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_A8_F183_I0_R1_S38_L004_R1_0012,389,110238,821,395100.0%100.0 bases100 bases94.9%
errorsqtrim-IND_KHP_HOT_A8_F183_I0_R1_S38_L004_R2_0012,389,088237,978,812100.0%99.6 bases100 bases93.1%
total4,778,198476,800,207100.0%99.8 bases100 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65296.42.098.2%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≤ 100000100004
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 ≤ 50002037
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.091

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.65755

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 input03:26:20 13 Jan 201703:27:10 13 Jan 201750 seconds
Read alignment to reference genome03:27:10 13 Jan 201703:29:59 13 Jan 20172 minutes 49 seconds
Preprocessing alignments for candidate junction identification03:29:59 13 Jan 201703:31:40 13 Jan 20171 minute 41 seconds
Preliminary analysis of coverage distribution03:31:40 13 Jan 201703:33:33 13 Jan 20171 minute 53 seconds
Identifying junction candidates03:33:33 13 Jan 201703:55:28 13 Jan 201721 minutes 55 seconds
Re-alignment to junction candidates03:55:28 13 Jan 201703:56:07 13 Jan 201739 seconds
Resolving alignments with junction candidates03:56:07 13 Jan 201703:58:56 13 Jan 20172 minutes 49 seconds
Creating BAM files03:58:56 13 Jan 201704:00:05 13 Jan 20171 minute 9 seconds
Tabulating error counts04:00:05 13 Jan 201704:02:05 13 Jan 20172 minutes 0 seconds
Re-calibrating base error rates04:02:05 13 Jan 201704:02:05 13 Jan 20170 seconds
Examining read alignment evidence04:02:05 13 Jan 201705:00:43 13 Jan 201758 minutes 38 seconds
Polymorphism statistics05:00:43 13 Jan 201705:00:47 13 Jan 20174 seconds
Output05:00:47 13 Jan 201705:03:07 13 Jan 20172 minutes 20 seconds
Total 1 hour 36 minutes 47 seconds