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_I1_R1_S66_L004_R1_0012,341,126234,054,225100.0%100.0 bases100 bases93.4%
errorsqtrim-IND_KHP_HOT_A12_F204_I1_R1_S66_L004_R2_0012,341,117233,871,242100.0%99.9 bases100 bases93.3%
total4,682,243467,925,467100.0%99.9 bases100 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65293.22.197.9%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≤ 100000100061
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 ≤ 50001380
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.062

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.66774

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 input12:05:30 05 Jan 201712:06:19 05 Jan 201749 seconds
Read alignment to reference genome12:06:19 05 Jan 201712:09:04 05 Jan 20172 minutes 45 seconds
Preprocessing alignments for candidate junction identification12:09:04 05 Jan 201712:10:47 05 Jan 20171 minute 43 seconds
Preliminary analysis of coverage distribution12:10:47 05 Jan 201712:12:31 05 Jan 20171 minute 44 seconds
Identifying junction candidates12:12:31 05 Jan 201712:27:30 05 Jan 201714 minutes 59 seconds
Re-alignment to junction candidates12:27:30 05 Jan 201712:28:06 05 Jan 201736 seconds
Resolving alignments with junction candidates12:28:06 05 Jan 201712:30:57 05 Jan 20172 minutes 51 seconds
Creating BAM files12:30:57 05 Jan 201712:31:57 05 Jan 20171 minute 0 seconds
Tabulating error counts12:31:57 05 Jan 201712:34:09 05 Jan 20172 minutes 12 seconds
Re-calibrating base error rates12:34:09 05 Jan 201712:34:09 05 Jan 20170 seconds
Examining read alignment evidence12:34:09 05 Jan 201712:48:28 05 Jan 201714 minutes 19 seconds
Polymorphism statistics12:48:28 05 Jan 201712:48:28 05 Jan 20170 seconds
Output12:48:28 05 Jan 201712:49:35 05 Jan 20171 minute 7 seconds
Total 44 minutes 5 seconds