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-PUTR3-1_S3_L001_R1_00110,9451,647,258100.0%150.5 bases151 bases99.1%
errorsqtrim-PUTR3-1_S8_L001_R1_0011,646,955247,880,909100.0%150.5 bases151 bases99.6%
errorsqtrim-PUTR3-1_S8_L001_R2_0011,646,780247,679,955100.0%150.4 bases151 bases98.7%
errorsqtrim-PUTR3-1_S3_L001_R2_00110,9441,646,129100.0%150.4 bases151 bases98.3%
total3,315,624498,854,251100.0%150.5 bases151 bases99.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652106.91.898.3%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≤ 100000619
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 ≤ 500026
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.71880

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 input14:39:57 03 Jan 201714:41:16 03 Jan 20171 minute 19 seconds
Read alignment to reference genome14:41:16 03 Jan 201714:51:48 03 Jan 201710 minutes 32 seconds
Preprocessing alignments for candidate junction identification14:51:48 03 Jan 201714:53:48 03 Jan 20172 minutes 0 seconds
Preliminary analysis of coverage distribution14:53:48 03 Jan 201714:57:14 03 Jan 20173 minutes 26 seconds
Identifying junction candidates14:57:14 03 Jan 201714:57:15 03 Jan 20171 second
Re-alignment to junction candidates14:57:15 03 Jan 201714:59:35 03 Jan 20172 minutes 20 seconds
Resolving alignments with junction candidates14:59:35 03 Jan 201715:03:08 03 Jan 20173 minutes 33 seconds
Creating BAM files15:03:08 03 Jan 201715:05:27 03 Jan 20172 minutes 19 seconds
Tabulating error counts15:05:27 03 Jan 201715:08:36 03 Jan 20173 minutes 9 seconds
Re-calibrating base error rates15:08:36 03 Jan 201715:08:37 03 Jan 20171 second
Examining read alignment evidence15:08:37 03 Jan 201715:31:21 03 Jan 201722 minutes 44 seconds
Polymorphism statistics15:31:21 03 Jan 201715:31:23 03 Jan 20172 seconds
Output15:31:23 03 Jan 201715:31:47 03 Jan 201724 seconds
Total 51 minutes 50 seconds