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-PUTR5-8_S11_L001_R1_0011,466,907220,658,064100.0%150.4 bases151 bases99.8%
errorsqtrim-PUTR5-8_S11_L001_R2_0011,466,863220,551,518100.0%150.4 bases151 bases99.2%
total2,933,770441,209,582100.0%150.4 bases151 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65294.61.498.3%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≤ 100000617
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 ≤ 500025
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_0009130.74396

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 input16:59:05 03 Jan 201717:00:16 03 Jan 20171 minute 11 seconds
Read alignment to reference genome17:00:17 03 Jan 201717:09:39 03 Jan 20179 minutes 22 seconds
Preprocessing alignments for candidate junction identification17:09:39 03 Jan 201717:11:28 03 Jan 20171 minute 49 seconds
Preliminary analysis of coverage distribution17:11:28 03 Jan 201717:14:32 03 Jan 20173 minutes 4 seconds
Identifying junction candidates17:14:32 03 Jan 201717:14:33 03 Jan 20171 second
Re-alignment to junction candidates17:14:33 03 Jan 201717:16:33 03 Jan 20172 minutes 0 seconds
Resolving alignments with junction candidates17:16:33 03 Jan 201717:19:37 03 Jan 20173 minutes 4 seconds
Creating BAM files17:19:37 03 Jan 201717:21:44 03 Jan 20172 minutes 7 seconds
Tabulating error counts17:21:44 03 Jan 201717:24:38 03 Jan 20172 minutes 54 seconds
Re-calibrating base error rates17:24:38 03 Jan 201717:24:38 03 Jan 20170 seconds
Examining read alignment evidence17:24:38 03 Jan 201717:44:56 03 Jan 201720 minutes 18 seconds
Polymorphism statistics17:44:56 03 Jan 201717:44:58 03 Jan 20172 seconds
Output17:44:58 03 Jan 201717:45:19 03 Jan 201721 seconds
Total 46 minutes 13 seconds