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-IL41_S49_L001_R1_0011,891,438284,742,63499.4%150.5 bases151 bases99.3%
errorsALE-IL41_S49_L001_R2_0011,894,026285,122,07199.6%150.5 bases151 bases97.0%
errorsALE-IL41_S49_L002_R1_0011,884,794283,758,83599.4%150.6 bases151 bases99.3%
errorsALE-IL41_S49_L002_R2_0011,887,685284,178,43999.6%150.5 bases151 bases97.1%
errorsALE-IL41_S49_L003_R1_0011,912,729287,970,18099.7%150.6 bases151 bases99.0%
errorsALE-IL41_S49_L003_R2_0011,912,630287,918,81699.7%150.5 bases151 bases96.6%
errorsALE-IL41_S49_L004_R1_0011,929,793290,554,48599.7%150.6 bases151 bases99.2%
errorsALE-IL41_S49_L004_R2_0011,927,617290,201,08899.6%150.5 bases151 bases97.5%
total15,240,7122,294,446,54899.6%150.5 bases151 bases98.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707483.43.998.2%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≤ 10000020443
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 ≤ 5000166
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.30525

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 input22:20:52 18 Oct 201622:36:19 18 Oct 201615 minutes 27 seconds
Read alignment to reference genome22:36:32 18 Oct 201600:38:49 19 Oct 20162 hours 2 minutes 17 seconds
Preprocessing alignments for candidate junction identification00:38:49 19 Oct 201601:16:50 19 Oct 201638 minutes 1 second
Preliminary analysis of coverage distribution01:16:50 19 Oct 201601:56:52 19 Oct 201640 minutes 2 seconds
Identifying junction candidates01:56:52 19 Oct 201601:57:14 19 Oct 201622 seconds
Re-alignment to junction candidates01:57:14 19 Oct 201602:30:12 19 Oct 201632 minutes 58 seconds
Resolving alignments with junction candidates02:30:12 19 Oct 201603:40:30 19 Oct 20161 hour 10 minutes 18 seconds
Creating BAM files03:40:30 19 Oct 201604:02:52 19 Oct 201622 minutes 22 seconds
Tabulating error counts04:02:52 19 Oct 201604:21:27 19 Oct 201618 minutes 35 seconds
Re-calibrating base error rates04:21:27 19 Oct 201604:21:30 19 Oct 20163 seconds
Examining read alignment evidence04:21:30 19 Oct 201606:57:18 19 Oct 20162 hours 35 minutes 48 seconds
Polymorphism statistics06:57:18 19 Oct 201606:57:21 19 Oct 20163 seconds
Output06:57:21 19 Oct 201606:59:49 19 Oct 20162 minutes 28 seconds
Total 8 hours 38 minutes 44 seconds