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_A9_F049_I1_R1_S32_L004_R1_0013,887,448388,619,103100.0%100.0 bases100 bases93.6%
errorsqtrim-IND_KHP_HOT_A9_F049_I1_R1_S32_L004_R2_0013,887,412388,001,583100.0%99.8 bases100 bases92.9%
total7,774,860776,620,686100.0%99.9 bases100 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652155.42.098.1%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≤ 100000100008
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 ≤ 5000696
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.032

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52123

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 input12:33:23 04 Jan 201712:34:46 04 Jan 20171 minute 23 seconds
Read alignment to reference genome12:34:47 04 Jan 201712:39:29 04 Jan 20174 minutes 42 seconds
Preprocessing alignments for candidate junction identification12:39:29 04 Jan 201712:42:23 04 Jan 20172 minutes 54 seconds
Preliminary analysis of coverage distribution12:42:23 04 Jan 201712:45:19 04 Jan 20172 minutes 56 seconds
Identifying junction candidates12:45:19 04 Jan 201712:47:12 04 Jan 20171 minute 53 seconds
Re-alignment to junction candidates12:47:12 04 Jan 201712:48:05 04 Jan 201753 seconds
Resolving alignments with junction candidates12:48:05 04 Jan 201712:52:38 04 Jan 20174 minutes 33 seconds
Creating BAM files12:52:38 04 Jan 201712:54:23 04 Jan 20171 minute 45 seconds
Tabulating error counts12:54:23 04 Jan 201712:57:40 04 Jan 20173 minutes 17 seconds
Re-calibrating base error rates12:57:40 04 Jan 201712:57:41 04 Jan 20171 second
Examining read alignment evidence12:57:41 04 Jan 201713:21:04 04 Jan 201723 minutes 23 seconds
Polymorphism statistics13:21:04 04 Jan 201713:21:08 04 Jan 20174 seconds
Output13:21:08 04 Jan 201713:21:52 04 Jan 201744 seconds
Total 48 minutes 28 seconds