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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Xyl4_S4_L001_R1_001_10252015821,563156,667,88499.9%190.7 bases200 bases99.7%
errorsSSW-NXT-Xyl4_S4_L001_R2_001_10252015821,480119,768,24699.9%145.8 bases150 bases98.7%
errorsSSW-NXT-Xyl4_S4_L001_R2_001_10112015639,70182,567,60299.9%129.1 bases132 bases98.6%
errorsSSW-NXT-Xyl4_S4_L001_R1_001_10112015639,73887,929,76299.9%137.4 bases141 bases99.6%
total2,922,482446,933,49499.9%152.9 bases200 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65294.23.1100.0%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≤ 1000005195
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 ≤ 5000150
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_0009130.80204

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 input22:12:37 27 Oct 201522:13:34 27 Oct 201557 seconds
Read alignment to reference genome22:13:34 27 Oct 201522:16:41 27 Oct 20153 minutes 7 seconds
Preprocessing alignments for candidate junction identification22:16:41 27 Oct 201522:17:54 27 Oct 20151 minute 13 seconds
Preliminary analysis of coverage distribution22:17:54 27 Oct 201522:21:14 27 Oct 20153 minutes 20 seconds
Identifying junction candidates22:21:14 27 Oct 201522:21:14 27 Oct 20150 seconds
Re-alignment to junction candidates22:21:14 27 Oct 201522:22:06 27 Oct 201552 seconds
Resolving alignments with junction candidates22:22:06 27 Oct 201522:25:46 27 Oct 20153 minutes 40 seconds
Creating BAM files22:25:46 27 Oct 201522:27:36 27 Oct 20151 minute 50 seconds
Tabulating error counts22:27:36 27 Oct 201522:30:58 27 Oct 20153 minutes 22 seconds
Re-calibrating base error rates22:30:58 27 Oct 201522:31:02 27 Oct 20154 seconds
Examining read alignment evidence22:31:02 27 Oct 201523:03:50 27 Oct 201532 minutes 48 seconds
Polymorphism statistics23:03:50 27 Oct 201523:03:51 27 Oct 20151 second
Output23:03:51 27 Oct 201523:05:24 27 Oct 20151 minute 33 seconds
Total 52 minutes 47 seconds