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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL031_S31_R1_001.good.fq9,648,0651,220,756,226100.0%126.5 bases128 bases99.4%
errorsPAL031_S31_R2_001.good.fq9,648,0651,220,756,226100.0%126.5 bases128 bases98.6%
total19,296,1302,441,512,452100.0%126.5 bases128 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3794530.7129.8100.0%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≤ 10000032934
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 8
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000165
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.081

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.00645

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 input02:49:35 15 Nov 201702:53:29 15 Nov 20173 minutes 54 seconds
Read alignment to reference genome02:53:29 15 Nov 201703:04:49 15 Nov 201711 minutes 20 seconds
Preprocessing alignments for candidate junction identification03:04:49 15 Nov 201703:11:43 15 Nov 20176 minutes 54 seconds
Preliminary analysis of coverage distribution03:11:43 15 Nov 201703:22:29 15 Nov 201710 minutes 46 seconds
Identifying junction candidates03:22:29 15 Nov 201703:22:37 15 Nov 20178 seconds
Re-alignment to junction candidates03:22:37 15 Nov 201703:25:57 15 Nov 20173 minutes 20 seconds
Resolving alignments with junction candidates03:25:57 15 Nov 201703:39:15 15 Nov 201713 minutes 18 seconds
Creating BAM files03:39:15 15 Nov 201703:45:26 15 Nov 20176 minutes 11 seconds
Tabulating error counts03:45:26 15 Nov 201703:56:13 15 Nov 201710 minutes 47 seconds
Re-calibrating base error rates03:56:14 15 Nov 201703:56:15 15 Nov 20171 second
Examining read alignment evidence03:56:15 15 Nov 201705:16:46 15 Nov 20171 hour 20 minutes 31 seconds
Polymorphism statistics05:16:46 15 Nov 201705:16:55 15 Nov 20179 seconds
Output05:16:55 15 Nov 201705:19:20 15 Nov 20172 minutes 25 seconds
Total 2 hours 29 minutes 44 seconds