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_A16_F048_I0_R1_S84_L004_R1_0014,198,820419,727,947100.0%100.0 bases100 bases94.1%
errorsqtrim-IND_KHP_HOT_A16_F048_I0_R1_S84_L004_R2_0014,198,791418,332,860100.0%99.6 bases100 bases92.2%
total8,397,611838,060,807100.0%99.8 bases100 bases93.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652171.14.398.0%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≤ 100000100002
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 ≤ 5000517
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.023

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.50170

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 input19:49:06 13 Jan 201719:50:37 13 Jan 20171 minute 31 seconds
Read alignment to reference genome19:50:37 13 Jan 201719:55:53 13 Jan 20175 minutes 16 seconds
Preprocessing alignments for candidate junction identification19:55:53 13 Jan 201719:59:03 13 Jan 20173 minutes 10 seconds
Preliminary analysis of coverage distribution19:59:03 13 Jan 201720:02:28 13 Jan 20173 minutes 25 seconds
Identifying junction candidates20:02:28 13 Jan 201720:04:24 13 Jan 20171 minute 56 seconds
Re-alignment to junction candidates20:04:24 13 Jan 201720:05:18 13 Jan 201754 seconds
Resolving alignments with junction candidates20:05:18 13 Jan 201720:10:24 13 Jan 20175 minutes 6 seconds
Creating BAM files20:10:24 13 Jan 201720:12:24 13 Jan 20172 minutes 0 seconds
Tabulating error counts20:12:24 13 Jan 201720:15:57 13 Jan 20173 minutes 33 seconds
Re-calibrating base error rates20:15:57 13 Jan 201720:15:58 13 Jan 20171 second
Examining read alignment evidence20:15:58 13 Jan 201722:17:47 13 Jan 20172 hours 1 minute 49 seconds
Polymorphism statistics22:17:47 13 Jan 201722:17:55 13 Jan 20178 seconds
Output22:17:55 13 Jan 201722:19:49 13 Jan 20171 minute 54 seconds
Total 2 hours 30 minutes 43 seconds