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-IL12_S16_L004_R2_0011,693,943255,031,31799.6%150.6 bases151 bases96.5%
errorsALE-IL12_S16_L001_R2_0011,690,675254,511,77099.6%150.5 bases151 bases96.0%
errorsALE-IL12_S16_L001_R1_0011,680,706253,012,35299.0%150.5 bases151 bases98.2%
errorsALE-IL12_S16_L002_R2_0011,678,969252,768,06699.6%150.5 bases151 bases96.2%
errorsALE-IL12_S16_L004_R1_0011,691,424254,667,51699.5%150.6 bases151 bases98.0%
errorsALE-IL12_S16_L003_R2_0011,708,949257,270,54699.7%150.5 bases151 bases95.6%
errorsALE-IL12_S16_L002_R1_0011,671,544251,652,24899.2%150.6 bases151 bases98.2%
errorsALE-IL12_S16_L003_R1_0011,705,747256,812,38299.5%150.6 bases151 bases97.6%
total13,521,9572,035,726,19799.5%150.5 bases151 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652426.13.2100.0%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≤ 10000043283
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 ≤ 5000169
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.34196

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 input07:02:22 21 Apr 201607:09:09 21 Apr 20166 minutes 47 seconds
Read alignment to reference genome07:09:09 21 Apr 201607:24:37 21 Apr 201615 minutes 28 seconds
Preprocessing alignments for candidate junction identification07:24:37 21 Apr 201607:30:41 21 Apr 20166 minutes 4 seconds
Preliminary analysis of coverage distribution07:30:41 21 Apr 201607:45:23 21 Apr 201614 minutes 42 seconds
Identifying junction candidates07:45:23 21 Apr 201607:45:27 21 Apr 20164 seconds
Re-alignment to junction candidates07:45:27 21 Apr 201607:48:27 21 Apr 20163 minutes 0 seconds
Resolving alignments with junction candidates07:48:27 21 Apr 201608:09:08 21 Apr 201620 minutes 41 seconds
Creating BAM files08:09:08 21 Apr 201608:31:47 21 Apr 201622 minutes 39 seconds
Tabulating error counts08:31:47 21 Apr 201608:46:41 21 Apr 201614 minutes 54 seconds
Re-calibrating base error rates08:46:41 21 Apr 201608:46:47 21 Apr 20166 seconds
Examining read alignment evidence08:46:47 21 Apr 201610:42:33 21 Apr 20161 hour 55 minutes 46 seconds
Polymorphism statistics10:42:33 21 Apr 201610:42:36 21 Apr 20163 seconds
Output10:42:36 21 Apr 201610:46:31 21 Apr 20163 minutes 55 seconds
Total 3 hours 44 minutes 9 seconds