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_A11_F256_I1_R1_S63_L004_R2_0013,479,104346,994,347100.0%99.7 bases100 bases92.1%
errorsqtrim-IND_KHP_HOT_A11_F256_I1_R1_S63_L004_R1_0013,479,160347,795,647100.0%100.0 bases100 bases92.1%
total6,958,264694,789,994100.0%99.9 bases100 bases92.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652136.51.898.1%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 ≤ 50001741
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.078

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.55895

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 input11:25:18 04 Jan 201711:26:29 04 Jan 20171 minute 11 seconds
Read alignment to reference genome11:26:30 04 Jan 201711:32:42 04 Jan 20176 minutes 12 seconds
Preprocessing alignments for candidate junction identification11:32:42 04 Jan 201711:35:24 04 Jan 20172 minutes 42 seconds
Preliminary analysis of coverage distribution11:35:24 04 Jan 201711:38:07 04 Jan 20172 minutes 43 seconds
Identifying junction candidates11:38:07 04 Jan 201712:00:34 04 Jan 201722 minutes 27 seconds
Re-alignment to junction candidates12:00:34 04 Jan 201712:01:29 04 Jan 201755 seconds
Resolving alignments with junction candidates12:01:29 04 Jan 201712:05:34 04 Jan 20174 minutes 5 seconds
Creating BAM files12:05:34 04 Jan 201712:07:24 04 Jan 20171 minute 50 seconds
Tabulating error counts12:07:24 04 Jan 201712:10:16 04 Jan 20172 minutes 52 seconds
Re-calibrating base error rates12:10:16 04 Jan 201712:10:17 04 Jan 20171 second
Examining read alignment evidence12:10:17 04 Jan 201712:31:21 04 Jan 201721 minutes 4 seconds
Polymorphism statistics12:31:21 04 Jan 201712:31:25 04 Jan 20174 seconds
Output12:31:26 04 Jan 201712:33:22 04 Jan 20171 minute 56 seconds
Total 1 hour 8 minutes 2 seconds