breseq  version 0.31.0  revision 69e7c3c0fa11
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL036_S36_R2_001.good.fq4,574,852581,531,041100.0%127.1 bases128 bases98.6%
errorsPAL036_S36_R1_001.good.fq4,574,852581,531,041100.0%127.1 bases128 bases99.3%
total9,149,7041,163,062,082100.0%127.1 bases128 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3792144.227.4100.0%Synthetic bacterium JCVI-Syn3.0 strain 6d, complete genome.
total543,379100.0%

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≤ 10000027537
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 6
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000159
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.078

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.02840

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

Software Versions

programversion
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input17:25:58 14 Nov 201717:27:51 14 Nov 20171 minute 53 seconds
Read alignment to reference genome17:27:51 14 Nov 201717:33:15 14 Nov 20175 minutes 24 seconds
Preprocessing alignments for candidate junction identification17:33:15 14 Nov 201717:36:34 14 Nov 20173 minutes 19 seconds
Preliminary analysis of coverage distribution17:36:34 14 Nov 201717:41:40 14 Nov 20175 minutes 6 seconds
Identifying junction candidates17:41:40 14 Nov 201717:41:48 14 Nov 20178 seconds
Re-alignment to junction candidates17:41:48 14 Nov 201717:43:15 14 Nov 20171 minute 27 seconds
Resolving alignments with junction candidates17:43:15 14 Nov 201717:49:26 14 Nov 20176 minutes 11 seconds
Creating BAM files17:49:26 14 Nov 201717:52:24 14 Nov 20172 minutes 58 seconds
Tabulating error counts17:52:24 14 Nov 201717:57:35 14 Nov 20175 minutes 11 seconds
Re-calibrating base error rates17:57:35 14 Nov 201717:57:37 14 Nov 20172 seconds
Examining read alignment evidence17:57:37 14 Nov 201718:35:15 14 Nov 201737 minutes 38 seconds
Polymorphism statistics18:35:15 14 Nov 201718:35:18 14 Nov 20173 seconds
Output18:35:18 14 Nov 201718:36:30 14 Nov 20171 minute 12 seconds
Total 1 hour 10 minutes 32 seconds