breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-1-163-3-1_S3_L001_R2_0011,129,274339,089,20999.9%300.3 bases301 bases76.9%
errorsSSW-KHP-SSW-1-163-3-1_S3_L001_R1_0011,130,708339,848,050100.0%300.6 bases301 bases79.6%
total2,259,982678,937,25999.9%300.4 bases301 bases78.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652113.52.1100.0%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≤ 1000007913
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 ≤ 500026
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86258

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 input21:32:23 05 Mar 201621:33:36 05 Mar 20161 minute 13 seconds
Read alignment to reference genome21:33:37 05 Mar 201621:39:58 05 Mar 20166 minutes 21 seconds
Preprocessing alignments for candidate junction identification21:39:58 05 Mar 201621:41:05 05 Mar 20161 minute 7 seconds
Preliminary analysis of coverage distribution21:41:05 05 Mar 201621:43:59 05 Mar 20162 minutes 54 seconds
Identifying junction candidates21:43:59 05 Mar 201621:44:01 05 Mar 20162 seconds
Re-alignment to junction candidates21:44:01 05 Mar 201621:44:33 05 Mar 201632 seconds
Resolving alignments with junction candidates21:44:33 05 Mar 201621:47:10 05 Mar 20162 minutes 37 seconds
Creating BAM files21:47:10 05 Mar 201621:48:52 05 Mar 20161 minute 42 seconds
Tabulating error counts21:48:52 05 Mar 201621:51:49 05 Mar 20162 minutes 57 seconds
Re-calibrating base error rates21:51:49 05 Mar 201621:51:50 05 Mar 20161 second
Examining read alignment evidence21:51:50 05 Mar 201622:13:29 05 Mar 201621 minutes 39 seconds
Polymorphism statistics22:13:29 05 Mar 201622:13:29 05 Mar 20160 seconds
Output22:13:29 05 Mar 201622:14:03 05 Mar 201634 seconds
Total 41 minutes 39 seconds