breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1351685_R1.good.fq3,386,278426,504,724100.0%126.0 bases126 bases99.5%
errorsERR1351685_R2.good.fq3,386,278426,504,724100.0%126.0 bases126 bases99.3%
total6,772,556853,009,448100.0%126.0 bases126 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,469168.32.293.3%Escherichia coli BW25113, complete genome.
coveragedistributionKX0775368,1877926.3120.36.7%Vector pCBB, complete sequence.
total4,639,656100.0%

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≤ 10000017631
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 ≤ 5000163
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.52548
KX0775360.01052

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input12:36:50 30 Mar 202112:38:43 30 Mar 20211 minute 53 seconds
Read alignment to reference genome12:38:44 30 Mar 202112:52:54 30 Mar 202114 minutes 10 seconds
Preprocessing alignments for candidate junction identification12:52:54 30 Mar 202112:54:30 30 Mar 20211 minute 36 seconds
Preliminary analysis of coverage distribution12:54:30 30 Mar 202112:58:13 30 Mar 20213 minutes 43 seconds
Identifying junction candidates12:58:13 30 Mar 202112:58:15 30 Mar 20212 seconds
Re-alignment to junction candidates12:58:15 30 Mar 202113:02:57 30 Mar 20214 minutes 42 seconds
Resolving best read alignments13:02:57 30 Mar 202113:05:09 30 Mar 20212 minutes 12 seconds
Creating BAM files13:05:09 30 Mar 202113:08:22 30 Mar 20213 minutes 13 seconds
Tabulating error counts13:08:22 30 Mar 202113:09:50 30 Mar 20211 minute 28 seconds
Re-calibrating base error rates13:09:50 30 Mar 202113:09:51 30 Mar 20211 second
Examining read alignment evidence13:09:51 30 Mar 202113:24:50 30 Mar 202114 minutes 59 seconds
Polymorphism statistics13:24:50 30 Mar 202113:24:50 30 Mar 20210 seconds
Output13:24:50 30 Mar 202113:25:21 30 Mar 202131 seconds
Total 48 minutes 30 seconds