breseq  version 0.28.1  revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL13_S17_L001_R1_0011,844,464277,666,40499.1%150.5 bases151 bases98.3%
errorsALE-IL13_S17_L001_R2_0011,853,709279,052,91699.6%150.5 bases151 bases96.1%
errorsALE-IL13_S17_L002_R1_0011,835,083276,276,24099.2%150.6 bases151 bases98.3%
errorsALE-IL13_S17_L002_R2_0011,841,757277,277,00199.6%150.6 bases151 bases96.2%
errorsALE-IL13_S17_L003_R1_0011,868,026281,242,17599.6%150.6 bases151 bases97.9%
errorsALE-IL13_S17_L003_R2_0011,869,873281,491,80599.7%150.5 bases151 bases95.8%
errorsALE-IL13_S17_L004_R1_0011,851,272278,732,92399.6%150.6 bases151 bases98.2%
errorsALE-IL13_S17_L004_R2_0011,852,268278,863,68199.6%150.6 bases151 bases96.7%
total14,816,4522,230,603,14599.5%150.5 bases151 bases97.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707468.65.298.2%Escherichia coli DH1, complete genome.
total4,630,707100.0%

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≤ 10000011209
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 ≤ 5000196
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.31601

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 input15:15:54 18 Oct 201615:22:50 18 Oct 20166 minutes 56 seconds
Read alignment to reference genome15:22:50 18 Oct 201616:37:20 18 Oct 20161 hour 14 minutes 30 seconds
Preprocessing alignments for candidate junction identification16:37:21 18 Oct 201617:12:20 18 Oct 201634 minutes 59 seconds
Preliminary analysis of coverage distribution17:12:20 18 Oct 201617:54:30 18 Oct 201642 minutes 10 seconds
Identifying junction candidates17:54:30 18 Oct 201617:55:01 18 Oct 201631 seconds
Re-alignment to junction candidates17:55:01 18 Oct 201618:21:09 18 Oct 201626 minutes 8 seconds
Resolving alignments with junction candidates18:21:09 18 Oct 201619:17:04 18 Oct 201655 minutes 55 seconds
Creating BAM files19:17:04 18 Oct 201619:43:18 18 Oct 201626 minutes 14 seconds
Tabulating error counts19:43:18 18 Oct 201620:01:43 18 Oct 201618 minutes 25 seconds
Re-calibrating base error rates20:01:43 18 Oct 201620:01:48 18 Oct 20165 seconds
Examining read alignment evidence20:01:48 18 Oct 201622:00:20 18 Oct 20161 hour 58 minutes 32 seconds
Polymorphism statistics22:00:20 18 Oct 201622:00:22 18 Oct 20162 seconds
Output22:00:22 18 Oct 201622:02:28 18 Oct 20162 minutes 6 seconds
Total 6 hours 46 minutes 33 seconds