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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL035_S35_R2_001.good.fq7,951,5501,010,129,313100.0%127.0 bases128 bases98.6%
errorsPAL035_S35_R1_001.good.fq7,951,5501,010,129,313100.0%127.0 bases128 bases99.3%
total15,903,1002,020,258,626100.0%127.0 bases128 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3793703.629.5100.0%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≤ 10000042916
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 10
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000185
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.091

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.00858

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 input12:29:44 14 Nov 201712:32:54 14 Nov 20173 minutes 10 seconds
Read alignment to reference genome12:32:54 14 Nov 201712:42:14 14 Nov 20179 minutes 20 seconds
Preprocessing alignments for candidate junction identification12:42:14 14 Nov 201712:48:01 14 Nov 20175 minutes 47 seconds
Preliminary analysis of coverage distribution12:48:01 14 Nov 201712:56:50 14 Nov 20178 minutes 49 seconds
Identifying junction candidates12:56:50 14 Nov 201712:57:00 14 Nov 201710 seconds
Re-alignment to junction candidates12:57:00 14 Nov 201712:59:34 14 Nov 20172 minutes 34 seconds
Resolving alignments with junction candidates12:59:34 14 Nov 201713:10:35 14 Nov 201711 minutes 1 second
Creating BAM files13:10:35 14 Nov 201713:15:43 14 Nov 20175 minutes 8 seconds
Tabulating error counts13:15:43 14 Nov 201713:24:39 14 Nov 20178 minutes 56 seconds
Re-calibrating base error rates13:24:39 14 Nov 201713:24:42 14 Nov 20173 seconds
Examining read alignment evidence13:24:42 14 Nov 201714:30:23 14 Nov 20171 hour 5 minutes 41 seconds
Polymorphism statistics14:30:23 14 Nov 201714:30:30 14 Nov 20177 seconds
Output14:30:30 14 Nov 201714:32:34 14 Nov 20172 minutes 4 seconds
Total 2 hours 2 minutes 50 seconds