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-HMDA3-6_S6_L001_R1_0011,282,680192,951,941100.0%150.4 bases151 bases99.5%
errorsqtrim-HMDA3-6_S6_L001_R2_0011,282,613192,752,673100.0%150.3 bases151 bases98.4%
total2,565,293385,704,614100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65282.51.498.3%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≤ 1000001920
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 ≤ 500028
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.77239

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 input15:00:42 03 Jan 201715:01:38 03 Jan 201756 seconds
Read alignment to reference genome15:01:39 03 Jan 201715:09:54 03 Jan 20178 minutes 15 seconds
Preprocessing alignments for candidate junction identification15:09:54 03 Jan 201715:11:20 03 Jan 20171 minute 26 seconds
Preliminary analysis of coverage distribution15:11:20 03 Jan 201715:14:04 03 Jan 20172 minutes 44 seconds
Identifying junction candidates15:14:04 03 Jan 201715:14:04 03 Jan 20170 seconds
Re-alignment to junction candidates15:14:04 03 Jan 201715:15:45 03 Jan 20171 minute 41 seconds
Resolving alignments with junction candidates15:15:45 03 Jan 201715:18:36 03 Jan 20172 minutes 51 seconds
Creating BAM files15:18:36 03 Jan 201715:20:30 03 Jan 20171 minute 54 seconds
Tabulating error counts15:20:30 03 Jan 201715:22:50 03 Jan 20172 minutes 20 seconds
Re-calibrating base error rates15:22:50 03 Jan 201715:22:51 03 Jan 20171 second
Examining read alignment evidence15:22:51 03 Jan 201715:41:06 03 Jan 201718 minutes 15 seconds
Polymorphism statistics15:41:06 03 Jan 201715:41:07 03 Jan 20171 second
Output15:41:07 03 Jan 201715:41:27 03 Jan 201720 seconds
Total 40 minutes 44 seconds