breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL10_S14_L003_R1_0011,691,220254,581,99199.6%150.5 bases151 bases98.5%
errorsALE-IL10_S14_L001_R1_0011,668,170251,090,89899.3%150.5 bases151 bases98.9%
errorsALE-IL10_S14_L002_R1_0011,663,871250,459,77699.4%150.5 bases151 bases98.9%
errorsALE-IL10_S14_L004_R2_0011,685,748253,764,11899.6%150.5 bases151 bases97.2%
errorsALE-IL10_S14_L004_R1_0011,685,502253,738,24199.6%150.5 bases151 bases98.8%
errorsALE-IL10_S14_L003_R2_0011,692,307254,722,62999.7%150.5 bases151 bases96.3%
errorsALE-IL10_S14_L001_R2_0011,673,226251,850,08699.6%150.5 bases151 bases96.7%
errorsALE-IL10_S14_L002_R2_0011,667,258250,964,30399.6%150.5 bases151 bases96.8%
total13,427,3022,021,172,04299.5%150.5 bases151 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652424.93.1100.0%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≤ 1000004449
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 ≤ 5000186
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.33828

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
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
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 input03:11:17 21 Apr 201603:18:02 21 Apr 20166 minutes 45 seconds
Read alignment to reference genome03:18:03 21 Apr 201603:47:54 21 Apr 201629 minutes 51 seconds
Preprocessing alignments for candidate junction identification03:47:54 21 Apr 201603:54:24 21 Apr 20166 minutes 30 seconds
Preliminary analysis of coverage distribution03:54:24 21 Apr 201604:15:51 21 Apr 201621 minutes 27 seconds
Identifying junction candidates04:15:51 21 Apr 201604:15:56 21 Apr 20165 seconds
Re-alignment to junction candidates04:15:56 21 Apr 201604:20:38 21 Apr 20164 minutes 42 seconds
Resolving alignments with junction candidates04:20:38 21 Apr 201604:51:15 21 Apr 201630 minutes 37 seconds
Creating BAM files04:51:15 21 Apr 201605:06:15 21 Apr 201615 minutes 0 seconds
Tabulating error counts05:06:15 21 Apr 201605:18:35 21 Apr 201612 minutes 20 seconds
Re-calibrating base error rates05:18:35 21 Apr 201605:18:40 21 Apr 20165 seconds
Examining read alignment evidence05:18:40 21 Apr 201606:59:45 21 Apr 20161 hour 41 minutes 5 seconds
Polymorphism statistics06:59:45 21 Apr 201606:59:47 21 Apr 20162 seconds
Output06:59:47 21 Apr 201607:02:21 21 Apr 20162 minutes 34 seconds
Total 3 hours 51 minutes 3 seconds