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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Xyl1_S1_L001_R2_001_10112015860,067109,889,36699.8%127.8 bases132 bases99.2%
errorsSSW-NXT-Xyl1_S1_L001_R2_001_102520151,097,924157,530,69699.8%143.5 bases150 bases99.4%
errorsSSW-NXT-Xyl1_S1_L001_R1_001_10112015860,106116,886,28799.9%135.9 bases141 bases99.7%
errorsSSW-NXT-Xyl1_S1_L001_R1_001_102520151,098,018203,644,95799.8%185.5 bases200 bases99.7%
total3,916,115587,951,30699.8%150.1 bases200 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652118.33.8100.0%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≤ 1000005762
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 ≤ 5000172
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.75695

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 input21:13:45 27 Oct 201521:15:54 27 Oct 20152 minutes 9 seconds
Read alignment to reference genome21:15:54 27 Oct 201521:23:07 27 Oct 20157 minutes 13 seconds
Preprocessing alignments for candidate junction identification21:23:08 27 Oct 201521:25:27 27 Oct 20152 minutes 19 seconds
Preliminary analysis of coverage distribution21:25:27 27 Oct 201521:29:24 27 Oct 20153 minutes 57 seconds
Identifying junction candidates21:29:24 27 Oct 201521:29:27 27 Oct 20153 seconds
Re-alignment to junction candidates21:29:27 27 Oct 201521:30:44 27 Oct 20151 minute 17 seconds
Resolving alignments with junction candidates21:30:44 27 Oct 201521:35:30 27 Oct 20154 minutes 46 seconds
Creating BAM files21:35:30 27 Oct 201521:37:39 27 Oct 20152 minutes 9 seconds
Tabulating error counts21:37:39 27 Oct 201521:41:09 27 Oct 20153 minutes 30 seconds
Re-calibrating base error rates21:41:09 27 Oct 201521:41:12 27 Oct 20153 seconds
Examining read alignment evidence21:41:12 27 Oct 201522:11:19 27 Oct 201530 minutes 7 seconds
Polymorphism statistics22:11:19 27 Oct 201522:11:19 27 Oct 20150 seconds
Output22:11:19 27 Oct 201522:12:37 27 Oct 20151 minute 18 seconds
Total 58 minutes 51 seconds