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_A9_F255_I1_R1_S61_L004_R1_0013,058,226305,725,277100.0%100.0 bases100 bases93.3%
errorsqtrim-IND_KHP_HOT_A9_F255_I1_R1_S61_L004_R2_0013,058,183305,232,203100.0%99.8 bases100 bases93.0%
total6,116,409610,957,480100.0%99.9 bases100 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652120.72.198.2%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≤ 100000100046
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000634
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.029

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.58909

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 input06:14:04 05 Jan 201706:15:07 05 Jan 20171 minute 3 seconds
Read alignment to reference genome06:15:08 05 Jan 201706:18:49 05 Jan 20173 minutes 41 seconds
Preprocessing alignments for candidate junction identification06:18:49 05 Jan 201706:21:05 05 Jan 20172 minutes 16 seconds
Preliminary analysis of coverage distribution06:21:05 05 Jan 201706:23:25 05 Jan 20172 minutes 20 seconds
Identifying junction candidates06:23:25 05 Jan 201706:24:46 05 Jan 20171 minute 21 seconds
Re-alignment to junction candidates06:24:46 05 Jan 201706:25:27 05 Jan 201741 seconds
Resolving alignments with junction candidates06:25:27 05 Jan 201706:29:01 05 Jan 20173 minutes 34 seconds
Creating BAM files06:29:01 05 Jan 201706:30:23 05 Jan 20171 minute 22 seconds
Tabulating error counts06:30:23 05 Jan 201706:32:57 05 Jan 20172 minutes 34 seconds
Re-calibrating base error rates06:32:57 05 Jan 201706:32:58 05 Jan 20171 second
Examining read alignment evidence06:32:58 05 Jan 201706:51:31 05 Jan 201718 minutes 33 seconds
Polymorphism statistics06:51:31 05 Jan 201706:51:34 05 Jan 20173 seconds
Output06:51:34 05 Jan 201706:52:28 05 Jan 201754 seconds
Total 38 minutes 23 seconds