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-GLUT7-7-rerun_S19_L001_R2_0011,069,036160,738,776100.0%150.4 bases151 bases98.8%
errorsqtrim-GLUT7-7-rerun_S19_L001_R1_0011,069,215160,857,894100.0%150.4 bases151 bases99.8%
total2,138,251321,596,670100.0%150.4 bases151 bases99.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65268.91.398.3%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≤ 100000274
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_0009130.80411

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 input23:04:17 02 Jan 201723:04:48 02 Jan 201731 seconds
Read alignment to reference genome23:04:48 02 Jan 201723:08:46 02 Jan 20173 minutes 58 seconds
Preprocessing alignments for candidate junction identification23:08:46 02 Jan 201723:09:40 02 Jan 201754 seconds
Preliminary analysis of coverage distribution23:09:40 02 Jan 201723:11:17 02 Jan 20171 minute 37 seconds
Identifying junction candidates23:11:17 02 Jan 201723:11:17 02 Jan 20170 seconds
Re-alignment to junction candidates23:11:17 02 Jan 201723:12:12 02 Jan 201755 seconds
Resolving alignments with junction candidates23:12:12 02 Jan 201723:13:44 02 Jan 20171 minute 32 seconds
Creating BAM files23:13:44 02 Jan 201723:15:00 02 Jan 20171 minute 16 seconds
Tabulating error counts23:15:00 02 Jan 201723:16:24 02 Jan 20171 minute 24 seconds
Re-calibrating base error rates23:16:24 02 Jan 201723:16:24 02 Jan 20170 seconds
Examining read alignment evidence23:16:24 02 Jan 201723:27:11 02 Jan 201710 minutes 47 seconds
Polymorphism statistics23:27:11 02 Jan 201723:27:12 02 Jan 20171 second
Output23:27:12 02 Jan 201723:27:29 02 Jan 201717 seconds
Total 23 minutes 12 seconds