Search for Variation information by Variation ID:

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

Detailed information for vg1208480617:

Variant ID: vg1208480617 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8480617
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AAACCGGGACTAAAGGGGGGTTACGAACCGGGACTACAAAGGGTTTCTCCACCAGTGCTTCCGCTGGAATGATTTCTCTGTTAAAATTTGTCGGTCCCTA[C/G]
AACATCGTTCAGAAGAAGAATGATGTAGCACATCGAGTTAGGACATCATTTTAATCCATGCGGGTTGGTGGTGAGTGTAACAACCAGCCAGTTCAAAGCC

Reverse complement sequence

GGCTTTGAACTGGCTGGTTGTTACACTCACCACCAACCCGCATGGATTAAAATGATGTCCTAACTCGATGTGCTACATCATTCTTCTTCTGAACGATGTT[G/C]
TAGGGACCGACAAATTTTAACAGAGAAATCATTCCAGCGGAAGCACTGGTGGAGAAACCCTTTGTAGTCCCGGTTCGTAACCCCCCTTTAGTCCCGGTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.40%	27.00%	3.39%	0.28%	NA
All Indica	2759	60.70%	36.30%	2.61%	0.36%	NA
All Japonica	1512	96.60%	3.30%	0.13%	0.00%	NA
Aus	269	15.20%	62.10%	21.93%	0.74%	NA
Indica I	595	62.50%	36.60%	0.50%	0.34%	NA
Indica II	465	52.50%	45.20%	2.37%	0.00%	NA
Indica III	913	65.00%	29.90%	4.38%	0.77%	NA
Indica Intermediate	786	59.40%	38.20%	2.29%	0.13%	NA
Temperate Japonica	767	94.70%	5.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.00%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	32.30%	44.80%	21.88%	1.04%	NA
Intermediate	90	78.90%	14.40%	6.67%	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
vg1208480617	C -> DEL	N	N	silent_mutation	Average:43.1; most accessible tissue: Minghui63 root, score: 80.366	N	N	N	N
vg1208480617	C -> G	LOC_Os12g14820.1	downstream_gene_variant ; 556.0bp to feature; MODIFIER	silent_mutation	Average:43.1; most accessible tissue: Minghui63 root, score: 80.366	N	N	N	N
vg1208480617	C -> G	LOC_Os12g14820-LOC_Os12g14830	intergenic_region ; MODIFIER	silent_mutation	Average:43.1; most accessible tissue: Minghui63 root, score: 80.366	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208480617	7.51E-08	NA	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
vg1208480617	8.34E-09	1.49E-12	mr1425	Ind_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
vg1208480617	NA	6.10E-06	mr1558	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
vg1208480617	NA	3.67E-06	mr1002_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
vg1208480617	NA	6.30E-08	mr1683_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
vg1208480617	NA	1.64E-08	mr1864_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