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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsKT2440_Van_A2_F110_I0_R1_S62_L001_R1_001.good.fq338,79243,159,217100.0%127.4 bases135 bases94.3%
errorsKT2440_Van_A2_F110_I0_R1_S62_L001_R2_001.good.fq338,79243,159,353100.0%127.4 bases135 bases91.4%
errorsKT2440_Van_A2_F110_I0_R1_S62_L002_R1_001.good.fq333,66742,572,642100.0%127.6 bases135 bases95.5%
errorsKT2440_Van_A2_F110_I0_R1_S62_L002_R2_001.good.fq333,66742,570,724100.0%127.6 bases135 bases93.7%
errorsKT2440_Van_A2_F110_I0_R1_S62_L003_R1_001.good.fq339,86443,405,745100.0%127.7 bases135 bases94.1%
errorsKT2440_Van_A2_F110_I0_R1_S62_L003_R2_001.good.fq339,86443,404,479100.0%127.7 bases135 bases92.1%
errorsKT2440_Van_A2_F110_I0_R1_S62_L004_R1_001.good.fq339,50643,199,319100.0%127.2 bases135 bases95.5%
errorsKT2440_Van_A2_F110_I0_R1_S62_L004_R2_001.good.fq339,50643,198,704100.0%127.2 bases135 bases93.8%
total2,703,658344,670,183100.0%127.5 bases135 bases93.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionKT24406,185,27651.83.2100.0%tig00000001|arrow.
total6,185,276100.0%

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≤ 1000001096
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 ≤ 500051
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
KT24400.86799

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 input21:59:24 01 May 202322:00:09 01 May 202345 seconds
Read alignment to reference genome22:00:09 01 May 202322:05:53 01 May 20235 minutes 44 seconds
Preprocessing alignments for candidate junction identification22:05:53 01 May 202322:06:26 01 May 202333 seconds
Preliminary analysis of coverage distribution22:06:26 01 May 202322:08:00 01 May 20231 minute 34 seconds
Identifying junction candidates22:08:00 01 May 202322:08:00 01 May 20230 seconds
Re-alignment to junction candidates22:08:00 01 May 202322:09:15 01 May 20231 minute 15 seconds
Resolving best read alignments22:09:15 01 May 202322:10:01 01 May 202346 seconds
Creating BAM files22:10:01 01 May 202322:11:26 01 May 20231 minute 25 seconds
Tabulating error counts22:11:26 01 May 202322:11:55 01 May 202329 seconds
Re-calibrating base error rates22:11:55 01 May 202322:11:58 01 May 20233 seconds
Examining read alignment evidence22:11:58 01 May 202322:34:20 01 May 202322 minutes 22 seconds
Polymorphism statistics22:34:20 01 May 202322:34:21 01 May 20231 second
Output22:34:21 01 May 202322:34:52 01 May 202331 seconds
Total 35 minutes 28 seconds