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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL039_S39_R1_001.good.fq5,548,721704,854,137100.0%127.0 bases128 bases99.4%
errorsPAL039_S39_R2_001.good.fq5,548,721704,854,137100.0%127.0 bases128 bases98.5%
total11,097,4421,409,708,274100.0%127.0 bases128 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3792595.055.7100.0%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≤ 10000020826
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 5
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000201
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.099

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.02441

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 input18:36:30 14 Nov 201718:38:46 14 Nov 20172 minutes 16 seconds
Read alignment to reference genome18:38:46 14 Nov 201718:45:16 14 Nov 20176 minutes 30 seconds
Preprocessing alignments for candidate junction identification18:45:16 14 Nov 201718:49:19 14 Nov 20174 minutes 3 seconds
Preliminary analysis of coverage distribution18:49:19 14 Nov 201718:55:28 14 Nov 20176 minutes 9 seconds
Identifying junction candidates18:55:28 14 Nov 201718:55:42 14 Nov 201714 seconds
Re-alignment to junction candidates18:55:42 14 Nov 201718:57:33 14 Nov 20171 minute 51 seconds
Resolving alignments with junction candidates18:57:33 14 Nov 201719:05:16 14 Nov 20177 minutes 43 seconds
Creating BAM files19:05:16 14 Nov 201719:08:51 14 Nov 20173 minutes 35 seconds
Tabulating error counts19:08:51 14 Nov 201719:15:04 14 Nov 20176 minutes 13 seconds
Re-calibrating base error rates19:15:04 14 Nov 201719:15:06 14 Nov 20172 seconds
Examining read alignment evidence19:15:06 14 Nov 201720:00:45 14 Nov 201745 minutes 39 seconds
Polymorphism statistics20:00:45 14 Nov 201720:00:50 14 Nov 20175 seconds
Output20:00:50 14 Nov 201720:02:24 14 Nov 20171 minute 34 seconds
Total 1 hour 25 minutes 54 seconds