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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL032_S32_R2_001.good.fq7,247,268914,986,788100.0%126.3 bases128 bases98.5%
errorsPAL032_S32_R1_001.good.fq7,247,268914,986,788100.0%126.3 bases128 bases99.4%
total14,494,5361,829,973,576100.0%126.3 bases128 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3793359.241.6100.0%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≤ 10000027289
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 7
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000168
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.082

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.01149

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 input00:58:25 15 Nov 201701:01:19 15 Nov 20172 minutes 54 seconds
Read alignment to reference genome01:01:19 15 Nov 201701:09:48 15 Nov 20178 minutes 29 seconds
Preprocessing alignments for candidate junction identification01:09:48 15 Nov 201701:15:06 15 Nov 20175 minutes 18 seconds
Preliminary analysis of coverage distribution01:15:06 15 Nov 201701:23:08 15 Nov 20178 minutes 2 seconds
Identifying junction candidates01:23:08 15 Nov 201701:23:16 15 Nov 20178 seconds
Re-alignment to junction candidates01:23:16 15 Nov 201701:25:33 15 Nov 20172 minutes 17 seconds
Resolving alignments with junction candidates01:25:33 15 Nov 201701:35:33 15 Nov 201710 minutes 0 seconds
Creating BAM files01:35:33 15 Nov 201701:40:12 15 Nov 20174 minutes 39 seconds
Tabulating error counts01:40:12 15 Nov 201701:48:18 15 Nov 20178 minutes 6 seconds
Re-calibrating base error rates01:48:18 15 Nov 201701:48:20 15 Nov 20172 seconds
Examining read alignment evidence01:48:20 15 Nov 201702:47:44 15 Nov 201759 minutes 24 seconds
Polymorphism statistics02:47:44 15 Nov 201702:47:51 15 Nov 20177 seconds
Output02:47:51 15 Nov 201702:49:34 15 Nov 20171 minute 43 seconds
Total 1 hour 51 minutes 9 seconds