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_A10_F210_I0_R1_S77_L004_R1_0013,933,486392,858,612100.0%99.9 bases100 bases94.0%
errorsqtrim-IND_KHP_HOT_A10_F210_I0_R1_S77_L004_R2_0013,933,447391,884,128100.0%99.6 bases100 bases92.6%
total7,866,933784,742,740100.0%99.8 bases100 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652159.14.998.1%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≤ 100000100061
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 ≤ 50001929
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.086

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52120

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 input03:22:57 12 Jan 201703:24:42 12 Jan 20171 minute 45 seconds
Read alignment to reference genome03:24:43 12 Jan 201703:30:19 12 Jan 20175 minutes 36 seconds
Preprocessing alignments for candidate junction identification03:30:19 12 Jan 201703:33:21 12 Jan 20173 minutes 2 seconds
Preliminary analysis of coverage distribution03:33:21 12 Jan 201703:36:57 12 Jan 20173 minutes 36 seconds
Identifying junction candidates03:36:57 12 Jan 201704:01:31 12 Jan 201724 minutes 34 seconds
Re-alignment to junction candidates04:01:31 12 Jan 201704:02:50 12 Jan 20171 minute 19 seconds
Resolving alignments with junction candidates04:02:50 12 Jan 201704:07:46 12 Jan 20174 minutes 56 seconds
Creating BAM files04:07:46 12 Jan 201704:10:00 12 Jan 20172 minutes 14 seconds
Tabulating error counts04:10:00 12 Jan 201704:13:22 12 Jan 20173 minutes 22 seconds
Re-calibrating base error rates04:13:22 12 Jan 201704:13:23 12 Jan 20171 second
Examining read alignment evidence04:13:23 12 Jan 201706:33:01 12 Jan 20172 hours 19 minutes 38 seconds
Polymorphism statistics06:33:01 12 Jan 201706:33:09 12 Jan 20178 seconds
Output06:33:09 12 Jan 201706:36:10 12 Jan 20173 minutes 1 second
Total 3 hours 13 minutes 12 seconds