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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSvNSRound2_28_15_2_S136_L002_R1_001.good.fq1,317,015190,529,328100.0%144.7 bases149 bases96.8%
errorsSvNSRound2_28_15_2_S136_L002_R2_001.good.fq1,317,015190,529,328100.0%144.7 bases149 bases91.6%
total2,634,030381,058,656100.0%144.7 bases149 bases94.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_000913_3_pae_pgi4,640,91269.52.0100.0%Escherichia coli str. K-12 substr. MG1655, P. aerophilum pgi gene, complete genome.
total4,640,912100.0%

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≤ 10000016233
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 ≤ 5000100
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_000913_3_pae_pgi0.80658

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 input18:14:56 19 Dec 202018:17:31 19 Dec 20202 minutes 35 seconds
Read alignment to reference genome18:17:32 19 Dec 202018:42:15 19 Dec 202024 minutes 43 seconds
Preprocessing alignments for candidate junction identification18:42:15 19 Dec 202018:44:17 19 Dec 20202 minutes 2 seconds
Preliminary analysis of coverage distribution18:44:17 19 Dec 202018:50:01 19 Dec 20205 minutes 44 seconds
Identifying junction candidates18:50:01 19 Dec 202018:50:54 19 Dec 202053 seconds
Re-alignment to junction candidates18:50:54 19 Dec 202018:56:43 19 Dec 20205 minutes 49 seconds
Resolving best read alignments18:56:43 19 Dec 202018:59:57 19 Dec 20203 minutes 14 seconds
Creating BAM files18:59:57 19 Dec 202019:05:04 19 Dec 20205 minutes 7 seconds
Tabulating error counts19:05:04 19 Dec 202019:06:56 19 Dec 20201 minute 52 seconds
Re-calibrating base error rates19:06:56 19 Dec 202019:06:59 19 Dec 20203 seconds
Examining read alignment evidence19:06:59 19 Dec 202019:30:58 19 Dec 202023 minutes 59 seconds
Polymorphism statistics19:30:58 19 Dec 202019:31:00 19 Dec 20202 seconds
Output19:31:00 19 Dec 202019:31:53 19 Dec 202053 seconds
Total 1 hour 16 minutes 56 seconds