breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors5-Population-12-1-12_S6_L001_R1_001.good.fq1,261,066358,760,676100.0%284.5 bases289 bases99.6%
errors5-Population-12-1-12_S6_L001_R2_001.good.fq1,261,066358,817,381100.0%284.5 bases289 bases87.8%
total2,522,132717,578,057100.0%284.5 bases289 bases93.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652146.24.6100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 1000007130
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 ≤ 5000324
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.041

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84897

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≤ 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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input12:23:41 22 May 201912:24:20 22 May 201939 seconds
Read alignment to reference genome12:24:20 22 May 201912:38:17 22 May 201913 minutes 57 seconds
Preprocessing alignments for candidate junction identification12:38:17 22 May 201912:38:58 22 May 201941 seconds
Preliminary analysis of coverage distribution12:38:58 22 May 201912:41:18 22 May 20192 minutes 20 seconds
Identifying junction candidates12:41:18 22 May 201912:41:31 22 May 201913 seconds
Re-alignment to junction candidates12:41:31 22 May 201912:44:58 22 May 20193 minutes 27 seconds
Resolving best read alignments12:44:58 22 May 201912:46:13 22 May 20191 minute 15 seconds
Creating BAM files12:46:13 22 May 201912:48:14 22 May 20192 minutes 1 second
Tabulating error counts12:48:14 22 May 201912:49:12 22 May 201958 seconds
Re-calibrating base error rates12:49:12 22 May 201912:49:13 22 May 20191 second
Examining read alignment evidence12:49:13 22 May 201914:02:05 22 May 20191 hour 12 minutes 52 seconds
Polymorphism statistics14:02:05 22 May 201914:02:06 22 May 20191 second
Output14:02:06 22 May 201914:02:26 22 May 201920 seconds
Total 1 hour 38 minutes 45 seconds