561

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 input16:53:49 05 Mar 201616:54:16 05 Mar 201627 seconds
Read alignment to reference genome16:54:17 05 Mar 201616:56:17 05 Mar 20162 minutes 0 seconds
Preprocessing alignments for candidate junction identification16:56:17 05 Mar 201616:56:40 05 Mar 201623 seconds
Preliminary analysis of coverage distribution16:56:40 05 Mar 201616:57:37 05 Mar 201657 seconds
Identifying junction candidates16:57:37 05 Mar 201616:57:38 05 Mar 20161 second
Re-alignment to junction candidates16:57:38 05 Mar 201616:57:51 05 Mar 201613 seconds
Resolving alignments with junction candidates16:57:51 05 Mar 201616:58:43 05 Mar 201652 seconds
Creating BAM files16:58:43 05 Mar 201616:59:13 05 Mar 201630 seconds
Tabulating error counts16:59:13 05 Mar 201617:00:16 05 Mar 20161 minute 3 seconds
Re-calibrating base error rates17:00:16 05 Mar 201617:00:17 05 Mar 20161 second
Examining read alignment evidence17:00:17 05 Mar 201617:08:36 05 Mar 20168 minutes 19 seconds
Polymorphism statistics17:08:36 05 Mar 201617:08:36 05 Mar 20160 seconds
Output17:08:36 05 Mar 201617:08:57 05 Mar 201621 seconds
Total 15 minutes 7 seconds