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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSvNSRound3_8_9POP_S375_L002_R1_001.good.fq689,315102,521,342100.0%148.7 bases149 bases98.0%
errorsSvNSRound3_8_9POP_S375_L002_R2_001.good.fq689,315102,521,342100.0%148.7 bases149 bases79.1%
total1,378,630205,042,684100.0%148.7 bases149 bases88.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_000913_3_hsa_tpiA4,641,63438.91.8100.0%Escherichia coli str. K-12 substr. MG1655, H. sapien tpiA gene, complete genome.
total4,641,634100.0%

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≤ 1000001479
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500029
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_000913_3_hsa_tpiA0.89567

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input18:02:46 19 Dec 202018:04:02 19 Dec 20201 minute 16 seconds
Read alignment to reference genome18:04:03 19 Dec 202018:18:16 19 Dec 202014 minutes 13 seconds
Preprocessing alignments for candidate junction identification18:18:16 19 Dec 202018:19:09 19 Dec 202053 seconds
Preliminary analysis of coverage distribution18:19:09 19 Dec 202018:21:48 19 Dec 20202 minutes 39 seconds
Identifying junction candidates18:21:48 19 Dec 202018:21:48 19 Dec 20200 seconds
Re-alignment to junction candidates18:21:48 19 Dec 202018:24:23 19 Dec 20202 minutes 35 seconds
Resolving best read alignments18:24:23 19 Dec 202018:25:41 19 Dec 20201 minute 18 seconds
Creating BAM files18:25:41 19 Dec 202018:28:06 19 Dec 20202 minutes 25 seconds
Tabulating error counts18:28:06 19 Dec 202018:28:55 19 Dec 202049 seconds
Re-calibrating base error rates18:28:55 19 Dec 202018:28:58 19 Dec 20203 seconds
Examining read alignment evidence18:28:58 19 Dec 202019:33:34 19 Dec 20201 hour 4 minutes 36 seconds
Polymorphism statistics19:33:34 19 Dec 202019:33:35 19 Dec 20201 second
Output19:33:35 19 Dec 202019:33:55 19 Dec 202020 seconds
Total 1 hour 31 minutes 8 seconds