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-HEXA6-6_S14_L001_R1_0011,282,005192,882,276100.0%150.5 bases151 bases99.8%
errorsqtrim-HEXA6-6_S14_L001_R2_0011,281,990192,773,484100.0%150.4 bases151 bases99.2%
total2,563,995385,655,760100.0%150.4 bases151 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65282.81.398.3%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≤ 100000531
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 ≤ 500019
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.77081

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 input15:22:01 02 Jan 201715:22:50 02 Jan 201749 seconds
Read alignment to reference genome15:22:50 02 Jan 201715:29:58 02 Jan 20177 minutes 8 seconds
Preprocessing alignments for candidate junction identification15:29:58 02 Jan 201715:31:19 02 Jan 20171 minute 21 seconds
Preliminary analysis of coverage distribution15:31:19 02 Jan 201715:33:46 02 Jan 20172 minutes 27 seconds
Identifying junction candidates15:33:46 02 Jan 201715:33:47 02 Jan 20171 second
Re-alignment to junction candidates15:33:47 02 Jan 201715:35:20 02 Jan 20171 minute 33 seconds
Resolving alignments with junction candidates15:35:20 02 Jan 201715:37:42 02 Jan 20172 minutes 22 seconds
Creating BAM files15:37:42 02 Jan 201715:39:31 02 Jan 20171 minute 49 seconds
Tabulating error counts15:39:31 02 Jan 201715:41:33 02 Jan 20172 minutes 2 seconds
Re-calibrating base error rates15:41:33 02 Jan 201715:41:34 02 Jan 20171 second
Examining read alignment evidence15:41:34 02 Jan 201715:57:32 02 Jan 201715 minutes 58 seconds
Polymorphism statistics15:57:32 02 Jan 201715:57:33 02 Jan 20171 second
Output15:57:33 02 Jan 201715:57:51 02 Jan 201718 seconds
Total 35 minutes 50 seconds