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_A13_F052_I0_R1_S81_L004_R2_0013,820,254380,585,480100.0%99.6 bases100 bases92.0%
errorsqtrim-IND_KHP_HOT_A13_F052_I0_R1_S81_L004_R1_0013,820,279381,883,424100.0%100.0 bases100 bases94.0%
total7,640,533762,468,904100.0%99.8 bases100 bases93.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652152.31.898.1%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≤ 100000100063
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001843
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.083

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52866

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 input08:58:03 11 Jan 201708:59:27 11 Jan 20171 minute 24 seconds
Read alignment to reference genome08:59:28 11 Jan 201709:04:44 11 Jan 20175 minutes 16 seconds
Preprocessing alignments for candidate junction identification09:04:44 11 Jan 201709:07:34 11 Jan 20172 minutes 50 seconds
Preliminary analysis of coverage distribution09:07:34 11 Jan 201709:10:44 11 Jan 20173 minutes 10 seconds
Identifying junction candidates09:10:44 11 Jan 201709:40:57 11 Jan 201730 minutes 13 seconds
Re-alignment to junction candidates09:40:57 11 Jan 201709:42:09 11 Jan 20171 minute 12 seconds
Resolving alignments with junction candidates09:42:09 11 Jan 201709:46:57 11 Jan 20174 minutes 48 seconds
Creating BAM files09:46:57 11 Jan 201709:48:53 11 Jan 20171 minute 56 seconds
Tabulating error counts09:48:53 11 Jan 201709:52:08 11 Jan 20173 minutes 15 seconds
Re-calibrating base error rates09:52:08 11 Jan 201709:52:09 11 Jan 20171 second
Examining read alignment evidence09:52:09 11 Jan 201711:54:46 11 Jan 20172 hours 2 minutes 37 seconds
Polymorphism statistics11:54:46 11 Jan 201711:54:53 11 Jan 20177 seconds
Output11:54:53 11 Jan 201711:57:26 11 Jan 20172 minutes 33 seconds
Total 2 hours 59 minutes 22 seconds