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-PUTR7-7_S10_L001_R1_0011,476,346222,185,795100.0%150.5 bases151 bases99.7%
errorsqtrim-PUTR7-7_S16_L001_R1_001193,66129,141,545100.0%150.5 bases151 bases99.7%
errorsqtrim-PUTR7-7_S16_L001_R2_001193,65229,118,608100.0%150.4 bases151 bases98.6%
errorsqtrim-PUTR7-7_S10_L001_R2_0011,476,205222,030,519100.0%150.4 bases151 bases98.8%
total3,339,864502,476,467100.0%150.4 bases151 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652105.61.498.3%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≤ 100000896
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 ≤ 500018
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_0009130.71684

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 input13:10:42 03 Jan 201713:11:50 03 Jan 20171 minute 8 seconds
Read alignment to reference genome13:11:51 03 Jan 201713:22:31 03 Jan 201710 minutes 40 seconds
Preprocessing alignments for candidate junction identification13:22:31 03 Jan 201713:24:35 03 Jan 20172 minutes 4 seconds
Preliminary analysis of coverage distribution13:24:35 03 Jan 201713:27:57 03 Jan 20173 minutes 22 seconds
Identifying junction candidates13:27:57 03 Jan 201713:27:57 03 Jan 20170 seconds
Re-alignment to junction candidates13:27:57 03 Jan 201713:30:05 03 Jan 20172 minutes 8 seconds
Resolving alignments with junction candidates13:30:05 03 Jan 201713:33:39 03 Jan 20173 minutes 34 seconds
Creating BAM files13:33:39 03 Jan 201713:36:01 03 Jan 20172 minutes 22 seconds
Tabulating error counts13:36:01 03 Jan 201713:38:50 03 Jan 20172 minutes 49 seconds
Re-calibrating base error rates13:38:50 03 Jan 201713:38:51 03 Jan 20171 second
Examining read alignment evidence13:38:51 03 Jan 201714:02:05 03 Jan 201723 minutes 14 seconds
Polymorphism statistics14:02:05 03 Jan 201714:02:06 03 Jan 20171 second
Output14:02:06 03 Jan 201714:02:30 03 Jan 201724 seconds
Total 51 minutes 47 seconds