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_A7_F113_I0_R1_S35_L004_R1_0013,111,400311,032,705100.0%100.0 bases100 bases92.6%
errorsqtrim-IND_KHP_HOT_A7_F113_I0_R1_S35_L004_R2_0013,111,371310,218,110100.0%99.7 bases100 bases91.1%
total6,222,771621,250,815100.0%99.8 bases100 bases91.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652122.51.898.2%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≤ 100000100000
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 ≤ 50002097
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.094

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.59457

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 input18:28:42 10 Jan 201718:30:23 10 Jan 20171 minute 41 seconds
Read alignment to reference genome18:30:24 10 Jan 201718:34:45 10 Jan 20174 minutes 21 seconds
Preprocessing alignments for candidate junction identification18:34:45 10 Jan 201718:37:01 10 Jan 20172 minutes 16 seconds
Preliminary analysis of coverage distribution18:37:01 10 Jan 201718:39:38 10 Jan 20172 minutes 37 seconds
Identifying junction candidates18:39:38 10 Jan 201719:08:58 10 Jan 201729 minutes 20 seconds
Re-alignment to junction candidates19:08:58 10 Jan 201719:10:02 10 Jan 20171 minute 4 seconds
Resolving alignments with junction candidates19:10:02 10 Jan 201719:13:48 10 Jan 20173 minutes 46 seconds
Creating BAM files19:13:48 10 Jan 201719:15:20 10 Jan 20171 minute 32 seconds
Tabulating error counts19:15:20 10 Jan 201719:17:59 10 Jan 20172 minutes 39 seconds
Re-calibrating base error rates19:17:59 10 Jan 201719:18:00 10 Jan 20171 second
Examining read alignment evidence19:18:00 10 Jan 201720:38:45 10 Jan 20171 hour 20 minutes 45 seconds
Polymorphism statistics20:38:45 10 Jan 201720:38:49 10 Jan 20174 seconds
Output20:38:49 10 Jan 201720:41:09 10 Jan 20172 minutes 20 seconds
Total 2 hours 12 minutes 26 seconds