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Landmark or Region: Examples: 2L, 2R, 3L, 3R, X, net*.	(DGRP) Download Polymorphic sequences Annotate Restriction Sites Download Decorated FASTA File Download Sequence File Download Track Data
Data Source Drosophila Buzzatii Genome Project Population Display Demo Renderfarm demo (gbrowse_slave must be running!) Tutorial database Yeast chromosomes 1+2 (advanced) Yeast chromosomes 1+2 (basic) popDrowser - Drosophila Genome Variation Browser (DGRP Freeze1 dataset)	Scroll/Zoom:     Show 23.01 Mbp Show 5 Mbp Show 1 Mbp Show 200 kbp Show 100 kbp Show 50 kbp Show 20 kbp Show 10 kbp Show 5 kbp Show 2 kbp Show 1 kbp Show 200 bp Show 100 bp     Flip

 Overview

 Overview

 

 Region

 Region

 

 Details

 Details

 

  Recombination Rate (cM/Mb) [50kb window]  

  N's [100kb window]  

  Gene density [100kb window]  

  Transposon density [100kb window]  

  Pi [100kb window]  

  Divergence (dmel-dsim)[100kb window]  

  r2 (Zns)[100kb window]  

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 Tracks

 Tracks

 

 0.General 

 0.General 

 Reference annotations

 Reference annotations

 All on All off 

6-frame translation [?]	Insertion sites [?]	Transposons [?]
CDS [?]	mRNA [?]	tRNAs [?]
Chromosome Bands [?]	Noncoding RNAs [?]	UCSC-phastConsElements15way [?]
DNA_GC [?]	Orthologous [?]
Genes [?]	Pseudogenes [?]

 1.Recombination 

 1.Recombination 

 Recombination rate

 Recombination rate

 All on All off 

Recombination Rate (cM/Mb) [50kb window] [?]

 2.Density tracks 

 2.Density tracks 

 Gene density

 Gene density

 All on All off 

Gene density [100kb window] [?]

Gene density [10kb window] [?]

Gene density [50kb window] [?]

 Microsatellite density

 Microsatellite density

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Microsatellite density [100kb window] [?]

Microsatellite density [10kb window] [?]

Microsatellite density [50kb window] [?]

 Number of ambiguous bases

 Number of ambiguous bases

 All on All off 

N's [100bp window] [?]	N's [1kb window] [?]	N's [50kb window] [?]
N's [100kb window] [?]	N's [500bp window] [?]
N's [10kb window] [?]	N's [50bp window] [?]

 SNPs density [PDA]

 SNPs density [PDA]

 All on All off 

SNPs density [100kb window] [?]

 Transposon density

 Transposon density

 All on All off 

Transposon density [100kb window] [?]

Transposon density [10kb window] [?]

Transposon density [50kb window] [?]

 3.Nucleotide Variants

 3.Nucleotide Variants

 All on All off 

SNFs (Using PDA software) [?]

SNPs (Using PDA software) [?]

 4.Structural Variants

 4.Structural Variants

 All on All off 

Tlex2

 5.Summary Measures of nucleotide diversity 

 5.Summary Measures of nucleotide diversity 

 4fold Ps

 4fold Ps

 All on All off 

Ps of 4-fold positions per window [100kb window] [?]

Ps of 4-fold positions per window [10kb window] [?]

Ps of 4-fold positions per window [50kb window] [?]

 Divergence (dmel-dsim)

 Divergence (dmel-dsim)

 All on All off 

Divergence (dmel-dsim)[100bp window] [?]	Divergence (dmel-dsim)[1kb window] [?]	Divergence (dmel-dsim)[50kb window] [?]
Divergence (dmel-dsim)[100kb window] [?]	Divergence (dmel-dsim)[500bp window] [?]
Divergence (dmel-dsim)[10kb window] [?]	Divergence (dmel-dsim)[50bp window] [?]

 Divergence (dmel-dyak)

 Divergence (dmel-dyak)

 All on All off 

Divergence (dmel-dyak)[100bp window] [?]	Divergence (dmel-dyak)[1kb window] [?]	Divergence (dmel-dyak)[50kb window] [?]
Divergence (dmel-dyak)[100kb window] [?]	Divergence (dmel-dyak)[500bp window] [?]
Divergence (dmel-dyak)[10kb window] [?]	Divergence (dmel-dyak)[50bp window] [?]

 Eta

 Eta

 All on All off 

Eta [100bp window] [?]	Eta [1kb window] [?]	Eta [50kb window] [?]
Eta [100kb window] [?]	Eta [500bp window] [?]
Eta [10kb window] [?]	Eta [50bp window] [?]

 EtaE

 EtaE

 All on All off 

EtaE [100bp window] [?]	EtaE [1kb window] [?]	EtaE [50kb window] [?]
EtaE [100kb window] [?]	EtaE [500bp window] [?]
EtaE [10kb window] [?]	EtaE [50bp window] [?]

 Pi

 Pi

 All on All off 

Pi [100bp window] [?]	Pi [1kb window] [?]	Pi [50kb window] [?]
Pi [100kb window] [?]	Pi [500bp window] [?]
Pi [10kb window] [?]	Pi [50bp window] [?]

 S

 S

 All on All off 

S [100bp window] [?]	S [1kb window] [?]	S [50kb window] [?]
S [100kb window] [?]	S [500bp window] [?]
S [10kb window] [?]	S [50bp window] [?]

 Theta

 Theta

 All on All off 

Theta [100bp window] [?]	Theta [1kb window] [?]	Theta [50kb window] [?]
Theta [100kb window] [?]	Theta [500bp window] [?]
Theta [10kb window] [?]	Theta [50bp window] [?]

 6.Linkage Disequilibrium 

 6.Linkage Disequilibrium 

 R2

 R2

 All on All off 

r2 (Zns)[100bp window]	r2 (Zns)[1kb window] [?]	r2 (Zns)[50kb window] [?]
r2 (Zns)[100kb window] [?]	r2 (Zns)[500bp window]
r2 (Zns)[10kb window] [?]	r2 (Zns)[50bp window]

 7.Neutrality Tests 

 7.Neutrality Tests 

 McDonald-Kreitman Test for coding genes

 McDonald-Kreitman Test for coding genes

 All on All off 

MKT for coding genes dmel-dsim [?]

MKT for coding genes dmel-dsim (5% MAF discarded) [?]

 Analysis

 Analysis

 All on All off 

Restriction Sites

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

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Genomics, Bioinformatics and Evolution Group. Institut de Biologia i Biomedicina - IBB / Dept. of Genetics and Microbiology, Universitat Autonoma de Barcelona (UAB) [Contact us]
Molecular Evolutionary Genetics Group, Universitat de Barcelona (UB) [Contact us]

CITE US:
Ràmia M, Librado P, Casillas S, Rozas J, Barbadilla A.
PopDrowser: the Population Drosophila Browser.
Bioinformatics. 2012 Feb 15;28(4):595-6. Epub 2011 Dec 15.[Link]

Based on Generic Genome Browser version 2.x