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-COUM7-6_S18_L001_R1_001863,256129,829,064100.0%150.4 bases151 bases99.6%
errorsqtrim-COUM7-6_S18_L001_R2_001863,022129,547,638100.0%150.1 bases151 bases97.2%
total1,726,278259,376,702100.0%150.3 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65255.01.298.3%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≤ 1000001644
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 ≤ 500020
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.83988

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 input13:39:49 03 Jan 201713:40:24 03 Jan 201735 seconds
Read alignment to reference genome13:40:25 03 Jan 201713:46:11 03 Jan 20175 minutes 46 seconds
Preprocessing alignments for candidate junction identification13:46:11 03 Jan 201713:47:14 03 Jan 20171 minute 3 seconds
Preliminary analysis of coverage distribution13:47:14 03 Jan 201713:48:55 03 Jan 20171 minute 41 seconds
Identifying junction candidates13:48:55 03 Jan 201713:48:55 03 Jan 20170 seconds
Re-alignment to junction candidates13:48:55 03 Jan 201713:50:02 03 Jan 20171 minute 7 seconds
Resolving alignments with junction candidates13:50:02 03 Jan 201713:51:50 03 Jan 20171 minute 48 seconds
Creating BAM files13:51:50 03 Jan 201713:53:09 03 Jan 20171 minute 19 seconds
Tabulating error counts13:53:09 03 Jan 201713:54:52 03 Jan 20171 minute 43 seconds
Re-calibrating base error rates13:54:52 03 Jan 201713:54:53 03 Jan 20171 second
Examining read alignment evidence13:54:53 03 Jan 201714:08:10 03 Jan 201713 minutes 17 seconds
Polymorphism statistics14:08:10 03 Jan 201714:08:10 03 Jan 20170 seconds
Output14:08:10 03 Jan 201714:08:30 03 Jan 201720 seconds
Total 28 minutes 40 seconds