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_A5_F064_I0_R1_S25_L004_R2_0013,351,487334,524,560100.0%99.8 bases100 bases96.3%
errorsqtrim-IND_KHP_HOT_A5_F064_I0_R1_S25_L004_R1_0013,351,513335,046,168100.0%100.0 bases100 bases97.0%
total6,703,000669,570,728100.0%99.9 bases100 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652139.01.898.1%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≤ 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 ≤ 50001978
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_0009130.55250

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 input04:23:11 14 Jan 201704:24:20 14 Jan 20171 minute 9 seconds
Read alignment to reference genome04:24:21 14 Jan 201704:27:36 14 Jan 20173 minutes 15 seconds
Preprocessing alignments for candidate junction identification04:27:36 14 Jan 201704:30:01 14 Jan 20172 minutes 25 seconds
Preliminary analysis of coverage distribution04:30:01 14 Jan 201704:32:42 14 Jan 20172 minutes 41 seconds
Identifying junction candidates04:32:42 14 Jan 201704:51:15 14 Jan 201718 minutes 33 seconds
Re-alignment to junction candidates04:51:15 14 Jan 201704:52:03 14 Jan 201748 seconds
Resolving alignments with junction candidates04:52:03 14 Jan 201704:56:08 14 Jan 20174 minutes 5 seconds
Creating BAM files04:56:08 14 Jan 201704:57:41 14 Jan 20171 minute 33 seconds
Tabulating error counts04:57:41 14 Jan 201705:00:36 14 Jan 20172 minutes 55 seconds
Re-calibrating base error rates05:00:36 14 Jan 201705:00:37 14 Jan 20171 second
Examining read alignment evidence05:00:37 14 Jan 201706:06:30 14 Jan 20171 hour 5 minutes 53 seconds
Polymorphism statistics06:06:30 14 Jan 201706:06:34 14 Jan 20174 seconds
Output06:06:34 14 Jan 201706:08:34 14 Jan 20172 minutes 0 seconds
Total 1 hour 45 minutes 22 seconds