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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Ace4_S8_L001_R2_001_10112015439,53456,933,07799.9%129.5 bases132 bases98.9%
errorsSSW-NXT-Ace4_S8_L001_R1_001_10252015773,990148,017,76999.9%191.2 bases200 bases99.8%
errorsSSW-NXT-Ace4_S8_L001_R2_001_10252015773,942113,030,26799.9%146.0 bases150 bases98.9%
errorsSSW-NXT-Ace4_S8_L001_R1_001_10112015439,54860,659,29199.9%138.0 bases141 bases99.7%
total2,427,014378,640,40499.9%156.0 bases200 bases99.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65281.12.6100.0%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≤ 1000004424
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 ≤ 500098
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.82579

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 input23:05:25 27 Oct 201523:07:02 27 Oct 20151 minute 37 seconds
Read alignment to reference genome23:07:02 27 Oct 201523:09:33 27 Oct 20152 minutes 31 seconds
Preprocessing alignments for candidate junction identification23:09:33 27 Oct 201523:10:38 27 Oct 20151 minute 5 seconds
Preliminary analysis of coverage distribution23:10:38 27 Oct 201523:12:54 27 Oct 20152 minutes 16 seconds
Identifying junction candidates23:12:54 27 Oct 201523:12:55 27 Oct 20151 second
Re-alignment to junction candidates23:12:55 27 Oct 201523:13:44 27 Oct 201549 seconds
Resolving alignments with junction candidates23:13:44 27 Oct 201523:19:05 27 Oct 20155 minutes 21 seconds
Creating BAM files23:19:05 27 Oct 201523:20:47 27 Oct 20151 minute 42 seconds
Tabulating error counts23:20:47 27 Oct 201523:23:07 27 Oct 20152 minutes 20 seconds
Re-calibrating base error rates23:23:07 27 Oct 201523:23:10 27 Oct 20153 seconds
Examining read alignment evidence23:23:10 27 Oct 201523:40:52 27 Oct 201517 minutes 42 seconds
Polymorphism statistics23:40:52 27 Oct 201523:40:53 27 Oct 20151 second
Output23:40:53 27 Oct 201523:41:59 27 Oct 20151 minute 6 seconds
Total 36 minutes 34 seconds