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_A10_F169_I1_R1_S45_L004_R1_0014,182,610418,132,428100.0%100.0 bases100 bases97.0%
errorsqtrim-IND_KHP_HOT_A10_F169_I1_R1_S45_L004_R2_0014,182,565417,430,105100.0%99.8 bases100 bases96.6%
total8,365,175835,562,533100.0%99.9 bases100 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652169.82.798.1%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≤ 100000100127
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 ≤ 50001204
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.054

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.48262

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 input01:23:09 05 Jan 201701:24:39 05 Jan 20171 minute 30 seconds
Read alignment to reference genome01:24:39 05 Jan 201701:29:21 05 Jan 20174 minutes 42 seconds
Preprocessing alignments for candidate junction identification01:29:21 05 Jan 201701:32:23 05 Jan 20173 minutes 2 seconds
Preliminary analysis of coverage distribution01:32:23 05 Jan 201701:35:42 05 Jan 20173 minutes 19 seconds
Identifying junction candidates01:35:42 05 Jan 201701:45:47 05 Jan 201710 minutes 5 seconds
Re-alignment to junction candidates01:45:47 05 Jan 201701:46:47 05 Jan 20171 minute 0 seconds
Resolving alignments with junction candidates01:46:47 05 Jan 201701:51:48 05 Jan 20175 minutes 1 second
Creating BAM files01:51:48 05 Jan 201701:53:44 05 Jan 20171 minute 56 seconds
Tabulating error counts01:53:44 05 Jan 201701:57:24 05 Jan 20173 minutes 40 seconds
Re-calibrating base error rates01:57:24 05 Jan 201701:57:25 05 Jan 20171 second
Examining read alignment evidence01:57:25 05 Jan 201702:23:50 05 Jan 201726 minutes 25 seconds
Polymorphism statistics02:23:50 05 Jan 201702:23:51 05 Jan 20171 second
Output02:23:51 05 Jan 201702:25:01 05 Jan 20171 minute 10 seconds
Total 1 hour 1 minute 52 seconds