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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Xyl2_S2_L001_R1_001_10112015708,80398,336,35399.9%138.7 bases141 bases99.7%
errorsSSW-NXT-Xyl2_S2_L001_R2_001_10112015708,75992,242,38599.9%130.1 bases132 bases99.0%
errorsSSW-NXT-Xyl2_S2_L001_R2_001_10252015859,940126,620,40399.9%147.2 bases150 bases99.1%
errorsSSW-NXT-Xyl2_S2_L001_R1_001_10252015860,004166,376,00699.9%193.5 bases200 bases99.7%
total3,137,506483,575,14799.9%154.1 bases200 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652106.03.0100.0%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≤ 1000006777
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 ≤ 5000202
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.018

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.78826

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 input02:01:07 28 Oct 201502:02:55 28 Oct 20151 minute 48 seconds
Read alignment to reference genome02:02:55 28 Oct 201502:07:10 28 Oct 20154 minutes 15 seconds
Preprocessing alignments for candidate junction identification02:07:10 28 Oct 201502:08:35 28 Oct 20151 minute 25 seconds
Preliminary analysis of coverage distribution02:08:35 28 Oct 201502:11:45 28 Oct 20153 minutes 10 seconds
Identifying junction candidates02:11:45 28 Oct 201502:11:46 28 Oct 20151 second
Re-alignment to junction candidates02:11:46 28 Oct 201502:12:27 28 Oct 201541 seconds
Resolving alignments with junction candidates02:12:27 28 Oct 201502:14:45 28 Oct 20152 minutes 18 seconds
Creating BAM files02:14:45 28 Oct 201502:16:37 28 Oct 20151 minute 52 seconds
Tabulating error counts02:16:37 28 Oct 201502:19:39 28 Oct 20153 minutes 2 seconds
Re-calibrating base error rates02:19:39 28 Oct 201502:19:40 28 Oct 20151 second
Examining read alignment evidence02:19:40 28 Oct 201502:43:20 28 Oct 201523 minutes 40 seconds
Polymorphism statistics02:43:20 28 Oct 201502:43:20 28 Oct 20150 seconds
Output02:43:20 28 Oct 201502:44:41 28 Oct 20151 minute 21 seconds
Total 43 minutes 34 seconds