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-ADIP1-9_S2_L001_R1_0011,222,612183,999,831100.0%150.5 bases151 bases99.8%
errorsqtrim-ADIP1-9_S2_L001_R2_0011,222,581183,889,264100.0%150.4 bases151 bases99.2%
total2,445,193367,889,095100.0%150.5 bases151 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65279.01.398.3%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≤ 1000001068
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 ≤ 500030
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_0009130.77982

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 input19:21:17 03 Jan 201719:22:16 03 Jan 201759 seconds
Read alignment to reference genome19:22:16 03 Jan 201719:29:06 03 Jan 20176 minutes 50 seconds
Preprocessing alignments for candidate junction identification19:29:06 03 Jan 201719:30:33 03 Jan 20171 minute 27 seconds
Preliminary analysis of coverage distribution19:30:33 03 Jan 201719:32:56 03 Jan 20172 minutes 23 seconds
Identifying junction candidates19:32:56 03 Jan 201719:32:57 03 Jan 20171 second
Re-alignment to junction candidates19:32:57 03 Jan 201719:34:25 03 Jan 20171 minute 28 seconds
Resolving alignments with junction candidates19:34:25 03 Jan 201719:36:50 03 Jan 20172 minutes 25 seconds
Creating BAM files19:36:50 03 Jan 201719:38:28 03 Jan 20171 minute 38 seconds
Tabulating error counts19:38:28 03 Jan 201719:40:22 03 Jan 20171 minute 54 seconds
Re-calibrating base error rates19:40:22 03 Jan 201719:40:22 03 Jan 20170 seconds
Examining read alignment evidence19:40:22 03 Jan 201719:55:31 03 Jan 201715 minutes 9 seconds
Polymorphism statistics19:55:31 03 Jan 201719:55:31 03 Jan 20170 seconds
Output19:55:31 03 Jan 201719:55:53 03 Jan 201722 seconds
Total 34 minutes 36 seconds