Schema for H-C Coding Diffs - Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage
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Database: hg19 Primary Table: ntHumChimpCodingDiff Row Count: 11,345   Data last updated: 2010-12-14
Format description: Browser extensible data On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 591 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
chromStart | 877564 | int(10) unsigned | range | Start position in chromosome |
chromEnd | 877565 | int(10) unsigned | range | End position in chromosome |
name | 0A>3G(ATC>GTC) | varchar(255) | values | Name of item |
score | 300 | int(10) unsigned | range | Optional score, nominal range 0-1000 |
strand | + | char(1) | values | + or - |
thickStart | 877564 | int(10) unsigned | range | Start of where display should be thick (start codon) |
thickEnd | 877565 | int(10) unsigned | range | End of where display should be thick (stop codon) |
itemRgb | 46080 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRgb |
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591 | chr1 | 877564 | 877565 | 0A>3G(ATC>GTC) | 300 | + | 877564 | 877565 | 0,180,0 |
591 | chr1 | 878309 | 878310 | 0C>4T(GCT>GTT) | 400 | + | 878309 | 878310 | 0,180,0 |
591 | chr1 | 878652 | 878653 | 0G>2A(GTG>ATG) | 200 | + | 878652 | 878653 | 0,180,0 |
591 | chr1 | 879141 | 879142 | 0G>2C(AGC>ACC) | 200 | + | 879141 | 879142 | 0,180,0 |
591 | chr1 | 879144 | 879145 | 0C>2A(ACC>AAC) | 200 | + | 879144 | 879145 | 0,180,0 |
592 | chr1 | 949421 | 949422 | 0A>7G(AAC>AGC) | 700 | + | 949421 | 949422 | 0,180,0 |
593 | chr1 | 1139844 | 1139845 | 0G>5A(CGG>CAG) | 500 | - | 1139844 | 1139845 | 0,180,0 |
593 | chr1 | 1141920 | 1141921 | 0G>1C(GGG>CGG) | 100 | - | 1141920 | 1141921 | 0,180,0 |
593 | chr1 | 1149430 | 1149431 | 0C>3T(GCG>GTG) | 300 | - | 1149430 | 1149431 | 0,180,0 |
602 | chr1 | 2267932 | 2267933 | 0A>2G(ACA>GCA) | 200 | - | 2267932 | 2267933 | 0,180,0 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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H-C Coding Diffs (ntHumChimpCodingDiff) Track Description
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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
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