breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-PUTR7-9_S17_L001_R2_0011,706,083256,622,251100.0%150.4 bases151 bases99.3%
errorsqtrim-PUTR7-9_S17_L001_R1_0011,706,151256,732,613100.0%150.5 bases151 bases99.8%
total3,412,234513,354,864100.0%150.4 bases151 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652107.11.798.3%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≤ 100000607
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 ≤ 500032
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.71240

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 input20:55:49 03 Jan 201720:56:48 03 Jan 201759 seconds
Read alignment to reference genome20:56:49 03 Jan 201721:04:21 03 Jan 20177 minutes 32 seconds
Preprocessing alignments for candidate junction identification21:04:21 03 Jan 201721:05:52 03 Jan 20171 minute 31 seconds
Preliminary analysis of coverage distribution21:05:52 03 Jan 201721:08:52 03 Jan 20173 minutes 0 seconds
Identifying junction candidates21:08:52 03 Jan 201721:08:52 03 Jan 20170 seconds
Re-alignment to junction candidates21:08:52 03 Jan 201721:10:30 03 Jan 20171 minute 38 seconds
Resolving alignments with junction candidates21:10:30 03 Jan 201721:13:11 03 Jan 20172 minutes 41 seconds
Creating BAM files21:13:11 03 Jan 201721:15:15 03 Jan 20172 minutes 4 seconds
Tabulating error counts21:15:15 03 Jan 201721:17:37 03 Jan 20172 minutes 22 seconds
Re-calibrating base error rates21:17:37 03 Jan 201721:17:38 03 Jan 20171 second
Examining read alignment evidence21:17:38 03 Jan 201721:35:19 03 Jan 201717 minutes 41 seconds
Polymorphism statistics21:35:19 03 Jan 201721:35:20 03 Jan 20171 second
Output21:35:20 03 Jan 201721:35:39 03 Jan 201719 seconds
Total 39 minutes 49 seconds