Schema for H-C Coding Diffs - Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage
  Database: hg19    Primary Table: ntHumChimpCodingDiff    Row Count: 11,345   Data last updated: 2010-12-15
Format description: Browser extensible data
fieldexampleSQL type info description
bin 591smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 877564int(10) unsigned range Start position in chromosome
chromEnd 877565int(10) unsigned range End position in chromosome
name 0A>3G(ATC>GTC)varchar(255) values Name of item
score 300int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -
thickStart 877564int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 877565int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 46080int(10) unsigned range Used as itemRgb as of 2004-11-22

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
591chr18775648775650A>3G(ATC>GTC)300+8775648775650,180,0
591chr18783098783100C>4T(GCT>GTT)400+8783098783100,180,0
591chr18786528786530G>2A(GTG>ATG)200+8786528786530,180,0
591chr18791418791420G>2C(AGC>ACC)200+8791418791420,180,0
591chr18791448791450C>2A(ACC>AAC)200+8791448791450,180,0
592chr19494219494220A>7G(AAC>AGC)700+9494219494220,180,0
593chr1113984411398450G>5A(CGG>CAG)500-113984411398450,180,0
593chr1114192011419210G>1C(GGG>CGG)100-114192011419210,180,0
593chr1114943011494310C>3T(GCG>GTG)300-114943011494310,180,0
602chr1226793222679330A>2G(ACA>GCA)200-226793222679330,180,0

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

H-C Coding Diffs (ntHumChimpCodingDiff) Track Description
 

Description

This track displays Neandertal alleles for human-chimp protein-coding differences on the human lineage using orangutan as the outgroup to determine which allele is more likely to be ancestral.

Display Conventions and Configuration

Neandertal ancestral alleles are colored blue; derived (human) alleles are colored green.

The item names show the number of Neandertal reads for the ancestral and derived alleles, followed by the ancestral and derived codons enclosed in parentheses. For example, if no Neandertal reads matched the ancestral base G and three Neandertal reads matched the derived base A, and the ancestral and derived codons were GTA and ATA respectively, then the item name would be "0G>3A(GTA>ATA)". If N Neandertal reads match neither ancestral nor derived base, then a "+N?" is added before the codons (i.e. "0G>3A+N?(GTA>ATA)").

Methods

Neandertal DNA was extracted from a ~49,000-year-old bone (Sidrón 1253), which was excavated in El Sidrón cave, Asturias, Spain. Non-synonymous changes that occurred on the human lineage since the ancestral split with chimpanzee were identified by aligning human, chimpanzee and orangutan protein sequences for all orthologous proteins in HomoloGene (Build 58) . Comparison of these three species allowed the assignment of human/chimpanzee differences to their respective evolutionary lineages. An Agilent custom oligonucleotide array covering the 13,841 non-synonymous changes inferred to have occurred in the human lineage was designed and used to capture Neandertal sequences.

Reference

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 May 7;328(5979):723-5. PMID: 20448179; PMC: PMC3140021