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-OCTA5-8_S11_L001_R1_0011,043,177156,756,601100.0%150.3 bases151 bases95.1%
errorsqtrim-OCTA5-8_S11_L001_R2_0011,042,914156,585,581100.0%150.1 bases151 bases93.7%
total2,086,091313,342,182100.0%150.2 bases151 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65263.71.398.3%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≤ 1000003135
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 ≤ 500029
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_0009130.81718

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 input09:53:56 02 Jan 201709:56:10 02 Jan 20172 minutes 14 seconds
Read alignment to reference genome09:56:10 02 Jan 201710:02:28 02 Jan 20176 minutes 18 seconds
Preprocessing alignments for candidate junction identification10:02:28 02 Jan 201710:03:32 02 Jan 20171 minute 4 seconds
Preliminary analysis of coverage distribution10:03:32 02 Jan 201710:05:15 02 Jan 20171 minute 43 seconds
Identifying junction candidates10:05:15 02 Jan 201710:05:15 02 Jan 20170 seconds
Re-alignment to junction candidates10:05:15 02 Jan 201710:06:30 02 Jan 20171 minute 15 seconds
Resolving alignments with junction candidates10:06:30 02 Jan 201710:08:20 02 Jan 20171 minute 50 seconds
Creating BAM files10:08:20 02 Jan 201710:09:40 02 Jan 20171 minute 20 seconds
Tabulating error counts10:09:40 02 Jan 201710:11:12 02 Jan 20171 minute 32 seconds
Re-calibrating base error rates10:11:12 02 Jan 201710:11:13 02 Jan 20171 second
Examining read alignment evidence10:11:13 02 Jan 201710:23:29 02 Jan 201712 minutes 16 seconds
Polymorphism statistics10:23:29 02 Jan 201710:23:29 02 Jan 20170 seconds
Output10:23:29 02 Jan 201710:23:47 02 Jan 201718 seconds
Total 29 minutes 51 seconds