breseq  version 0.38.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors11109049673_S2060_Dung_Dnfi_c10.rawdata‡963,957192,791,40098.3%200.0 bases200 bases94.3%
total963,957192,791,40098.3%200.0 bases200 bases94.3%

‡ Read and base numbers are after long reads in this file were split to exactly 200 bases (extra bases discarded)

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0104734,686,13737.41.3100.0%Escherichia coli str. K-12 substr. DH10B, complete sequence.
total4,686,137100.0%

fit relative_variance 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≤ 100000100039
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 ≤ 5000864
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.074

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0104730.91267

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 cutoff0.8
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 polymorphismsNO
Skip indel polymorphisms in homopolymers runs of ≥4 bases
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.4.4
R4.1.1

Execution Times

stepstartendelapsed
Read and reference sequence file input10:34:32 29 Sep 202410:34:52 29 Sep 202420 seconds
Read alignment to reference genome10:34:52 29 Sep 202410:35:49 29 Sep 202457 seconds
Preprocessing alignments for candidate junction identification10:35:49 29 Sep 202410:36:10 29 Sep 202421 seconds
Preliminary analysis of coverage distribution10:36:10 29 Sep 202410:36:45 29 Sep 202435 seconds
Identifying junction candidates10:36:45 29 Sep 202410:37:06 29 Sep 202421 seconds
Re-alignment to junction candidates10:37:06 29 Sep 202410:37:21 29 Sep 202415 seconds
Resolving best read alignments10:37:21 29 Sep 202410:37:52 29 Sep 202431 seconds
Creating BAM files10:37:52 29 Sep 202410:38:19 29 Sep 202427 seconds
Tabulating error counts10:38:19 29 Sep 202410:38:48 29 Sep 202429 seconds
Re-calibrating base error rates10:38:48 29 Sep 202410:38:49 29 Sep 20241 second
Examining read alignment evidence10:38:49 29 Sep 202410:42:46 29 Sep 20243 minutes 57 seconds
Polymorphism statistics10:42:46 29 Sep 202410:42:47 29 Sep 20241 second
Output10:42:47 29 Sep 202410:42:58 29 Sep 202411 seconds
Output :: Mutation Prediction10:42:47 29 Sep 202410:42:51 29 Sep 20244 seconds
Output :: Mutation Annotation10:42:51 29 Sep 202410:42:51 29 Sep 20240 seconds
Total 8 minutes 30 seconds