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_A12_F204_I0_R1_S80_L004_R2_0014,278,471426,329,180100.0%99.6 bases100 bases93.3%
errorsqtrim-IND_KHP_HOT_A12_F204_I0_R1_S80_L004_R1_0014,278,495427,694,703100.0%100.0 bases100 bases95.1%
total8,556,966854,023,883100.0%99.8 bases100 bases94.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652174.32.998.1%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≤ 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 ≤ 50001830
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.082

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.49281

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 input15:59:55 13 Jan 201716:01:27 13 Jan 20171 minute 32 seconds
Read alignment to reference genome16:01:28 13 Jan 201716:06:29 13 Jan 20175 minutes 1 second
Preprocessing alignments for candidate junction identification16:06:29 13 Jan 201716:09:39 13 Jan 20173 minutes 10 seconds
Preliminary analysis of coverage distribution16:09:39 13 Jan 201716:13:06 13 Jan 20173 minutes 27 seconds
Identifying junction candidates16:13:06 13 Jan 201716:30:46 13 Jan 201717 minutes 40 seconds
Re-alignment to junction candidates16:30:46 13 Jan 201716:31:59 13 Jan 20171 minute 13 seconds
Resolving alignments with junction candidates16:31:59 13 Jan 201716:37:07 13 Jan 20175 minutes 8 seconds
Creating BAM files16:37:07 13 Jan 201716:39:10 13 Jan 20172 minutes 3 seconds
Tabulating error counts16:39:10 13 Jan 201716:42:45 13 Jan 20173 minutes 35 seconds
Re-calibrating base error rates16:42:45 13 Jan 201716:42:46 13 Jan 20171 second
Examining read alignment evidence16:42:46 13 Jan 201718:49:37 13 Jan 20172 hours 6 minutes 51 seconds
Polymorphism statistics18:49:37 13 Jan 201718:49:45 13 Jan 20178 seconds
Output18:49:45 13 Jan 201718:52:34 13 Jan 20172 minutes 49 seconds
Total 2 hours 52 minutes 38 seconds