Search for Variation information by Variation ID:

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

Detailed information for vg0228028944:

Variant ID: vg0228028944 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28028944
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

ACAATGACAGTGCTAACGGAGTGTGGCGTGGCGGCAATATAGAGGAATAATTCTTCATTAGGTTGGGGAGCAACAAGTACAGGGGGGTTTGATAGGTAGC[A/G]
CTTGAGTGCAATGAATGCCTCTTCGGCTTCCTATGTCCATACAAATTTGTCTTGTTTCTTCAACAGAGCGAAGAAAGGTTGTCCTCGTTCTCCCATCCTA

Reverse complement sequence

TAGGATGGGAGAACGAGGACAACCTTTCTTCGCTCTGTTGAAGAAACAAGACAAATTTGTATGGACATAGGAAGCCGAAGAGGCATTCATTGCACTCAAG[T/C]
GCTACCTATCAAACCCCCCTGTACTTGTTGCTCCCCAACCTAATGAAGAATTATTCCTCTATATTGCCGCCACGCCACACTCCGTTAGCACTGTCATTGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.70%	10.20%	22.24%	33.92%	NA
All Indica	2759	8.00%	3.20%	31.71%	57.12%	NA
All Japonica	1512	85.80%	13.00%	0.93%	0.20%	NA
Aus	269	4.80%	38.30%	54.65%	2.23%	NA
Indica I	595	5.20%	2.00%	24.87%	67.90%	NA
Indica II	465	4.90%	4.30%	38.28%	52.47%	NA
Indica III	913	11.10%	2.70%	31.54%	54.65%	NA
Indica Intermediate	786	8.40%	3.80%	33.21%	54.58%	NA
Temperate Japonica	767	99.60%	0.10%	0.00%	0.26%	NA
Tropical Japonica	504	60.30%	36.90%	2.58%	0.20%	NA
Japonica Intermediate	241	95.40%	4.10%	0.41%	0.00%	NA
VI/Aromatic	96	18.80%	80.20%	0.00%	1.04%	NA
Intermediate	90	46.70%	17.80%	16.67%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0228028944	A -> G	LOC_Os02g46000.1	missense_variant ; p.Cys262Arg; MODERATE	nonsynonymous_codon ; C262R	Average:20.617; most accessible tissue: Minghui63 root, score: 29.362	unknown	unknown	TOLERATED	1.00
vg0228028944	A -> DEL	LOC_Os02g46000.1	N	frameshift_variant	Average:20.617; most accessible tissue: Minghui63 root, score: 29.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228028944	NA	2.06E-06	mr1392	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
vg0228028944	NA	7.29E-12	mr1636	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
vg0228028944	NA	4.51E-40	mr1243_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
vg0228028944	NA	1.12E-06	mr1250_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
vg0228028944	NA	1.70E-19	mr1255_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
vg0228028944	3.99E-06	1.74E-34	mr1257_2	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
vg0228028944	NA	3.02E-23	mr1708_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
vg0228028944	NA	4.25E-06	mr1785_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
vg0228028944	NA	1.68E-17	mr1790_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
vg0228028944	NA	4.93E-09	mr1947_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