breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSample6_S6_L001_R2_0011,513,899225,748,19299.9%149.1 bases151 bases97.2%
errorsSample6_S6_L001_R1_0011,514,695225,854,339100.0%149.1 bases151 bases99.2%
total3,028,594451,602,53199.9%149.1 bases151 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65295.83.3100.0%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≤ 10000021513
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 ≤ 5000778
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.052

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.82052

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 input11:18:44 20 Apr 201611:19:49 20 Apr 20161 minute 5 seconds
Read alignment to reference genome11:19:50 20 Apr 201611:22:54 20 Apr 20163 minutes 4 seconds
Preprocessing alignments for candidate junction identification11:22:54 20 Apr 201611:24:08 20 Apr 20161 minute 14 seconds
Preliminary analysis of coverage distribution11:24:08 20 Apr 201611:27:05 20 Apr 20162 minutes 57 seconds
Identifying junction candidates11:27:05 20 Apr 201611:27:07 20 Apr 20162 seconds
Re-alignment to junction candidates11:27:07 20 Apr 201611:27:52 20 Apr 201645 seconds
Resolving alignments with junction candidates11:27:52 20 Apr 201611:30:30 20 Apr 20162 minutes 38 seconds
Creating BAM files11:30:30 20 Apr 201611:32:49 20 Apr 20162 minutes 19 seconds
Tabulating error counts11:32:49 20 Apr 201611:35:14 20 Apr 20162 minutes 25 seconds
Re-calibrating base error rates11:35:14 20 Apr 201611:35:14 20 Apr 20160 seconds
Examining read alignment evidence11:35:14 20 Apr 201611:55:59 20 Apr 201620 minutes 45 seconds
Polymorphism statistics11:55:59 20 Apr 201611:56:01 20 Apr 20162 seconds
Output11:56:01 20 Apr 201611:56:59 20 Apr 201658 seconds
Total 38 minutes 14 seconds