breseq  version 0.26.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Xyl3_S3_L001_R1_001_10112015571,54577,417,99799.8%135.5 bases141 bases98.7%
errorsSSW-NXT-Xyl3_S3_L001_R1_001_10252015707,216131,233,36099.8%185.6 bases200 bases98.8%
errorsSSW-NXT-Xyl3_S3_L001_R2_001_10112015571,51272,796,96199.8%127.4 bases132 bases97.8%
errorsSSW-NXT-Xyl3_S3_L001_R2_001_10252015707,139101,211,53199.8%143.1 bases150 bases98.0%
total2,557,412382,659,84999.8%149.6 bases200 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65282.33.2100.0%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≤ 1000002721
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 ≤ 500058
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_0009130.81993

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
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.1
Polymorphism minimum coverage each strand2
Polymorphism bias cutoff0.05
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 input23:42:00 27 Oct 201523:42:46 27 Oct 201546 seconds
Read alignment to reference genome23:42:46 27 Oct 201523:45:27 27 Oct 20152 minutes 41 seconds
Preprocessing alignments for candidate junction identification23:45:27 27 Oct 201523:46:32 27 Oct 20151 minute 5 seconds
Preliminary analysis of coverage distribution23:46:32 27 Oct 201523:49:02 27 Oct 20152 minutes 30 seconds
Identifying junction candidates23:49:02 27 Oct 201523:49:02 27 Oct 20150 seconds
Re-alignment to junction candidates23:49:02 27 Oct 201523:49:33 27 Oct 201531 seconds
Resolving alignments with junction candidates23:49:33 27 Oct 201523:51:08 27 Oct 20151 minute 35 seconds
Creating BAM files23:51:08 27 Oct 201523:52:35 27 Oct 20151 minute 27 seconds
Tabulating error counts23:52:35 27 Oct 201523:54:51 27 Oct 20152 minutes 16 seconds
Re-calibrating base error rates23:54:51 27 Oct 201523:54:53 27 Oct 20152 seconds
Examining read alignment evidence23:54:53 27 Oct 201500:15:55 28 Oct 201521 minutes 2 seconds
Polymorphism statistics00:15:55 28 Oct 201500:15:56 28 Oct 20151 second
Output00:15:56 28 Oct 201500:17:05 28 Oct 20151 minute 9 seconds
Total 35 minutes 5 seconds