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-12PD4-9_S8_L001_R1_0011,284,629193,015,849100.0%150.3 bases151 bases94.3%
errorsqtrim-12PD4-9_S8_L001_R2_0011,284,395192,814,937100.0%150.1 bases151 bases93.4%
errorsqtrim-12PD4-9_S11_L001_R2_001461,23269,289,402100.0%150.2 bases151 bases98.2%
errorsqtrim-12PD4-9_S11_L001_R1_001461,23969,334,641100.0%150.3 bases151 bases98.9%
total3,491,495524,454,829100.0%150.2 bases151 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652107.91.998.3%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≤ 1000004452
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_0009130.71671

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 input17:57:50 02 Jan 201717:58:40 02 Jan 201750 seconds
Read alignment to reference genome17:58:41 02 Jan 201718:05:17 02 Jan 20176 minutes 36 seconds
Preprocessing alignments for candidate junction identification18:05:17 02 Jan 201718:06:43 02 Jan 20171 minute 26 seconds
Preliminary analysis of coverage distribution18:06:43 02 Jan 201718:09:33 02 Jan 20172 minutes 50 seconds
Identifying junction candidates18:09:33 02 Jan 201718:09:34 02 Jan 20171 second
Re-alignment to junction candidates18:09:34 02 Jan 201718:11:14 02 Jan 20171 minute 40 seconds
Resolving alignments with junction candidates18:11:14 02 Jan 201718:13:48 02 Jan 20172 minutes 34 seconds
Creating BAM files18:13:48 02 Jan 201718:15:47 02 Jan 20171 minute 59 seconds
Tabulating error counts18:15:47 02 Jan 201718:18:00 02 Jan 20172 minutes 13 seconds
Re-calibrating base error rates18:18:00 02 Jan 201718:18:01 02 Jan 20171 second
Examining read alignment evidence18:18:01 02 Jan 201718:34:13 02 Jan 201716 minutes 12 seconds
Polymorphism statistics18:34:13 02 Jan 201718:34:15 02 Jan 20172 seconds
Output18:34:15 02 Jan 201718:34:51 02 Jan 201736 seconds
Total 37 minutes 0 seconds