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-PUTR8-10_S20_L001_R2_0011,455,063218,856,486100.0%150.4 bases151 bases99.1%
errorsqtrim-PUTR8-10_S20_L001_R1_0011,455,103218,964,276100.0%150.5 bases151 bases99.8%
total2,910,166437,820,762100.0%150.4 bases151 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65293.91.398.3%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≤ 100000675
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 ≤ 500043
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.74595

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 input19:37:30 03 Jan 201719:38:23 03 Jan 201753 seconds
Read alignment to reference genome19:38:23 03 Jan 201719:46:30 03 Jan 20178 minutes 7 seconds
Preprocessing alignments for candidate junction identification19:46:30 03 Jan 201719:47:58 03 Jan 20171 minute 28 seconds
Preliminary analysis of coverage distribution19:47:58 03 Jan 201719:50:48 03 Jan 20172 minutes 50 seconds
Identifying junction candidates19:50:48 03 Jan 201719:50:48 03 Jan 20170 seconds
Re-alignment to junction candidates19:50:48 03 Jan 201719:52:30 03 Jan 20171 minute 42 seconds
Resolving alignments with junction candidates19:52:30 03 Jan 201719:55:22 03 Jan 20172 minutes 52 seconds
Creating BAM files19:55:22 03 Jan 201719:57:20 03 Jan 20171 minute 58 seconds
Tabulating error counts19:57:20 03 Jan 201719:59:41 03 Jan 20172 minutes 21 seconds
Re-calibrating base error rates19:59:41 03 Jan 201719:59:43 03 Jan 20172 seconds
Examining read alignment evidence19:59:43 03 Jan 201720:17:26 03 Jan 201717 minutes 43 seconds
Polymorphism statistics20:17:26 03 Jan 201720:17:27 03 Jan 20171 second
Output20:17:27 03 Jan 201720:17:46 03 Jan 201719 seconds
Total 40 minutes 16 seconds