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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsB1C3_S146_R1_001.good.fq1,562,086103,916,521100.0%66.5 bases71 bases58.2%
total1,562,086103,916,521100.0%66.5 bases71 bases58.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionminE2,987,942[78.1][48.9]100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total2,987,942100.0%

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.

Fit failed Negative binomial fit failed for this reference sequence. It may have an unusual coverage depth distribution. JC and MC predictions may be less accurate.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000001820
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 ≤ 50001
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
minENA

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:55:03 10 Dec 201920:55:19 10 Dec 201916 seconds
Read alignment to reference genome20:55:19 10 Dec 201920:59:10 10 Dec 20193 minutes 51 seconds
Preprocessing alignments for candidate junction identification20:59:10 10 Dec 201920:59:23 10 Dec 201913 seconds
Preliminary analysis of coverage distribution20:59:23 10 Dec 201920:59:38 10 Dec 201915 seconds
Identifying junction candidates20:59:38 10 Dec 201920:59:39 10 Dec 20191 second
Re-alignment to junction candidates20:59:39 10 Dec 201921:00:08 10 Dec 201929 seconds
Resolving best read alignments21:00:08 10 Dec 201921:00:31 10 Dec 201923 seconds
Creating BAM files21:00:31 10 Dec 201921:00:45 10 Dec 201914 seconds
Tabulating error counts21:00:45 10 Dec 201921:00:50 10 Dec 20195 seconds
Re-calibrating base error rates21:00:50 10 Dec 201921:00:50 10 Dec 20190 seconds
Examining read alignment evidence21:00:50 10 Dec 201921:02:01 10 Dec 20191 minute 11 seconds
Polymorphism statistics21:02:01 10 Dec 201921:02:02 10 Dec 20191 second
Output21:02:02 10 Dec 201921:58:42 10 Dec 201956 minutes 40 seconds
Total 1 hour 3 minutes 39 seconds