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-12PD3-10_S8_L001_R2_001479,14071,650,009100.0%149.5 bases151 bases93.0%
errorsqtrim-12PD3-10_S6_L001_R2_0011,685,720252,328,790100.0%149.7 bases151 bases82.8%
errorsqtrim-12PD3-10_S8_L001_R1_001479,16071,718,810100.0%149.7 bases151 bases94.0%
errorsqtrim-12PD3-10_S6_L001_R1_0011,687,756252,958,619100.0%149.9 bases151 bases83.4%
total4,331,776648,656,228100.0%149.7 bases151 bases85.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652117.21.498.2%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≤ 1000001107
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500018
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.69220

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 input15:24:48 02 Jan 201715:26:08 02 Jan 20171 minute 20 seconds
Read alignment to reference genome15:26:09 02 Jan 201715:37:48 02 Jan 201711 minutes 39 seconds
Preprocessing alignments for candidate junction identification15:37:48 02 Jan 201715:39:48 02 Jan 20172 minutes 0 seconds
Preliminary analysis of coverage distribution15:39:48 02 Jan 201715:43:20 02 Jan 20173 minutes 32 seconds
Identifying junction candidates15:43:20 02 Jan 201715:43:21 02 Jan 20171 second
Re-alignment to junction candidates15:43:21 02 Jan 201715:45:49 02 Jan 20172 minutes 28 seconds
Resolving alignments with junction candidates15:45:49 02 Jan 201715:49:35 02 Jan 20173 minutes 46 seconds
Creating BAM files15:49:35 02 Jan 201715:52:08 02 Jan 20172 minutes 33 seconds
Tabulating error counts15:52:08 02 Jan 201715:55:13 02 Jan 20173 minutes 5 seconds
Re-calibrating base error rates15:55:13 02 Jan 201715:55:15 02 Jan 20172 seconds
Examining read alignment evidence15:55:15 02 Jan 201716:17:17 02 Jan 201722 minutes 2 seconds
Polymorphism statistics16:17:17 02 Jan 201716:17:18 02 Jan 20171 second
Output16:17:18 02 Jan 201716:18:16 02 Jan 201758 seconds
Total 53 minutes 27 seconds