Search for Variation information by Variation ID:

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

Detailed information for vg1012246009:

Variant ID: vg1012246009 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12246009
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TATTACCCATAGGAAAAATAAAGTCATCTTCGGCCATAATTAATTGGGAAAGCCTCATCACCCGATGACATTCGAAAATAATGCATAAGTTGAAATAAAA[C/T]
ATTAGCATTAAACGGGTTTAACATGCTCAAAGGATTGTTTGGGATCTGTGTGACTTACCTTGACCTTCTTCAAACGCTTTTGAACCTTTCTAAACGTAAA

Reverse complement sequence

TTTACGTTTAGAAAGGTTCAAAAGCGTTTGAAGAAGGTCAAGGTAAGTCACACAGATCCCAAACAATCCTTTGAGCATGTTAAACCCGTTTAATGCTAAT[G/A]
TTTTATTTCAACTTATGCATTATTTTCGAATGTCATCGGGTGATGAGGCTTTCCCAATTAATTATGGCCGAAGATGACTTTATTTTTCCTATGGGTAATA

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	51.20%	1.70%	19.83%	27.30%	NA
All Indica	2759	34.20%	2.70%	28.96%	34.18%	NA
All Japonica	1512	90.10%	0.00%	1.65%	8.20%	NA
Aus	269	12.60%	1.90%	30.48%	55.02%	NA
Indica I	595	15.80%	1.50%	25.04%	57.65%	NA
Indica II	465	41.70%	1.70%	24.30%	32.26%	NA
Indica III	913	36.10%	4.10%	35.82%	23.99%	NA
Indica Intermediate	786	41.30%	2.50%	26.72%	29.39%	NA
Temperate Japonica	767	97.40%	0.00%	0.26%	2.35%	NA
Tropical Japonica	504	82.70%	0.00%	2.98%	14.29%	NA
Japonica Intermediate	241	82.60%	0.00%	3.32%	14.11%	NA
VI/Aromatic	96	21.90%	0.00%	20.83%	57.29%	NA
Intermediate	90	65.60%	0.00%	12.22%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012246009	C -> T	LOC_Os10g23870.1	upstream_gene_variant ; 4587.0bp to feature; MODIFIER	silent_mutation	Average:11.225; most accessible tissue: Callus, score: 37.026	N	N	N	N
vg1012246009	C -> T	LOC_Os10g23880.1	intron_variant ; MODIFIER	silent_mutation	Average:11.225; most accessible tissue: Callus, score: 37.026	N	N	N	N
vg1012246009	C -> DEL	N	N	silent_mutation	Average:11.225; most accessible tissue: Callus, score: 37.026	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012246009	1.67E-07	NA	mr1244_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