Schema for 5% Lowest S - Selective Sweep Scan (S): 5% Smallest S scores
  Database: hg19    Primary Table: ntSssTop5p    Row Count: 212   Data last updated: 2010-12-14
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 12smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 29250635int(10) unsigned range Start position in chromosome
chromEnd 29582124int(10) unsigned range End position in chromosome
name -5.7648varchar(255) values Name of item
score 599int(10) unsigned range Optional score, nominal range 0-1000

Sample Rows
 
binchromchromStartchromEndnamescore
12chr12925063529582124-5.7648599
14chr14602653146214183-4.8403473
117chr14655451746718374-5.3036536
121chr15100817151235816-4.4165415
16chr16386206964092146-4.8096469
147chr17805271778289590-5.4671559
1234chr18506663385177704-4.5858438
163chr19463933694839130-4.6630449
165chr19722988897509581-5.1809520
166chr19805356298445381-6.5720709

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

5% Lowest S (ntSssTop5p) Track Description
 

Description

This track shows regions of the human genome with a strong signal for depletion of Neandertal-derived alleles (regions from the Sel Swp Scan (S) track with S scores in the lowest 5%), which may indicate an episode of positive selection in early humans.

Display Conventions and Configuration

Grayscale shading is used as a rough indicator of the strength of the score; the darker the item, the stronger its negative score. The strongest negative score (-8.7011) is shaded black, and the shading lightens from dark to light gray as the negative score weakens (weakest score is -4.3202).

Methods

Green et al. identified single-base sites that are polymorphic among five modern human genomes of diverse ancestry (in the Modern Human Seq track) plus the human reference genome, and determined ancestral or derived state of each single nucleotide polymorphism (SNP) by comparison with the chimpanzee genome. The SNPs are displayed in the S SNPs track. The human allele states were used to estimate an expected number of derived alleles in Neandertal in the 100,000-base window around each SNP, and a measure called the S score was developed, displayed in the Sel Swp Scan (S) track, to compare the observed number of Neandertal alleles in each window to the expected number. An S score significantly less than zero indicates a reduction of Neandertal-derived alleles (or an increase of human-derived alleles not found in Neandertal), consistent with the scenario of positive selection in the human lineage since divergence from Neandertals.

Genomic regions of 25,000 or more bases in which all polymorphic sites were at least 2 standard deviations below the expected value were identified, and S was recomputed on each such region. Regions with S scores in the lowest 5% (strongest negative scores) were prioritized for further analysis as described in Green et al..

Credits

This track was produced at UCSC using data generated by Ed Green.

References

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178