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-OCTA6-6_S14_L001_R2_0011,195,797179,657,714100.0%150.2 bases151 bases96.7%
errorsqtrim-OCTA6-6_S14_L001_R1_0011,196,061179,797,676100.0%150.3 bases151 bases97.3%
total2,391,858359,455,390100.0%150.3 bases151 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65275.21.498.3%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≤ 1000002287
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 ≤ 500032
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_0009130.78923

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 input11:45:21 02 Jan 201711:46:11 02 Jan 201750 seconds
Read alignment to reference genome11:46:11 02 Jan 201711:52:55 02 Jan 20176 minutes 44 seconds
Preprocessing alignments for candidate junction identification11:52:55 02 Jan 201711:54:05 02 Jan 20171 minute 10 seconds
Preliminary analysis of coverage distribution11:54:05 02 Jan 201711:56:18 02 Jan 20172 minutes 13 seconds
Identifying junction candidates11:56:18 02 Jan 201711:56:19 02 Jan 20171 second
Re-alignment to junction candidates11:56:19 02 Jan 201711:57:43 02 Jan 20171 minute 24 seconds
Resolving alignments with junction candidates11:57:43 02 Jan 201711:59:51 02 Jan 20172 minutes 8 seconds
Creating BAM files11:59:51 02 Jan 201712:01:27 02 Jan 20171 minute 36 seconds
Tabulating error counts12:01:27 02 Jan 201712:03:15 02 Jan 20171 minute 48 seconds
Re-calibrating base error rates12:03:15 02 Jan 201712:03:16 02 Jan 20171 second
Examining read alignment evidence12:03:16 02 Jan 201712:17:47 02 Jan 201714 minutes 31 seconds
Polymorphism statistics12:17:47 02 Jan 201712:17:48 02 Jan 20171 second
Output12:17:48 02 Jan 201712:18:36 02 Jan 201748 seconds
Total 33 minutes 15 seconds