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_A7_F113_I1_R1_S28_L004_R1_0013,872,549387,137,468100.0%100.0 bases100 bases93.9%
errorsqtrim-IND_KHP_HOT_A7_F113_I1_R1_S28_L004_R2_0013,872,532386,666,683100.0%99.8 bases100 bases93.0%
total7,745,081773,804,151100.0%99.9 bases100 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652155.01.998.0%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≤ 10000053950
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 ≤ 5000546
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.024

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52294

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 input09:35:14 05 Jan 201709:36:37 05 Jan 20171 minute 23 seconds
Read alignment to reference genome09:36:38 05 Jan 201709:41:05 05 Jan 20174 minutes 27 seconds
Preprocessing alignments for candidate junction identification09:41:05 05 Jan 201709:43:44 05 Jan 20172 minutes 39 seconds
Preliminary analysis of coverage distribution09:43:44 05 Jan 201709:46:42 05 Jan 20172 minutes 58 seconds
Identifying junction candidates09:46:42 05 Jan 201709:48:03 05 Jan 20171 minute 21 seconds
Re-alignment to junction candidates09:48:03 05 Jan 201709:48:52 05 Jan 201749 seconds
Resolving alignments with junction candidates09:48:52 05 Jan 201709:53:20 05 Jan 20174 minutes 28 seconds
Creating BAM files09:53:20 05 Jan 201709:55:03 05 Jan 20171 minute 43 seconds
Tabulating error counts09:55:03 05 Jan 201709:58:20 05 Jan 20173 minutes 17 seconds
Re-calibrating base error rates09:58:20 05 Jan 201709:58:20 05 Jan 20170 seconds
Examining read alignment evidence09:58:20 05 Jan 201710:21:34 05 Jan 201723 minutes 14 seconds
Polymorphism statistics10:21:34 05 Jan 201710:21:34 05 Jan 20170 seconds
Output10:21:34 05 Jan 201710:22:09 05 Jan 201735 seconds
Total 46 minutes 54 seconds