Search for Variation information by Variation ID:

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

Detailed information for vg0807716778:

Variant ID: vg0807716778 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7716778
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.54, C: 0.46, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGCACTGTTTGTATATATCTGCGCCCTCCCGTGGGTGGAGGTTCCTCTGTCGCTCGATCGTCAACTTGTCATTCGCCATCCTAATACTTGTTCGTTC[C/T]
CAATATTTTTGAGGTATTAAGAAAGTATGTTAAGATGATTATTGAAAGAAGTGTGTGATTGGTTGAAAAGAAAAAGTAGGTCAAAGAGAATAGTCAATAG

Reverse complement sequence

CTATTGACTATTCTCTTTGACCTACTTTTTCTTTTCAACCAATCACACACTTCTTTCAATAATCATCTTAACATACTTTCTTAATACCTCAAAAATATTG[G/A]
GAACGAACAAGTATTAGGATGGCGAATGACAAGTTGACGATCGAGCGACAGAGGAACCTCCACCCACGGGAGGGCGCAGATATATACAAACAGTGCATGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.60%	44.60%	0.32%	3.45%	NA
All Indica	2759	29.80%	65.00%	0.36%	4.78%	NA
All Japonica	1512	91.50%	8.20%	0.20%	0.07%	NA
Aus	269	60.20%	29.40%	0.00%	10.41%	NA
Indica I	595	3.50%	95.50%	0.17%	0.84%	NA
Indica II	465	56.10%	40.40%	0.22%	3.23%	NA
Indica III	913	34.60%	55.00%	0.22%	10.19%	NA
Indica Intermediate	786	28.60%	68.20%	0.76%	2.42%	NA
Temperate Japonica	767	96.90%	3.10%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	7.10%	0.20%	0.00%	NA
Japonica Intermediate	241	72.20%	26.60%	0.83%	0.41%	NA
VI/Aromatic	96	16.70%	82.30%	0.00%	1.04%	NA
Intermediate	90	58.90%	37.80%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807716778	C -> T	LOC_Os08g12990.1	upstream_gene_variant ; 153.0bp to feature; MODIFIER	silent_mutation	Average:59.131; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0807716778	C -> T	LOC_Os08g13000.1	upstream_gene_variant ; 1336.0bp to feature; MODIFIER	silent_mutation	Average:59.131; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0807716778	C -> T	LOC_Os08g12990-LOC_Os08g13000	intergenic_region ; MODIFIER	silent_mutation	Average:59.131; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0807716778	C -> DEL	N	N	silent_mutation	Average:59.131; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807716778	2.44E-06	2.44E-06	mr1008	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0807716778	1.59E-06	1.59E-06	mr1009	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
vg0807716778	NA	2.70E-07	mr1598	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0807716778	NA	7.05E-08	mr1124_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251