This track shows the reading frame of coding sequences in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows mRNA annotations in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows tRNA annotations in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows the G+C content when large windows are visualized, or the DNA sequence when zoomed in.
This track shows noncoding RNA annotations in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows the last version of the phastCons conservation track (Siepel et al. 20052) from the UCSC.
This track shows gene annotations in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows 6-frame protein translations in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
This track shows insertion sites of transposable elements in the Drosophila melanogaster reference genome (Smith et al. 2007 Science1) from Flybase.
This track shows insertion sites of transposable elements in the Drosophila melanogaster reference genome (Smith et al. 20071) from Flybase.
Using the estimations of Fiston-Lavier et al 201018
Coding nucleotides per window.
Number of genes in per window . Only "end" coordinate considered.
Number of microsatellites per window.
Sum of ambiguous nucleotides (N) per sliding window in all the 158 DGRP lines.
Number of SNPs in the population obtained with PDA (Casillas et al. 2006) per window.
Number of transposon per window (Only "end" coordinate considered).
Single Nucleotide Fixed differences: shows nucleotide positions in which all the Drosophila melanogaster strains have the same nucleotide and which is different from that in D. simulans.
Single Nucleotide Polymorphisms: shows nucleotide positions in which different strains of Drosophila melanogaster have different nucleotides. When the mouse is located over a SNP, more information is displayed including: the count and frequency of the different alleles, the ancestral allele (that which is shared with D. simulans, in case the D. simulans allele matches one of the D. melanogaster alleles), the derived allele frequency (the sum frequency of all D. melanogaster alleles other than the ancestral allele, when the ancestral allele can be inferred), the number of missing data for this position (the number of strains containing a gap or "N"), and an indication whether the polymorphism is a singleton or not (singleton means that only one D. melanogaster strain contains a nucleotide which is different from the others).
Divergence per site (Jukes-Cantor corrected) (Jukes and Cantor 19693) is the average number of nucleotide substitutions per site between Drosophila melanogaster and D. simulans with Jukes and Cantor correction. The correction is performed using the simplification indicated in Nei and Miller 1990, that is, the correction is performed directly on the uncorrected value and not in each pairwise comparison of two sequences.
Total (minimum) number of mutations (η) (Tajima 19964).
Number of singletons (Tajima 19964).
Derived Allele Frequency: a distribution of the frequency of derived alleles has been performed for all SNPs in the window excluding singletons (see SNPs). This track shows the frequency of the first class of the distribution (SNPs with a derived allele frequency < 10%).
Minor Allele Frequency (excluding singletons): a distribution of the frequency of the rarest allele has been performed for all SNPs in the window excluding singletons (see SNPs). This track shows the frequency of the first class of the distribution (SNPs with a minor allele frequency < 10%).
Nucleotide diversity (π) (Nei 19875) is the average number of nucleotide differences per site between two sequences.
Number of segregating (polymorphic) sites (Nei 19875).
Watterson's estimator of nucleotide diversity per site θw (based on Eta) (Tajima 19964).
D value averaged over all comparisons in the window (Lewontin and Kojima 19606).
D' value averaged over all comparisons in the window (Lewontin 19647).
Fu's Fs statistic (Fu 1997).
Number of haplotypes (Nei 19875).
Haplotype (gene) diversity (Nei 19875).
r2 value averaged over all comparisons in the window (i.e. ZnS statistic) (Hill and Robertson 19688; Kelly 19979).
Absolute D' value averaged over all comparisons in the window (Lewontin 19647).
Absolute D value averaged over all comparisons in the window (Lewontin and Kojima 19606).
The Fay & Wu's H test statistic (Fay and Wu 200010) is based on the differences between two estimators of θ: θk (or k), the average number of nucleotide differences between pairs of sequences, and θH, an estimator based on the frequency of the derived variants.
The Fu & Li's D test statistic (Fu and Li 199311) is based on the differences between ηe, the total number of mutations in external branches of the genealogy, and η, the total number of mutations.
The Fu & Li's F test statistic (Fu and Li 199311) is based on the differences between ηe, the total number of mutations in external branches of the genealogy, and η, the average number of nucleotide differences between pairs of sequences.
McDonald and Kreitman (1991) proposed a simple test of neutrality (the McDonald-Kreitman test, or MK test), which has become the basis of several methods to estimate the proportion of substitutions that have been fixed by positive selection rather than by genetic drift (Fay et al. 200112; Smith and Eyre-Walker 200213; Sawyer et al. 200314; Bierne and Eyre-Walker 200415; Welch 200616). The test compares the amount of variation within species to the divergence between species at two types of site: synonymous and nonsynonymous sites. The test assumes that all synonymous mutations are neutral, and that nonsynonymous mutations are either strongly deleterious, neutral, or strongly advantageous.
It is expected that the effects on fitness of a mutation are the same whether within a species or at any time along the ancestral history of two species back to the common ancestor. If this is true, and if all mutations are neutral, then the ratio of synonymous to nonsynonymous polymorphisms (Pn/Ps) is expected to equal the ratio of synonymous to nonsynonymous substitutions (Dn/Ds). This is the basis of the MK test. We can summarize the four values as a ratio of ratios termed the Neutrality Index (NI) (Rand and Kann 1996) as follows:
NI = (Pn/Ps) / (Dn/Ds)
Under neutrality, Dn/Ds equals Pn/Ps, and thus NI = 1. If NI < 1, there is an excess of fixation of amino acid replacements due to positive selection (Dn is higher than expected). If NI > 1, negative selection is preventing the fixation of harmful mutations (Dn is lower than expected). The test is therefore useful in assessing the relative importance of neutral drift and selection.
In this track, the MK test has been performed by comparing four-fold degenerate sites taken from all CDS annotations in the chromosome being visualized, to any other type of site (including noncoding sites) of the window.
The Tajima's D test statistic (Tajima 1989117) is based on the differences between the number of segregating sites and the average number of nucleotide differences, and it is used for testing the hypothesis that all mutations are selectively neutral.