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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL044_S44_R1_001.good.fq2,472,217313,855,535100.0%127.0 bases128 bases99.1%
errorsPAL044_S44_R2_001.good.fq2,472,217313,855,535100.0%127.0 bases128 bases97.9%
total4,944,434627,711,070100.0%127.0 bases128 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3791157.234.5100.0%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≤ 10000015176
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000114
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.056

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.09125

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 input16:48:03 14 Nov 201716:48:59 14 Nov 201756 seconds
Read alignment to reference genome16:48:59 14 Nov 201716:51:54 14 Nov 20172 minutes 55 seconds
Preprocessing alignments for candidate junction identification16:51:54 14 Nov 201716:53:39 14 Nov 20171 minute 45 seconds
Preliminary analysis of coverage distribution16:53:39 14 Nov 201716:56:22 14 Nov 20172 minutes 43 seconds
Identifying junction candidates16:56:22 14 Nov 201716:56:30 14 Nov 20178 seconds
Re-alignment to junction candidates16:56:30 14 Nov 201716:57:12 14 Nov 201742 seconds
Resolving alignments with junction candidates16:57:12 14 Nov 201717:00:30 14 Nov 20173 minutes 18 seconds
Creating BAM files17:00:30 14 Nov 201717:02:08 14 Nov 20171 minute 38 seconds
Tabulating error counts17:02:08 14 Nov 201717:04:55 14 Nov 20172 minutes 47 seconds
Re-calibrating base error rates17:04:55 14 Nov 201717:04:56 14 Nov 20171 second
Examining read alignment evidence17:04:56 14 Nov 201717:25:24 14 Nov 201720 minutes 28 seconds
Polymorphism statistics17:25:24 14 Nov 201717:25:26 14 Nov 20172 seconds
Output17:25:26 14 Nov 201717:25:58 14 Nov 201732 seconds
Total 37 minutes 55 seconds