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_F258_I0_R1_S79_L004_R2_0012,595,839258,692,321100.0%99.7 bases100 bases91.9%
errorsqtrim-IND_KHP_HOT_A16_F258_I0_R1_S79_L004_R1_0012,595,858259,490,387100.0%100.0 bases100 bases93.4%
total5,191,697518,182,708100.0%99.8 bases100 bases92.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652103.02.098.0%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≤ 100000100007
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 ≤ 50002079
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.093

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.63878

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 input09:15:49 13 Jan 201709:16:46 13 Jan 201757 seconds
Read alignment to reference genome09:16:46 13 Jan 201709:19:57 13 Jan 20173 minutes 11 seconds
Preprocessing alignments for candidate junction identification09:19:57 13 Jan 201709:21:51 13 Jan 20171 minute 54 seconds
Preliminary analysis of coverage distribution09:21:51 13 Jan 201709:23:56 13 Jan 20172 minutes 5 seconds
Identifying junction candidates09:23:56 13 Jan 201709:54:57 13 Jan 201731 minutes 1 second
Re-alignment to junction candidates09:54:57 13 Jan 201709:55:40 13 Jan 201743 seconds
Resolving alignments with junction candidates09:55:40 13 Jan 201709:58:45 13 Jan 20173 minutes 5 seconds
Creating BAM files09:58:45 13 Jan 201710:00:01 13 Jan 20171 minute 16 seconds
Tabulating error counts10:00:01 13 Jan 201710:02:09 13 Jan 20172 minutes 8 seconds
Re-calibrating base error rates10:02:09 13 Jan 201710:02:10 13 Jan 20171 second
Examining read alignment evidence10:02:10 13 Jan 201711:04:28 13 Jan 20171 hour 2 minutes 18 seconds
Polymorphism statistics11:04:28 13 Jan 201711:04:33 13 Jan 20175 seconds
Output11:04:33 13 Jan 201711:08:12 13 Jan 20173 minutes 39 seconds
Total 1 hour 52 minutes 23 seconds