breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors3_S3_L001_R1_001569,24785,160,335100.0%149.6 bases151 bases99.7%
errorsHM3_S13_L001_R1_0011,469,949221,250,890100.0%150.5 bases151 bases99.7%
errors3_S3_L001_R2_001569,24285,160,159100.0%149.6 bases151 bases98.7%
errorsHM3_S13_L001_R2_0011,469,952221,249,148100.0%150.5 bases151 bases98.0%
total4,078,390612,820,532100.0%150.3 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652129.82.8100.0%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≤ 1000007628
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 ≤ 5000359
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.024

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.68379

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 input23:52:40 20 Feb 201623:53:35 20 Feb 201655 seconds
Read alignment to reference genome23:53:35 20 Feb 201623:55:55 20 Feb 20162 minutes 20 seconds
Preprocessing alignments for candidate junction identification23:55:55 20 Feb 201623:57:20 20 Feb 20161 minute 25 seconds
Preliminary analysis of coverage distribution23:57:20 20 Feb 201600:01:03 21 Feb 20163 minutes 43 seconds
Identifying junction candidates00:01:03 21 Feb 201600:01:04 21 Feb 20161 second
Re-alignment to junction candidates00:01:04 21 Feb 201600:01:37 21 Feb 201633 seconds
Resolving alignments with junction candidates00:01:37 21 Feb 201600:04:47 21 Feb 20163 minutes 10 seconds
Creating BAM files00:04:47 21 Feb 201600:07:12 21 Feb 20162 minutes 25 seconds
Tabulating error counts00:07:12 21 Feb 201600:10:28 21 Feb 20163 minutes 16 seconds
Re-calibrating base error rates00:10:28 21 Feb 201600:10:30 21 Feb 20162 seconds
Examining read alignment evidence00:10:30 21 Feb 201600:31:54 21 Feb 201621 minutes 24 seconds
Polymorphism statistics00:31:54 21 Feb 201600:31:56 21 Feb 20162 seconds
Output00:31:56 21 Feb 201600:32:39 21 Feb 201643 seconds
Total 39 minutes 59 seconds