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_F112_I0_R1_S51_L004_R1_0012,750,040274,900,474100.0%100.0 bases100 bases95.9%
errorsqtrim-IND_KHP_HOT_A10_F112_I0_R1_S51_L004_R2_0012,750,022274,095,530100.0%99.7 bases100 bases94.3%
total5,500,062548,996,004100.0%99.8 bases100 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652112.51.898.1%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≤ 100000100119
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 ≤ 50001958
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.088

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.61559

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 input02:35:49 14 Jan 201702:36:47 14 Jan 201758 seconds
Read alignment to reference genome02:36:48 14 Jan 201702:39:34 14 Jan 20172 minutes 46 seconds
Preprocessing alignments for candidate junction identification02:39:34 14 Jan 201702:41:33 14 Jan 20171 minute 59 seconds
Preliminary analysis of coverage distribution02:41:33 14 Jan 201702:43:45 14 Jan 20172 minutes 12 seconds
Identifying junction candidates02:43:45 14 Jan 201703:09:52 14 Jan 201726 minutes 7 seconds
Re-alignment to junction candidates03:09:52 14 Jan 201703:10:31 14 Jan 201739 seconds
Resolving alignments with junction candidates03:10:31 14 Jan 201703:13:48 14 Jan 20173 minutes 17 seconds
Creating BAM files03:13:48 14 Jan 201703:15:08 14 Jan 20171 minute 20 seconds
Tabulating error counts03:15:08 14 Jan 201703:17:27 14 Jan 20172 minutes 19 seconds
Re-calibrating base error rates03:17:27 14 Jan 201703:17:28 14 Jan 20171 second
Examining read alignment evidence03:17:28 14 Jan 201704:21:04 14 Jan 20171 hour 3 minutes 36 seconds
Polymorphism statistics04:21:04 14 Jan 201704:21:07 14 Jan 20173 seconds
Output04:21:07 14 Jan 201704:23:11 14 Jan 20172 minutes 4 seconds
Total 1 hour 47 minutes 21 seconds