Search for Variation information by Variation ID:

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

Detailed information for vg0724427664:

Variant ID: vg0724427664 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24427664
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.31, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCAAAGATACTGGGAGCTAGAGATGAACCCATAATTACCATGGTTGAGCACATAAGGACAAAAATGATGGGTGATTTCAATAATAAGAGGGAAGGTG[T/C]
AGAAAGGGACAATTGGCAAATCCCACCAAATATATTAAAGAAGCTTGAGGCAGAGAAGAGAGAGGCAAGATATTGCAAATCTGTGTGTGCTGGTAGGGGC

Reverse complement sequence

GCCCCTACCAGCACACACAGATTTGCAATATCTTGCCTCTCTCTTCTCTGCCTCAAGCTTCTTTAATATATTTGGTGGGATTTGCCAATTGTCCCTTTCT[A/G]
CACCTTCCCTCTTATTATTGAAATCACCCATCATTTTTGTCCTTATGTGCTCAACCATGGTAATTATGGGTTCATCTCTAGCTCCCAGTATCTTTGAATT

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	83.00%	14.90%	2.05%	0.00%	NA
All Indica	2759	97.40%	1.90%	0.72%	0.00%	NA
All Japonica	1512	55.40%	40.20%	4.43%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	96.60%	1.90%	1.51%	0.00%	NA
Indica III	913	99.30%	0.30%	0.33%	0.00%	NA
Indica Intermediate	786	94.80%	3.90%	1.27%	0.00%	NA
Temperate Japonica	767	37.90%	61.10%	0.91%	0.00%	NA
Tropical Japonica	504	83.50%	7.50%	8.93%	0.00%	NA
Japonica Intermediate	241	51.90%	41.90%	6.22%	0.00%	NA
VI/Aromatic	96	88.50%	10.40%	1.04%	0.00%	NA
Intermediate	90	72.20%	17.80%	10.00%	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
vg0724427664	T -> C	LOC_Os07g40760.1	missense_variant ; p.Val925Ala; MODERATE	nonsynonymous_codon ; V925A	Average:9.595; most accessible tissue: Minghui63 root, score: 13.235	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724427664	1.29E-07	NA	mr1138	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
vg0724427664	8.95E-06	NA	mr1181	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
vg0724427664	7.68E-07	NA	mr1343	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
vg0724427664	8.25E-20	6.08E-15	mr1354	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
vg0724427664	1.01E-14	2.26E-11	mr1354	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
vg0724427664	2.14E-06	7.72E-06	mr1406	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
vg0724427664	NA	2.84E-08	mr1716	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
vg0724427664	2.77E-10	NA	mr1829	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
vg0724427664	1.23E-09	2.10E-06	mr1829	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
vg0724427664	NA	2.78E-07	mr1915	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
vg0724427664	NA	3.99E-06	mr1977	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
vg0724427664	8.45E-09	NA	mr1181_2	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
vg0724427664	1.84E-29	2.54E-16	mr1354_2	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
vg0724427664	1.33E-20	4.96E-11	mr1354_2	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
vg0724427664	NA	3.22E-06	mr1510_2	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
vg0724427664	5.01E-16	NA	mr1829_2	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
vg0724427664	5.50E-11	1.02E-08	mr1829_2	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
vg0724427664	6.94E-16	NA	mr1902_2	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
vg0724427664	6.13E-11	3.77E-08	mr1902_2	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