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_A3_F181_I0_R1_S21_L004_R2_0013,063,068305,647,699100.0%99.8 bases100 bases96.3%
errorsqtrim-IND_KHP_HOT_A3_F181_I0_R1_S21_L004_R1_0013,063,087306,209,434100.0%100.0 bases100 bases96.8%
total6,126,155611,857,133100.0%99.9 bases100 bases96.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652126.13.598.1%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≤ 100000100111
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 ≤ 50002191
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.098

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.58073

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 input12:29:56 14 Jan 201712:30:59 14 Jan 20171 minute 3 seconds
Read alignment to reference genome12:30:59 14 Jan 201712:33:55 14 Jan 20172 minutes 56 seconds
Preprocessing alignments for candidate junction identification12:33:55 14 Jan 201712:36:06 14 Jan 20172 minutes 11 seconds
Preliminary analysis of coverage distribution12:36:06 14 Jan 201712:38:31 14 Jan 20172 minutes 25 seconds
Identifying junction candidates12:38:31 14 Jan 201713:10:07 14 Jan 201731 minutes 36 seconds
Re-alignment to junction candidates13:10:07 14 Jan 201713:10:52 14 Jan 201745 seconds
Resolving alignments with junction candidates13:10:52 14 Jan 201713:14:34 14 Jan 20173 minutes 42 seconds
Creating BAM files13:14:34 14 Jan 201713:15:59 14 Jan 20171 minute 25 seconds
Tabulating error counts13:15:59 14 Jan 201713:18:37 14 Jan 20172 minutes 38 seconds
Re-calibrating base error rates13:18:37 14 Jan 201713:18:37 14 Jan 20170 seconds
Examining read alignment evidence13:18:37 14 Jan 201714:21:29 14 Jan 20171 hour 2 minutes 52 seconds
Polymorphism statistics14:21:29 14 Jan 201714:21:33 14 Jan 20174 seconds
Output14:21:33 14 Jan 201714:23:56 14 Jan 20172 minutes 23 seconds
Total 1 hour 54 minutes 0 seconds