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_A12_F056_I0_R1_S56_L004_R1_0014,138,131413,654,543100.0%100.0 bases100 bases94.8%
errorsqtrim-IND_KHP_HOT_A12_F056_I0_R1_S56_L004_R2_0014,138,104412,099,164100.0%99.6 bases100 bases92.5%
total8,276,235825,753,707100.0%99.8 bases100 bases93.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652170.310.798.1%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≤ 100000100019
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 ≤ 50002140
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.096

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.50805

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 input18:58:48 11 Jan 201719:00:34 11 Jan 20171 minute 46 seconds
Read alignment to reference genome19:00:35 11 Jan 201719:05:36 11 Jan 20175 minutes 1 second
Preprocessing alignments for candidate junction identification19:05:36 11 Jan 201719:08:35 11 Jan 20172 minutes 59 seconds
Preliminary analysis of coverage distribution19:08:35 11 Jan 201719:11:57 11 Jan 20173 minutes 22 seconds
Identifying junction candidates19:11:57 11 Jan 201719:36:45 11 Jan 201724 minutes 48 seconds
Re-alignment to junction candidates19:36:45 11 Jan 201719:38:10 11 Jan 20171 minute 25 seconds
Resolving alignments with junction candidates19:38:10 11 Jan 201719:43:14 11 Jan 20175 minutes 4 seconds
Creating BAM files19:43:14 11 Jan 201719:45:20 11 Jan 20172 minutes 6 seconds
Tabulating error counts19:45:20 11 Jan 201719:48:52 11 Jan 20173 minutes 32 seconds
Re-calibrating base error rates19:48:52 11 Jan 201719:48:53 11 Jan 20171 second
Examining read alignment evidence19:48:53 11 Jan 201722:00:08 11 Jan 20172 hours 11 minutes 15 seconds
Polymorphism statistics22:00:08 11 Jan 201722:00:16 11 Jan 20178 seconds
Output22:00:16 11 Jan 201722:03:34 11 Jan 20173 minutes 18 seconds
Total 3 hours 4 minutes 45 seconds