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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Ace3_S7_L001_R2_001_10252015827,110121,614,36899.9%147.0 bases150 bases98.3%
errorsSSW-NXT-Ace3_S7_L001_R1_001_10252015827,179159,958,31299.9%193.4 bases200 bases99.7%
errorsSSW-NXT-Ace3_S7_L001_R1_001_10112015746,506103,475,44199.9%138.6 bases141 bases99.7%
errorsSSW-NXT-Ace3_S7_L001_R2_001_10112015746,47297,067,35399.9%130.0 bases132 bases98.0%
total3,147,267482,115,47499.9%153.2 bases200 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652103.63.8100.0%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≤ 1000006284
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 ≤ 5000143
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79545

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 input01:04:57 28 Oct 201501:06:17 28 Oct 20151 minute 20 seconds
Read alignment to reference genome01:06:17 28 Oct 201501:12:20 28 Oct 20156 minutes 3 seconds
Preprocessing alignments for candidate junction identification01:12:20 28 Oct 201501:14:22 28 Oct 20152 minutes 2 seconds
Preliminary analysis of coverage distribution01:14:22 28 Oct 201501:18:32 28 Oct 20154 minutes 10 seconds
Identifying junction candidates01:18:32 28 Oct 201501:18:33 28 Oct 20151 second
Re-alignment to junction candidates01:18:33 28 Oct 201501:19:45 28 Oct 20151 minute 12 seconds
Resolving alignments with junction candidates01:19:45 28 Oct 201501:23:04 28 Oct 20153 minutes 19 seconds
Creating BAM files01:23:04 28 Oct 201501:25:35 28 Oct 20152 minutes 31 seconds
Tabulating error counts01:25:35 28 Oct 201501:29:54 28 Oct 20154 minutes 19 seconds
Re-calibrating base error rates01:29:54 28 Oct 201501:29:58 28 Oct 20154 seconds
Examining read alignment evidence01:29:58 28 Oct 201501:59:23 28 Oct 201529 minutes 25 seconds
Polymorphism statistics01:59:23 28 Oct 201501:59:24 28 Oct 20151 second
Output01:59:24 28 Oct 201502:01:07 28 Oct 20151 minute 43 seconds
Total 56 minutes 10 seconds