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-1-163-5-1_S5_L001_R1_0011,255,637377,404,282100.0%300.6 bases301 bases83.6%
errorsSSW-KHP-SSW-1-163-5-1_S5_L001_R2_0011,253,936376,482,64699.9%300.2 bases301 bases80.9%
total2,509,573753,886,92899.9%300.4 bases301 bases82.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652131.62.3100.0%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≤ 1000008561
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 ≤ 500034
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84003

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 input15:18:36 05 Mar 201615:19:53 05 Mar 20161 minute 17 seconds
Read alignment to reference genome15:19:53 05 Mar 201615:26:26 05 Mar 20166 minutes 33 seconds
Preprocessing alignments for candidate junction identification15:26:26 05 Mar 201615:27:41 05 Mar 20161 minute 15 seconds
Preliminary analysis of coverage distribution15:27:41 05 Mar 201615:30:58 05 Mar 20163 minutes 17 seconds
Identifying junction candidates15:30:58 05 Mar 201615:31:00 05 Mar 20162 seconds
Re-alignment to junction candidates15:31:00 05 Mar 201615:31:36 05 Mar 201636 seconds
Resolving alignments with junction candidates15:31:36 05 Mar 201615:34:42 05 Mar 20163 minutes 6 seconds
Creating BAM files15:34:42 05 Mar 201615:36:36 05 Mar 20161 minute 54 seconds
Tabulating error counts15:36:36 05 Mar 201615:40:02 05 Mar 20163 minutes 26 seconds
Re-calibrating base error rates15:40:02 05 Mar 201615:40:03 05 Mar 20161 second
Examining read alignment evidence15:40:03 05 Mar 201616:04:42 05 Mar 201624 minutes 39 seconds
Polymorphism statistics16:04:42 05 Mar 201616:04:42 05 Mar 20160 seconds
Output16:04:42 05 Mar 201616:05:19 05 Mar 201637 seconds
Total 46 minutes 43 seconds