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-IL44_S52_L001_R1_0011,473,607221,844,21899.3%150.5 bases151 bases99.1%
errorsALE-IL44_S52_L001_R2_0011,478,424222,558,38499.6%150.5 bases151 bases97.0%
errorsALE-IL44_S52_L002_R1_0011,463,567220,346,65199.3%150.6 bases151 bases99.1%
errorsALE-IL44_S52_L002_R2_0011,468,337221,055,85199.6%150.5 bases151 bases97.1%
errorsALE-IL44_S52_L003_R1_0011,492,946224,775,02999.6%150.6 bases151 bases98.7%
errorsALE-IL44_S52_L003_R2_0011,494,437224,975,47099.7%150.5 bases151 bases96.6%
errorsALE-IL44_S52_L004_R1_0011,484,751223,553,52999.7%150.6 bases151 bases99.0%
errorsALE-IL44_S52_L004_R2_0011,484,905223,559,98199.7%150.6 bases151 bases97.5%
total11,840,9741,782,669,11399.6%150.6 bases151 bases98.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707375.84.298.2%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≤ 10000014799
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 ≤ 5000121
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.37672

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 input22:21:30 18 Oct 201622:34:29 18 Oct 201612 minutes 59 seconds
Read alignment to reference genome22:34:32 18 Oct 201623:52:55 18 Oct 20161 hour 18 minutes 23 seconds
Preprocessing alignments for candidate junction identification23:52:55 18 Oct 201600:01:24 19 Oct 20168 minutes 29 seconds
Preliminary analysis of coverage distribution00:01:24 19 Oct 201600:18:08 19 Oct 201616 minutes 44 seconds
Identifying junction candidates00:18:08 19 Oct 201600:18:45 19 Oct 201637 seconds
Re-alignment to junction candidates00:18:47 19 Oct 201600:56:09 19 Oct 201637 minutes 22 seconds
Resolving alignments with junction candidates00:56:09 19 Oct 201602:25:41 19 Oct 20161 hour 29 minutes 32 seconds
Creating BAM files02:25:41 19 Oct 201602:48:41 19 Oct 201623 minutes 0 seconds
Tabulating error counts02:48:41 19 Oct 201602:58:52 19 Oct 201610 minutes 11 seconds
Re-calibrating base error rates02:58:52 19 Oct 201602:58:56 19 Oct 20164 seconds
Examining read alignment evidence02:58:56 19 Oct 201604:11:25 19 Oct 20161 hour 12 minutes 29 seconds
Polymorphism statistics04:11:25 19 Oct 201604:11:27 19 Oct 20162 seconds
Output04:11:27 19 Oct 201604:14:38 19 Oct 20163 minutes 11 seconds
Total 5 hours 53 minutes 3 seconds