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_A4_F191_I0_R1_S24_L004_R2_0013,462,062345,540,502100.0%99.8 bases100 bases96.5%
errorsqtrim-IND_KHP_HOT_A4_F191_I0_R1_S24_L004_R1_0013,462,091346,105,856100.0%100.0 bases100 bases97.2%
total6,924,153691,646,358100.0%99.9 bases100 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652142.73.398.0%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≤ 100000100007
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 ≤ 5000672
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.030

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.54420

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 input01:51:44 13 Jan 201701:53:01 13 Jan 20171 minute 17 seconds
Read alignment to reference genome01:53:02 13 Jan 201701:56:56 13 Jan 20173 minutes 54 seconds
Preprocessing alignments for candidate junction identification01:56:56 13 Jan 201701:59:29 13 Jan 20172 minutes 33 seconds
Preliminary analysis of coverage distribution01:59:29 13 Jan 201702:02:18 13 Jan 20172 minutes 49 seconds
Identifying junction candidates02:02:18 13 Jan 201702:04:01 13 Jan 20171 minute 43 seconds
Re-alignment to junction candidates02:04:01 13 Jan 201702:04:50 13 Jan 201749 seconds
Resolving alignments with junction candidates02:04:50 13 Jan 201702:08:59 13 Jan 20174 minutes 9 seconds
Creating BAM files02:08:59 13 Jan 201702:10:36 13 Jan 20171 minute 37 seconds
Tabulating error counts02:10:36 13 Jan 201702:13:39 13 Jan 20173 minutes 3 seconds
Re-calibrating base error rates02:13:39 13 Jan 201702:13:40 13 Jan 20171 second
Examining read alignment evidence02:13:40 13 Jan 201703:24:59 13 Jan 20171 hour 11 minutes 19 seconds
Polymorphism statistics03:24:59 13 Jan 201703:25:02 13 Jan 20173 seconds
Output03:25:02 13 Jan 201703:26:19 13 Jan 20171 minute 17 seconds
Total 1 hour 34 minutes 34 seconds