Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1021649601:

Variant ID: vg1021649601 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 21649601
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCCTTTTTGCGGATTCTGCTCGAGAGCAGATTCCAATCCGCGCTTCGTGATTCTACGGCCGAGTCAAGAGGATATGGTTGGAGATGGCTCTGATACCA[G/A]
ATTGTTAGAACCCTAGCACTCGATTTCACCACGAACTCAAGAACACGATAGGTAGCTGGAACTTTGTATTTCTCTCACGATCCAACAGGATCGGAGCCGC

Reverse complement sequence

GCGGCTCCGATCCTGTTGGATCGTGAGAGAAATACAAAGTTCCAGCTACCTATCGTGTTCTTGAGTTCGTGGTGAAATCGAGTGCTAGGGTTCTAACAAT[C/T]
TGGTATCAGAGCCATCTCCAACCATATCCTCTTGACTCGGCCGTAGAATCACGAAGCGCGGATTGGAATCTGCTCTCGAGCAGAATCCGCAAAAAGGGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	3.90%	0.32%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	87.40%	11.60%	0.99%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.30%	1.80%	0.91%	0.00%	NA
Tropical Japonica	504	72.80%	25.80%	1.39%	0.00%	NA
Japonica Intermediate	241	86.70%	12.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1021649601	G -> A	LOC_Os10g40400.1	upstream_gene_variant ; 217.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021649601	G -> A	LOC_Os10g40410.1	upstream_gene_variant ; 2432.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021649601	G -> A	LOC_Os10g40410.2	upstream_gene_variant ; 2432.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021649601	G -> A	LOC_Os10g40400-LOC_Os10g40410	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1021649601	6.49E-06	5.95E-08	mr1444_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251