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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsE1C1_S162_R1_001.good.fq88,7065,065,445100.0%57.1 bases62 bases74.7%
total88,7065,065,445100.0%57.1 bases62 bases74.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionW3110S.gb4,646,334[33.8][22.7]100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total4,646,334100.0%

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≤ 100000281
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 0
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50000
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
W3110S.gbNA

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 input23:50:04 09 Dec 201923:50:06 09 Dec 20192 seconds
Read alignment to reference genome23:50:06 09 Dec 201923:51:16 09 Dec 20191 minute 10 seconds
Preprocessing alignments for candidate junction identification23:51:16 09 Dec 201923:51:17 09 Dec 20191 second
Preliminary analysis of coverage distribution23:51:17 09 Dec 201923:51:19 09 Dec 20192 seconds
Identifying junction candidates23:51:19 09 Dec 201923:51:19 09 Dec 20190 seconds
Re-alignment to junction candidates23:51:19 09 Dec 201923:51:19 09 Dec 20190 seconds
Resolving best read alignments23:51:19 09 Dec 201923:51:20 09 Dec 20191 second
Creating BAM files23:51:20 09 Dec 201923:51:21 09 Dec 20191 second
Tabulating error counts23:51:21 09 Dec 201923:51:22 09 Dec 20191 second
Re-calibrating base error rates23:51:22 09 Dec 201923:51:22 09 Dec 20190 seconds
Examining read alignment evidence23:51:22 09 Dec 201923:51:52 09 Dec 201930 seconds
Polymorphism statistics23:51:52 09 Dec 201923:51:53 09 Dec 20191 second
Output23:51:53 09 Dec 201900:04:30 10 Dec 201912 minutes 37 seconds
Total 14 minutes 26 seconds