Search for Variation information by Variation ID:

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

Detailed information for vg1209004418:

Variant ID: vg1209004418 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004418
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, G: 0.36, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCG[A/G]
TGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATG

Reverse complement sequence

CATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCA[T/C]
CGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGC

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	39.70%	38.20%	0.38%	21.71%	NA
All Indica	2759	54.00%	10.50%	0.65%	34.87%	NA
All Japonica	1512	4.40%	94.50%	0.00%	1.06%	NA
Aus	269	81.40%	5.60%	0.00%	13.01%	NA
Indica I	595	36.10%	21.30%	0.34%	42.18%	NA
Indica II	465	51.60%	11.80%	1.51%	35.05%	NA
Indica III	913	65.10%	3.10%	0.22%	31.65%	NA
Indica Intermediate	786	56.00%	10.20%	0.89%	32.95%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.60%	95.60%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	36.70%	53.30%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004418	A -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:40.821; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg1209004418	A -> G	LOC_Os12g15770.1	missense_variant ; p.Ser74Pro; MODERATE	nonsynonymous_codon ; S74P	Average:40.821; most accessible tissue: Zhenshan97 young leaf, score: 69.723	unknown	unknown	TOLERATED	0.79

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004418	NA	2.67E-08	mr1425	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
vg1209004418	NA	1.84E-07	mr1659	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