Search for Variation information by Variation ID:

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

Detailed information for vg1214765715:

Variant ID: vg1214765715 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14765715
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGAATGGGATCGTAAGGGGTTTCCCTCAGTATTGCGTTGACGGCTCTGATGTGCTGGGCCGGAGTAGTCACTTGATTCTCCGCTTCCGCATTGGTGC[G/A]
CGCTGACGTGCCGACATCGTCGATAGCCAATACCTCACGCGGCGTACTCGTTGTTGATGATCCATAGTCTTCGATCAGGTGCAAGACTGATGGTTCGTGG

Reverse complement sequence

CCACGAACCATCAGTCTTGCACCTGATCGAAGACTATGGATCATCAACAACGAGTACGCCGCGTGAGGTATTGGCTATCGACGATGTCGGCACGTCAGCG[C/T]
GCACCAATGCGGAAGCGGAGAATCAAGTGACTACTCCGGCCCAGCACATCAGAGCCGTCAACGCAATACTGAGGGAAACCCCTTACGATCCCATTCTGAA

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	82.10%	17.10%	0.80%	0.08%	NA
All Indica	2759	79.80%	18.80%	1.30%	0.04%	NA
All Japonica	1512	86.30%	13.40%	0.07%	0.20%	NA
Aus	269	82.20%	17.80%	0.00%	0.00%	NA
Indica I	595	74.30%	23.40%	2.35%	0.00%	NA
Indica II	465	78.90%	17.80%	3.23%	0.00%	NA
Indica III	913	82.60%	17.30%	0.11%	0.00%	NA
Indica Intermediate	786	81.40%	17.70%	0.76%	0.13%	NA
Temperate Japonica	767	96.90%	3.10%	0.00%	0.00%	NA
Tropical Japonica	504	70.80%	28.60%	0.20%	0.40%	NA
Japonica Intermediate	241	85.10%	14.50%	0.00%	0.41%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1214765715	G -> DEL	LOC_Os12g25510.1	N	frameshift_variant	Average:27.732; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1214765715	G -> A	LOC_Os12g25510.1	missense_variant ; p.Arg355Cys; MODERATE	nonsynonymous_codon ; R355C	Average:27.732; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	unknown	unknown	TOLERATED	0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214765715	NA	8.06E-07	mr1411	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
vg1214765715	NA	6.31E-07	mr1489	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
vg1214765715	4.19E-06	4.19E-06	mr1898	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