breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSvNSRound4_4_69_undiluted_S2271_L007_R1_001.good.fq22629,127100.0%128.9 bases129 bases1.3%
errorsSvNSRound4_4_69_undiluted_S2271_L007_R2_001.good.fq22629,127100.0%128.9 bases129 bases0.9%
errorsSvNSRound4_4_69_undiluted_S2271_L008_R1_001.good.fq15119,195100.0%127.1 bases129 bases6.0%
errorsSvNSRound4_4_69_undiluted_S2271_L008_R2_001.good.fq15119,195100.0%127.1 bases129 bases6.0%
total75496,644100.0%128.2 bases129 bases3.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_000913_3_bme_pgi4,641,653NANA100.0%Escherichia coli str. K-12 substr. MG1655, B. melitensis pgi gene, complete genome.
total4,641,653100.0%

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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 0
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50000
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_000913_3_bme_pgi1.00000

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input17:40:55 19 Dec 202017:40:59 19 Dec 20204 seconds
Read alignment to reference genome17:41:00 19 Dec 202017:41:12 19 Dec 202012 seconds
Preprocessing alignments for candidate junction identification17:41:12 19 Dec 202017:41:12 19 Dec 20200 seconds
Preliminary analysis of coverage distribution17:41:12 19 Dec 202017:41:16 19 Dec 20204 seconds
Identifying junction candidates17:41:16 19 Dec 202017:41:16 19 Dec 20200 seconds
Re-alignment to junction candidates17:41:16 19 Dec 202017:41:16 19 Dec 20200 seconds
Resolving best read alignments17:41:16 19 Dec 202017:41:17 19 Dec 20201 second
Creating BAM files17:41:17 19 Dec 202017:41:17 19 Dec 20200 seconds
Tabulating error counts17:41:17 19 Dec 202017:41:17 19 Dec 20200 seconds
Re-calibrating base error rates17:41:17 19 Dec 202017:41:22 19 Dec 20205 seconds
Examining read alignment evidence17:41:22 19 Dec 202017:41:28 19 Dec 20206 seconds
Polymorphism statistics17:41:28 19 Dec 202017:41:29 19 Dec 20201 second
Output17:41:29 19 Dec 202017:41:43 19 Dec 202014 seconds
Total 47 seconds