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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL6_S6_L003_R2_0011,503,324225,972,30999.7%150.3 bases151 bases95.5%
errorsALE-IL6_S6_L004_R1_0011,491,137224,183,23399.6%150.3 bases151 bases98.8%
errorsALE-IL6_S6_L002_R2_0011,476,828222,000,22999.6%150.3 bases151 bases96.1%
errorsALE-IL6_S6_L004_R2_0011,492,196224,327,73199.7%150.3 bases151 bases96.7%
errorsALE-IL6_S6_L003_R1_0011,500,023225,499,80399.5%150.3 bases151 bases98.3%
errorsALE-IL6_S6_L001_R1_0011,479,650222,410,78699.1%150.3 bases151 bases98.8%
errorsALE-IL6_S6_L001_R2_0011,487,387223,574,08799.6%150.3 bases151 bases95.9%
errorsALE-IL6_S6_L002_R1_0011,469,744220,938,22599.1%150.3 bases151 bases98.8%
total11,900,2891,788,906,40399.5%150.3 bases151 bases97.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652371.54.0100.0%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≤ 1000008338
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 ≤ 5000623
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.041

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.37715

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 input04:02:02 22 Apr 201604:06:46 22 Apr 20164 minutes 44 seconds
Read alignment to reference genome04:06:47 22 Apr 201604:16:48 22 Apr 201610 minutes 1 second
Preprocessing alignments for candidate junction identification04:16:48 22 Apr 201604:22:44 22 Apr 20165 minutes 56 seconds
Preliminary analysis of coverage distribution04:22:44 22 Apr 201604:38:53 22 Apr 201616 minutes 9 seconds
Identifying junction candidates04:38:53 22 Apr 201604:38:55 22 Apr 20162 seconds
Re-alignment to junction candidates04:38:55 22 Apr 201604:41:34 22 Apr 20162 minutes 39 seconds
Resolving alignments with junction candidates04:41:34 22 Apr 201604:54:14 22 Apr 201612 minutes 40 seconds
Creating BAM files04:54:14 22 Apr 201605:03:04 22 Apr 20168 minutes 50 seconds
Tabulating error counts05:03:04 22 Apr 201605:13:09 22 Apr 201610 minutes 5 seconds
Re-calibrating base error rates05:13:09 22 Apr 201605:13:12 22 Apr 20163 seconds
Examining read alignment evidence05:13:12 22 Apr 201606:52:01 22 Apr 20161 hour 38 minutes 49 seconds
Polymorphism statistics06:52:01 22 Apr 201606:52:05 22 Apr 20164 seconds
Output06:52:05 22 Apr 201606:55:01 22 Apr 20162 minutes 56 seconds
Total 2 hours 52 minutes 58 seconds