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-IL4_S4_L001_R2_0011,651,955248,600,15599.6%150.5 bases151 bases95.4%
errorsALE-IL4_S4_L003_R2_0011,669,587251,266,97099.7%150.5 bases151 bases95.0%
errorsALE-IL4_S4_L002_R1_0011,634,684246,017,98999.1%150.5 bases151 bases98.4%
errorsALE-IL4_S4_L002_R2_0011,642,296247,163,78799.6%150.5 bases151 bases95.5%
errorsALE-IL4_S4_L001_R1_0011,643,394247,314,83899.0%150.5 bases151 bases98.5%
errorsALE-IL4_S4_L004_R2_0011,657,912249,523,54099.6%150.5 bases151 bases95.9%
errorsALE-IL4_S4_L004_R1_0011,656,730249,359,44399.5%150.5 bases151 bases98.3%
errorsALE-IL4_S4_L003_R1_0011,667,133250,919,28899.5%150.5 bases151 bases97.9%
total13,223,6911,990,166,01099.5%150.5 bases151 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652413.04.0100.0%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≤ 1000009652
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 ≤ 5000225
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_0009130.34794

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 input21:30:23 21 Apr 201621:35:39 21 Apr 20165 minutes 16 seconds
Read alignment to reference genome21:35:39 21 Apr 201621:47:43 21 Apr 201612 minutes 4 seconds
Preprocessing alignments for candidate junction identification21:47:43 21 Apr 201621:53:38 21 Apr 20165 minutes 55 seconds
Preliminary analysis of coverage distribution21:53:38 21 Apr 201622:07:28 21 Apr 201613 minutes 50 seconds
Identifying junction candidates22:07:28 21 Apr 201622:07:30 21 Apr 20162 seconds
Re-alignment to junction candidates22:07:30 21 Apr 201622:10:15 21 Apr 20162 minutes 45 seconds
Resolving alignments with junction candidates22:10:15 21 Apr 201622:24:24 21 Apr 201614 minutes 9 seconds
Creating BAM files22:24:24 21 Apr 201622:32:33 21 Apr 20168 minutes 9 seconds
Tabulating error counts22:32:33 21 Apr 201622:43:07 21 Apr 201610 minutes 34 seconds
Re-calibrating base error rates22:43:07 21 Apr 201622:43:09 21 Apr 20162 seconds
Examining read alignment evidence22:43:09 21 Apr 201600:26:51 22 Apr 20161 hour 43 minutes 42 seconds
Polymorphism statistics00:26:51 22 Apr 201600:26:53 22 Apr 20162 seconds
Output00:26:53 22 Apr 201600:28:35 22 Apr 20161 minute 42 seconds
Total 2 hours 58 minutes 12 seconds