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_A16_F048_I1_R1_S70_L004_R2_0012,602,294259,897,679100.0%99.9 bases100 bases90.5%
errorsqtrim-IND_KHP_HOT_A16_F048_I1_R1_S70_L004_R1_0012,602,312260,155,858100.0%100.0 bases100 bases91.0%
total5,204,606520,053,537100.0%99.9 bases100 bases90.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652101.21.897.8%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≤ 100000100051
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 ≤ 50001769
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.079

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.64693

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 input23:59:48 04 Jan 201700:00:45 05 Jan 201757 seconds
Read alignment to reference genome00:00:45 05 Jan 201700:03:53 05 Jan 20173 minutes 8 seconds
Preprocessing alignments for candidate junction identification00:03:53 05 Jan 201700:05:44 05 Jan 20171 minute 51 seconds
Preliminary analysis of coverage distribution00:05:44 05 Jan 201700:07:40 05 Jan 20171 minute 56 seconds
Identifying junction candidates00:07:40 05 Jan 201700:25:02 05 Jan 201717 minutes 22 seconds
Re-alignment to junction candidates00:25:02 05 Jan 201700:25:43 05 Jan 201741 seconds
Resolving alignments with junction candidates00:25:43 05 Jan 201700:28:48 05 Jan 20173 minutes 5 seconds
Creating BAM files00:28:48 05 Jan 201700:29:55 05 Jan 20171 minute 7 seconds
Tabulating error counts00:29:55 05 Jan 201700:32:02 05 Jan 20172 minutes 7 seconds
Re-calibrating base error rates00:32:02 05 Jan 201700:32:02 05 Jan 20170 seconds
Examining read alignment evidence00:32:02 05 Jan 201700:47:27 05 Jan 201715 minutes 25 seconds
Polymorphism statistics00:47:27 05 Jan 201700:47:28 05 Jan 20171 second
Output00:47:28 05 Jan 201700:48:40 05 Jan 20171 minute 12 seconds
Total 48 minutes 52 seconds