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-IL38_S46_L001_R1_0012,307,225347,272,58499.7%150.5 bases151 bases99.5%
errorsALE-IL38_S46_L001_R2_0012,306,469347,140,39399.7%150.5 bases151 bases98.0%
errorsALE-IL38_S46_L002_R1_0012,289,378344,601,06199.7%150.5 bases151 bases99.5%
errorsALE-IL38_S46_L002_R2_0012,288,366344,424,76599.7%150.5 bases151 bases98.1%
errorsALE-IL38_S46_L003_R1_0012,324,990349,974,71899.8%150.5 bases151 bases99.4%
errorsALE-IL38_S46_L003_R2_0012,324,058349,790,72099.8%150.5 bases151 bases97.7%
errorsALE-IL38_S46_L004_R1_0012,308,570347,520,48899.8%150.5 bases151 bases99.4%
errorsALE-IL38_S46_L004_R2_0012,307,018347,252,96899.8%150.5 bases151 bases98.3%
total18,456,0742,777,977,69799.8%150.5 bases151 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707588.74.998.2%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≤ 10000025852
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 ≤ 5000311
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.25517

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 input22:20:11 18 Oct 201622:34:37 18 Oct 201614 minutes 26 seconds
Read alignment to reference genome22:34:53 18 Oct 201601:04:03 19 Oct 20162 hours 29 minutes 10 seconds
Preprocessing alignments for candidate junction identification01:04:03 19 Oct 201601:30:26 19 Oct 201626 minutes 23 seconds
Preliminary analysis of coverage distribution01:30:26 19 Oct 201602:15:10 19 Oct 201644 minutes 44 seconds
Identifying junction candidates02:15:10 19 Oct 201602:15:41 19 Oct 201631 seconds
Re-alignment to junction candidates02:15:42 19 Oct 201602:54:50 19 Oct 201639 minutes 8 seconds
Resolving alignments with junction candidates02:54:50 19 Oct 201604:14:24 19 Oct 20161 hour 19 minutes 34 seconds
Creating BAM files04:14:24 19 Oct 201604:35:15 19 Oct 201620 minutes 51 seconds
Tabulating error counts04:35:15 19 Oct 201605:03:35 19 Oct 201628 minutes 20 seconds
Re-calibrating base error rates05:03:35 19 Oct 201605:03:40 19 Oct 20165 seconds
Examining read alignment evidence05:03:40 19 Oct 201607:38:52 19 Oct 20162 hours 35 minutes 12 seconds
Polymorphism statistics07:38:52 19 Oct 201607:38:54 19 Oct 20162 seconds
Output07:38:54 19 Oct 201607:40:48 19 Oct 20161 minute 54 seconds
Total 9 hours 20 minutes 20 seconds