Search for Variation information by Variation ID:

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

Detailed information for vg1004365897:

Variant ID: vg1004365897 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4365897
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAAATAGTATATTTAATCTAATGATCTAAAATATAGAGTCCACCAATTTAAGTGAAAATCGACGGTGAGATTGAACGTGCCATGTGGCGGCTTATGA[G/A]
CGTTTGTAGGATACCACATGGTGGTTTAGGAGCGTTTGTAGGAAGTTTAATAGACTTTTAGTTTATAATAATAGATAGATAGAAGATTATGGATTTAATG

Reverse complement sequence

CATTAAATCCATAATCTTCTATCTATCTATTATTATAAACTAAAAGTCTATTAAACTTCCTACAAACGCTCCTAAACCACCATGTGGTATCCTACAAACG[C/T]
TCATAAGCCGCCACATGGCACGTTCAATCTCACCGTCGATTTTCACTTAAATTGGTGGACTCTATATTTTAGATCATTAGATTAAATATACTATTTAAAA

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	35.30%	16.10%	2.01%	46.66%	NA
All Indica	2759	24.00%	16.40%	0.91%	58.64%	NA
All Japonica	1512	62.30%	1.20%	4.56%	31.94%	NA
Aus	269	1.10%	93.30%	0.00%	5.58%	NA
Indica I	595	32.90%	42.40%	2.52%	22.18%	NA
Indica II	465	32.90%	10.50%	0.22%	56.34%	NA
Indica III	913	11.10%	3.40%	0.00%	85.54%	NA
Indica Intermediate	786	27.10%	15.40%	1.15%	56.36%	NA
Temperate Japonica	767	81.90%	0.40%	6.52%	11.21%	NA
Tropical Japonica	504	29.80%	2.00%	2.18%	66.07%	NA
Japonica Intermediate	241	68.00%	2.10%	3.32%	26.56%	NA
VI/Aromatic	96	30.20%	19.80%	0.00%	50.00%	NA
Intermediate	90	32.20%	21.10%	1.11%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004365897	G -> A	LOC_Os10g08060.1	upstream_gene_variant ; 2882.0bp to feature; MODIFIER	silent_mutation	Average:36.527; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1004365897	G -> A	LOC_Os10g08050.1	downstream_gene_variant ; 1553.0bp to feature; MODIFIER	silent_mutation	Average:36.527; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1004365897	G -> A	LOC_Os10g08040-LOC_Os10g08050	intergenic_region ; MODIFIER	silent_mutation	Average:36.527; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg1004365897	G -> DEL	N	N	silent_mutation	Average:36.527; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004365897	3.95E-06	NA	mr1128	Ind_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