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_A8_F183_I1_R1_S31_L004_R1_0013,357,398335,643,554100.0%100.0 bases100 bases94.9%
errorsqtrim-IND_KHP_HOT_A8_F183_I1_R1_S31_L004_R2_0013,357,379335,218,400100.0%99.8 bases100 bases94.3%
total6,714,777670,861,954100.0%99.9 bases100 bases94.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652136.12.098.1%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≤ 100000100019
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 ≤ 50001799
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.081

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.55883

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Execution Times

stepstartendelapsed
Read and reference sequence file input21:33:48 04 Jan 201721:35:00 04 Jan 20171 minute 12 seconds
Read alignment to reference genome21:35:01 04 Jan 201721:39:34 04 Jan 20174 minutes 33 seconds
Preprocessing alignments for candidate junction identification21:39:34 04 Jan 201721:42:02 04 Jan 20172 minutes 28 seconds
Preliminary analysis of coverage distribution21:42:02 04 Jan 201721:44:43 04 Jan 20172 minutes 41 seconds
Identifying junction candidates21:44:43 04 Jan 201722:03:42 04 Jan 201718 minutes 59 seconds
Re-alignment to junction candidates22:03:42 04 Jan 201722:04:39 04 Jan 201757 seconds
Resolving alignments with junction candidates22:04:39 04 Jan 201722:08:41 04 Jan 20174 minutes 2 seconds
Creating BAM files22:08:41 04 Jan 201722:10:11 04 Jan 20171 minute 30 seconds
Tabulating error counts22:10:11 04 Jan 201722:13:00 04 Jan 20172 minutes 49 seconds
Re-calibrating base error rates22:13:00 04 Jan 201722:13:01 04 Jan 20171 second
Examining read alignment evidence22:13:01 04 Jan 201722:33:21 04 Jan 201720 minutes 20 seconds
Polymorphism statistics22:33:21 04 Jan 201722:33:24 04 Jan 20173 seconds
Output22:33:24 04 Jan 201722:35:05 04 Jan 20171 minute 41 seconds
Total 1 hour 1 minute 16 seconds