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_A11_F056_I0_R1_S53_L004_R2_0013,392,746338,161,043100.0%99.7 bases100 bases94.7%
errorsqtrim-IND_KHP_HOT_A11_F056_I0_R1_S53_L004_R1_0013,392,775339,154,792100.0%100.0 bases100 bases95.9%
total6,785,521677,315,835100.0%99.8 bases100 bases95.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652141.23.998.1%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≤ 100000100041
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 ≤ 5000757
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.034

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.55593

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 input22:03:35 11 Jan 201722:04:51 11 Jan 20171 minute 16 seconds
Read alignment to reference genome22:04:52 11 Jan 201722:09:39 11 Jan 20174 minutes 47 seconds
Preprocessing alignments for candidate junction identification22:09:39 11 Jan 201722:12:09 11 Jan 20172 minutes 30 seconds
Preliminary analysis of coverage distribution22:12:09 11 Jan 201722:15:02 11 Jan 20172 minutes 53 seconds
Identifying junction candidates22:15:02 11 Jan 201722:17:02 11 Jan 20172 minutes 0 seconds
Re-alignment to junction candidates22:17:02 11 Jan 201722:17:55 11 Jan 201753 seconds
Resolving alignments with junction candidates22:17:55 11 Jan 201722:22:05 11 Jan 20174 minutes 10 seconds
Creating BAM files22:22:05 11 Jan 201722:23:49 11 Jan 20171 minute 44 seconds
Tabulating error counts22:23:49 11 Jan 201722:27:16 11 Jan 20173 minutes 27 seconds
Re-calibrating base error rates22:27:16 11 Jan 201722:27:18 11 Jan 20172 seconds
Examining read alignment evidence22:27:18 11 Jan 201723:59:14 11 Jan 20171 hour 31 minutes 56 seconds
Polymorphism statistics23:59:14 11 Jan 201723:59:20 11 Jan 20176 seconds
Output23:59:20 11 Jan 201700:00:58 12 Jan 20171 minute 38 seconds
Total 1 hour 57 minutes 22 seconds