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-12PD2-9_S4_L001_R2_0011,929,397289,860,204100.0%150.2 bases151 bases96.0%
errorsqtrim-12PD2-9_S5_L001_R1_001547,30182,135,887100.0%150.1 bases151 bases98.2%
errorsqtrim-12PD2-9_S5_L001_R2_001547,28082,033,977100.0%149.9 bases151 bases96.8%
errorsqtrim-12PD2-9_S4_L001_R1_0011,930,136290,129,558100.0%150.3 bases151 bases96.6%
total4,954,114744,159,626100.0%150.2 bases151 bases96.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652150.81.898.3%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≤ 1000001390
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 ≤ 500016
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.62847

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 input16:48:01 02 Jan 201716:49:16 02 Jan 20171 minute 15 seconds
Read alignment to reference genome16:49:17 02 Jan 201716:59:27 02 Jan 201710 minutes 10 seconds
Preprocessing alignments for candidate junction identification16:59:27 02 Jan 201717:01:31 02 Jan 20172 minutes 4 seconds
Preliminary analysis of coverage distribution17:01:31 02 Jan 201717:05:38 02 Jan 20174 minutes 7 seconds
Identifying junction candidates17:05:38 02 Jan 201717:05:39 02 Jan 20171 second
Re-alignment to junction candidates17:05:39 02 Jan 201717:07:55 02 Jan 20172 minutes 16 seconds
Resolving alignments with junction candidates17:07:55 02 Jan 201717:11:37 02 Jan 20173 minutes 42 seconds
Creating BAM files17:11:37 02 Jan 201717:14:29 02 Jan 20172 minutes 52 seconds
Tabulating error counts17:14:29 02 Jan 201717:17:43 02 Jan 20173 minutes 14 seconds
Re-calibrating base error rates17:17:43 02 Jan 201717:17:44 02 Jan 20171 second
Examining read alignment evidence17:17:44 02 Jan 201717:40:34 02 Jan 201722 minutes 50 seconds
Polymorphism statistics17:40:34 02 Jan 201717:40:36 02 Jan 20172 seconds
Output17:40:36 02 Jan 201717:41:32 02 Jan 201756 seconds
Total 53 minutes 30 seconds