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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsE2C3_S167_R1_001.good.fq1,652,08391,175,929100.0%55.2 bases62 bases58.3%
total1,652,08391,175,929100.0%55.2 bases62 bases58.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionW3110S.gb4,646,334[53.4][47.6]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≤ 1000005573
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
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)
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 input14:24:08 10 Dec 201914:24:25 10 Dec 201917 seconds
Read alignment to reference genome14:24:25 10 Dec 201914:36:27 10 Dec 201912 minutes 2 seconds
Preprocessing alignments for candidate junction identification14:36:27 10 Dec 201914:36:45 10 Dec 201918 seconds
Preliminary analysis of coverage distribution14:36:45 10 Dec 201914:36:59 10 Dec 201914 seconds
Identifying junction candidates14:36:59 10 Dec 201914:37:00 10 Dec 20191 second
Re-alignment to junction candidates14:37:00 10 Dec 201914:37:31 10 Dec 201931 seconds
Resolving best read alignments14:37:31 10 Dec 201914:37:57 10 Dec 201926 seconds
Creating BAM files14:37:57 10 Dec 201914:38:10 10 Dec 201913 seconds
Tabulating error counts14:38:10 10 Dec 201914:38:14 10 Dec 20194 seconds
Re-calibrating base error rates14:38:14 10 Dec 201914:38:15 10 Dec 20191 second
Examining read alignment evidence14:38:15 10 Dec 201914:39:30 10 Dec 20191 minute 15 seconds
Polymorphism statistics14:39:30 10 Dec 201914:39:31 10 Dec 20191 second
Output14:39:31 10 Dec 201916:12:19 10 Dec 20191 hour 32 minutes 48 seconds
Total 1 hour 48 minutes 11 seconds