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_A4_F244_I1_R1_S59_L004_R1_0013,036,563303,559,811100.0%100.0 bases100 bases93.5%
errorsqtrim-IND_KHP_HOT_A4_F244_I1_R1_S59_L004_R2_0013,036,536303,052,955100.0%99.8 bases100 bases93.6%
total6,073,099606,612,766100.0%99.9 bases100 bases93.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652120.61.998.1%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 ≤ 50001128
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.050

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.59105

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 input14:44:14 04 Jan 201714:45:20 04 Jan 20171 minute 6 seconds
Read alignment to reference genome14:45:21 04 Jan 201714:48:57 04 Jan 20173 minutes 36 seconds
Preprocessing alignments for candidate junction identification14:48:57 04 Jan 201714:51:12 04 Jan 20172 minutes 15 seconds
Preliminary analysis of coverage distribution14:51:12 04 Jan 201714:53:32 04 Jan 20172 minutes 20 seconds
Identifying junction candidates14:53:32 04 Jan 201715:00:06 04 Jan 20176 minutes 34 seconds
Re-alignment to junction candidates15:00:06 04 Jan 201715:00:51 04 Jan 201745 seconds
Resolving alignments with junction candidates15:00:51 04 Jan 201715:04:22 04 Jan 20173 minutes 31 seconds
Creating BAM files15:04:22 04 Jan 201715:05:44 04 Jan 20171 minute 22 seconds
Tabulating error counts15:05:44 04 Jan 201715:08:15 04 Jan 20172 minutes 31 seconds
Re-calibrating base error rates15:08:15 04 Jan 201715:08:16 04 Jan 20171 second
Examining read alignment evidence15:08:16 04 Jan 201715:26:40 04 Jan 201718 minutes 24 seconds
Polymorphism statistics15:26:40 04 Jan 201715:26:43 04 Jan 20173 seconds
Output15:26:43 04 Jan 201715:28:00 04 Jan 20171 minute 17 seconds
Total 43 minutes 45 seconds