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_A4_F125_I0_R1_S23_L004_R1_0012,659,799265,716,672100.0%99.9 bases100 bases96.3%
errorsqtrim-IND_KHP_HOT_A4_F125_I0_R1_S23_L004_R2_0012,659,767265,330,252100.0%99.8 bases100 bases95.9%
total5,319,566531,046,924100.0%99.8 bases100 bases96.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652108.62.298.1%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≤ 100000100092
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 ≤ 50002025
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.090

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.62125

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input04:22:43 11 Jan 201704:23:39 11 Jan 201756 seconds
Read alignment to reference genome04:23:40 11 Jan 201704:27:12 11 Jan 20173 minutes 32 seconds
Preprocessing alignments for candidate junction identification04:27:12 11 Jan 201704:29:08 11 Jan 20171 minute 56 seconds
Preliminary analysis of coverage distribution04:29:08 11 Jan 201704:31:30 11 Jan 20172 minutes 22 seconds
Identifying junction candidates04:31:30 11 Jan 201705:01:23 11 Jan 201729 minutes 53 seconds
Re-alignment to junction candidates05:01:23 11 Jan 201705:02:14 11 Jan 201751 seconds
Resolving alignments with junction candidates05:02:14 11 Jan 201705:05:38 11 Jan 20173 minutes 24 seconds
Creating BAM files05:05:38 11 Jan 201705:07:22 11 Jan 20171 minute 44 seconds
Tabulating error counts05:07:22 11 Jan 201705:09:42 11 Jan 20172 minutes 20 seconds
Re-calibrating base error rates05:09:42 11 Jan 201705:09:43 11 Jan 20171 second
Examining read alignment evidence05:09:43 11 Jan 201706:21:42 11 Jan 20171 hour 11 minutes 59 seconds
Polymorphism statistics06:21:42 11 Jan 201706:21:45 11 Jan 20173 seconds
Output06:21:45 11 Jan 201706:24:02 11 Jan 20172 minutes 17 seconds
Total 2 hours 1 minute 18 seconds