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-OCTA1-9_S3_L001_R2_0011,045,081156,995,572100.0%150.2 bases151 bases96.5%
errorsqtrim-OCTA1-9_S3_L001_R1_0011,045,378157,144,831100.0%150.3 bases151 bases97.2%
total2,090,459314,140,403100.0%150.3 bases151 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65265.61.698.3%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≤ 100000409
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 ≤ 500011
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_0009130.81310

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 input14:59:25 02 Jan 201715:00:05 02 Jan 201740 seconds
Read alignment to reference genome15:00:06 02 Jan 201715:06:18 02 Jan 20176 minutes 12 seconds
Preprocessing alignments for candidate junction identification15:06:18 02 Jan 201715:07:21 02 Jan 20171 minute 3 seconds
Preliminary analysis of coverage distribution15:07:21 02 Jan 201715:09:09 02 Jan 20171 minute 48 seconds
Identifying junction candidates15:09:09 02 Jan 201715:09:09 02 Jan 20170 seconds
Re-alignment to junction candidates15:09:09 02 Jan 201715:10:19 02 Jan 20171 minute 10 seconds
Resolving alignments with junction candidates15:10:19 02 Jan 201715:12:11 02 Jan 20171 minute 52 seconds
Creating BAM files15:12:11 02 Jan 201715:13:35 02 Jan 20171 minute 24 seconds
Tabulating error counts15:13:35 02 Jan 201715:15:14 02 Jan 20171 minute 39 seconds
Re-calibrating base error rates15:15:14 02 Jan 201715:15:15 02 Jan 20171 second
Examining read alignment evidence15:15:15 02 Jan 201715:28:11 02 Jan 201712 minutes 56 seconds
Polymorphism statistics15:28:11 02 Jan 201715:28:12 02 Jan 20171 second
Output15:28:12 02 Jan 201715:28:26 02 Jan 201714 seconds
Total 29 minutes 0 seconds