breseq  version 0.32.1  revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsT1000_488_GATCATTC-AGCCAACT.R2.good.fq619,82469,996,243100.0%112.9 bases139 bases95.2%
errorsT1000_488_GATCATTC-AGCCAACT.R1.good.fq619,82469,996,243100.0%112.9 bases139 bases95.3%
total1,239,648139,992,486100.0%112.9 bases139 bases95.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65227.93.4100.0%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≤ 1000001418
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 ≤ 5000293
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.018

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89723

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 cutoff0.75
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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input00:03:20 20 Jul 201800:03:34 20 Jul 201814 seconds
Read alignment to reference genome00:03:34 20 Jul 201800:04:16 20 Jul 201842 seconds
Preprocessing alignments for candidate junction identification00:04:16 20 Jul 201800:04:32 20 Jul 201816 seconds
Preliminary analysis of coverage distribution00:04:32 20 Jul 201800:05:02 20 Jul 201830 seconds
Identifying junction candidates00:05:02 20 Jul 201800:05:03 20 Jul 20181 second
Re-alignment to junction candidates00:05:03 20 Jul 201800:05:12 20 Jul 20189 seconds
Resolving best read alignments00:05:12 20 Jul 201800:05:39 20 Jul 201827 seconds
Creating BAM files00:05:39 20 Jul 201800:06:04 20 Jul 201825 seconds
Tabulating error counts00:06:04 20 Jul 201800:06:15 20 Jul 201811 seconds
Re-calibrating base error rates00:06:15 20 Jul 201800:06:16 20 Jul 20181 second
Examining read alignment evidence00:06:16 20 Jul 201800:08:40 20 Jul 20182 minutes 24 seconds
Polymorphism statistics00:08:40 20 Jul 201800:08:40 20 Jul 20180 seconds
Output00:08:40 20 Jul 201800:08:49 20 Jul 20189 seconds
Total 5 minutes 29 seconds