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_A4_F053_I1_R1_S15_L004_R2_0012,828,537282,481,935100.0%99.9 bases100 bases93.6%
errorsqtrim-IND_KHP_HOT_A4_F053_I1_R1_S15_L004_R1_0012,828,564282,777,013100.0%100.0 bases100 bases94.4%
total5,657,101565,258,948100.0%99.9 bases100 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652112.22.798.1%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≤ 10000037516
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001324
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.059

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.61109

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 input17:29:36 04 Jan 201717:30:39 04 Jan 20171 minute 3 seconds
Read alignment to reference genome17:30:40 04 Jan 201717:33:59 04 Jan 20173 minutes 19 seconds
Preprocessing alignments for candidate junction identification17:33:59 04 Jan 201717:36:09 04 Jan 20172 minutes 10 seconds
Preliminary analysis of coverage distribution17:36:09 04 Jan 201717:38:16 04 Jan 20172 minutes 7 seconds
Identifying junction candidates17:38:16 04 Jan 201717:38:35 04 Jan 201719 seconds
Re-alignment to junction candidates17:38:35 04 Jan 201717:39:21 04 Jan 201746 seconds
Resolving alignments with junction candidates17:39:21 04 Jan 201717:42:40 04 Jan 20173 minutes 19 seconds
Creating BAM files17:42:40 04 Jan 201717:43:53 04 Jan 20171 minute 13 seconds
Tabulating error counts17:43:53 04 Jan 201717:46:18 04 Jan 20172 minutes 25 seconds
Re-calibrating base error rates17:46:18 04 Jan 201717:46:18 04 Jan 20170 seconds
Examining read alignment evidence17:46:18 04 Jan 201718:03:32 04 Jan 201717 minutes 14 seconds
Polymorphism statistics18:03:32 04 Jan 201718:03:32 04 Jan 20170 seconds
Output18:03:32 04 Jan 201718:04:07 04 Jan 201735 seconds
Total 34 minutes 30 seconds