breseq  version 0.26.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors433WJAAXX_6_1_pf_REL8595M20,616,201721,567,035100.0%35.0 bases35 bases96.4%
total20,616,201721,567,035100.0%35.0 bases35 bases96.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812156.68.4100.0%Escherichia coli strain REL606.
total4,629,812100.0%

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≤ 100000100000
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 ≤ 5000888
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.21582

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Polymorphism E-value cutoff2
Polymorphism frequency cutoffOFF
Polymorphism minimum coverage each strand2
Polymorphism bias cutoff0.001
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input09:49:41 26 Jul 201509:52:08 26 Jul 20152 minutes 27 seconds
Read alignment to reference genome09:52:08 26 Jul 201512:50:32 26 Jul 20152 hours 58 minutes 24 seconds
Preprocessing alignments for candidate junction identification12:50:32 26 Jul 201513:01:09 26 Jul 201510 minutes 37 seconds
Preliminary analysis of coverage distribution13:01:09 26 Jul 201513:07:26 26 Jul 20156 minutes 17 seconds
Identifying junction candidates13:07:26 26 Jul 201513:07:38 26 Jul 201512 seconds
Re-alignment to junction candidates13:07:38 26 Jul 201513:12:22 26 Jul 20154 minutes 44 seconds
Resolving alignments with junction candidates13:12:22 26 Jul 201513:24:15 26 Jul 201511 minutes 53 seconds
Creating BAM files13:24:15 26 Jul 201513:30:16 26 Jul 20156 minutes 1 second
Tabulating error counts13:30:16 26 Jul 201513:32:03 26 Jul 20151 minute 47 seconds
Re-calibrating base error rates13:32:03 26 Jul 201513:32:04 26 Jul 20151 second
Examining read alignment evidence13:32:04 26 Jul 201514:26:23 26 Jul 201554 minutes 19 seconds
Polymorphism statistics14:26:23 26 Jul 201514:26:58 26 Jul 201535 seconds
Output14:26:58 26 Jul 201514:29:44 26 Jul 20152 minutes 46 seconds
Total 4 hours 40 minutes 3 seconds