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-12PD4-6_S7_L001_R2_0011,420,065213,386,716100.0%150.3 bases151 bases96.6%
errorsqtrim-12PD4-6_S9_L001_R1_001573,72386,264,377100.0%150.4 bases151 bases99.4%
errorsqtrim-12PD4-6_S7_L001_R1_0011,420,214213,537,368100.0%150.4 bases151 bases97.2%
errorsqtrim-12PD4-6_S9_L001_R2_001573,71586,203,668100.0%150.3 bases151 bases98.7%
total3,987,717599,392,129100.0%150.3 bases151 bases97.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652123.01.498.3%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≤ 100000984
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 ≤ 500014
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_0009130.68033

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 input09:32:32 02 Jan 201709:34:09 02 Jan 20171 minute 37 seconds
Read alignment to reference genome09:34:10 02 Jan 201709:45:35 02 Jan 201711 minutes 25 seconds
Preprocessing alignments for candidate junction identification09:45:35 02 Jan 201709:47:40 02 Jan 20172 minutes 5 seconds
Preliminary analysis of coverage distribution09:47:40 02 Jan 201709:51:26 02 Jan 20173 minutes 46 seconds
Identifying junction candidates09:51:26 02 Jan 201709:51:26 02 Jan 20170 seconds
Re-alignment to junction candidates09:51:26 02 Jan 201709:53:54 02 Jan 20172 minutes 28 seconds
Resolving alignments with junction candidates09:53:54 02 Jan 201709:57:21 02 Jan 20173 minutes 27 seconds
Creating BAM files09:57:21 02 Jan 201710:00:02 02 Jan 20172 minutes 41 seconds
Tabulating error counts10:00:02 02 Jan 201710:03:07 02 Jan 20173 minutes 5 seconds
Re-calibrating base error rates10:03:07 02 Jan 201710:03:09 02 Jan 20172 seconds
Examining read alignment evidence10:03:09 02 Jan 201710:26:09 02 Jan 201723 minutes 0 seconds
Polymorphism statistics10:26:09 02 Jan 201710:26:11 02 Jan 20172 seconds
Output10:26:11 02 Jan 201710:26:36 02 Jan 201725 seconds
Total 54 minutes 3 seconds