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-IND_KHP_HOT_A4_F244_I0_R1_S74_L004_R2_0012,920,057290,856,761100.0%99.6 bases100 bases92.4%
errorsqtrim-IND_KHP_HOT_A4_F244_I0_R1_S74_L004_R1_0012,920,076291,901,919100.0%100.0 bases100 bases94.3%
total5,840,133582,758,680100.0%99.8 bases100 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652114.41.998.1%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≤ 100000100048
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000772
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.035

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.60700

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input11:08:19 13 Jan 201711:09:20 13 Jan 20171 minute 1 second
Read alignment to reference genome11:09:21 13 Jan 201711:12:56 13 Jan 20173 minutes 35 seconds
Preprocessing alignments for candidate junction identification11:12:56 13 Jan 201711:15:01 13 Jan 20172 minutes 5 seconds
Preliminary analysis of coverage distribution11:15:01 13 Jan 201711:17:21 13 Jan 20172 minutes 20 seconds
Identifying junction candidates11:17:21 13 Jan 201711:21:24 13 Jan 20174 minutes 3 seconds
Re-alignment to junction candidates11:21:24 13 Jan 201711:22:06 13 Jan 201742 seconds
Resolving alignments with junction candidates11:22:06 13 Jan 201711:25:32 13 Jan 20173 minutes 26 seconds
Creating BAM files11:25:32 13 Jan 201711:26:57 13 Jan 20171 minute 25 seconds
Tabulating error counts11:26:57 13 Jan 201711:29:26 13 Jan 20172 minutes 29 seconds
Re-calibrating base error rates11:29:26 13 Jan 201711:29:26 13 Jan 20170 seconds
Examining read alignment evidence11:29:26 13 Jan 201712:44:16 13 Jan 20171 hour 14 minutes 50 seconds
Polymorphism statistics12:44:16 13 Jan 201712:44:22 13 Jan 20176 seconds
Output12:44:22 13 Jan 201712:46:11 13 Jan 20171 minute 49 seconds
Total 1 hour 37 minutes 51 seconds