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-COUM4-2_S8_L001_R2_0011,145,147171,688,813100.0%149.9 bases151 bases93.6%
errorsqtrim-COUM4-2_S8_L001_R1_0011,145,690172,312,904100.0%150.4 bases151 bases98.3%
total2,290,837344,001,717100.0%150.2 bases151 bases95.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65270.52.998.2%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≤ 100000682
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 ≤ 500022
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_0009130.80120

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 input15:53:04 03 Jan 201715:53:51 03 Jan 201747 seconds
Read alignment to reference genome15:53:52 03 Jan 201716:01:24 03 Jan 20177 minutes 32 seconds
Preprocessing alignments for candidate junction identification16:01:24 03 Jan 201716:02:43 03 Jan 20171 minute 19 seconds
Preliminary analysis of coverage distribution16:02:43 03 Jan 201716:04:50 03 Jan 20172 minutes 7 seconds
Identifying junction candidates16:04:50 03 Jan 201716:04:50 03 Jan 20170 seconds
Re-alignment to junction candidates16:04:50 03 Jan 201716:06:26 03 Jan 20171 minute 36 seconds
Resolving alignments with junction candidates16:06:26 03 Jan 201716:08:30 03 Jan 20172 minutes 4 seconds
Creating BAM files16:08:30 03 Jan 201716:10:08 03 Jan 20171 minute 38 seconds
Tabulating error counts16:10:08 03 Jan 201716:12:08 03 Jan 20172 minutes 0 seconds
Re-calibrating base error rates16:12:08 03 Jan 201716:12:09 03 Jan 20171 second
Examining read alignment evidence16:12:09 03 Jan 201716:28:17 03 Jan 201716 minutes 8 seconds
Polymorphism statistics16:28:17 03 Jan 201716:28:18 03 Jan 20171 second
Output16:28:18 03 Jan 201716:28:40 03 Jan 201722 seconds
Total 35 minutes 35 seconds