breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-IND_KHP_HOT_A16_F201_I1_R1_S72_L004_R1_0013,407,816340,690,678100.0%100.0 bases100 bases93.0%
errorsqtrim-IND_KHP_HOT_A16_F201_I1_R1_S72_L004_R2_0013,407,803340,416,757100.0%99.9 bases100 bases92.8%
total6,815,619681,107,435100.0%99.9 bases100 bases92.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652135.02.398.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 100000100000
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 ≤ 5000861
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.038

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.56519

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input02:25:01 05 Jan 201702:26:15 05 Jan 20171 minute 14 seconds
Read alignment to reference genome02:26:16 05 Jan 201702:30:11 05 Jan 20173 minutes 55 seconds
Preprocessing alignments for candidate junction identification02:30:11 05 Jan 201702:32:37 05 Jan 20172 minutes 26 seconds
Preliminary analysis of coverage distribution02:32:37 05 Jan 201702:35:11 05 Jan 20172 minutes 34 seconds
Identifying junction candidates02:35:11 05 Jan 201702:40:13 05 Jan 20175 minutes 2 seconds
Re-alignment to junction candidates02:40:13 05 Jan 201702:41:00 05 Jan 201747 seconds
Resolving alignments with junction candidates02:41:00 05 Jan 201702:45:01 05 Jan 20174 minutes 1 second
Creating BAM files02:45:01 05 Jan 201702:46:30 05 Jan 20171 minute 29 seconds
Tabulating error counts02:46:30 05 Jan 201702:49:32 05 Jan 20173 minutes 2 seconds
Re-calibrating base error rates02:49:32 05 Jan 201702:49:34 05 Jan 20172 seconds
Examining read alignment evidence02:49:34 05 Jan 201703:11:39 05 Jan 201722 minutes 5 seconds
Polymorphism statistics03:11:39 05 Jan 201703:11:40 05 Jan 20171 second
Output03:11:40 05 Jan 201703:12:36 05 Jan 201756 seconds
Total 47 minutes 34 seconds