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Detailed information for vg1221819145:

Variant ID: vg1221819145 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21819145
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.27, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAAATTACATGGTTACCCTTATGATAGGGACATTACAGTGGGTATACAAGGTCTTGTTTTACATTCGTGGGCTCTGAGATGGTCTTCCTGGGCCGGCC[T/C]
ATTAGGTGGCGAAGGGCCCCCCATGGACCACCGAGCTCCTCGAGCCCTATGACCGAAGGCCTTCTTCATTCGGGGCTTCGGCTTCATGGAATGCTTGACG

Reverse complement sequence

CGTCAAGCATTCCATGAAGCCGAAGCCCCGAATGAAGAAGGCCTTCGGTCATAGGGCTCGAGGAGCTCGGTGGTCCATGGGGGGCCCTTCGCCACCTAAT[A/G]
GGCCGGCCCAGGAAGACCATCTCAGAGCCCACGAATGTAAAACAAGACCTTGTATACCCACTGTAATGTCCCTATCATAAGGGTAACCATGTAATTTTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.00%	4.80%	1.50%	29.69%	NA
All Indica	2759	45.70%	7.90%	2.28%	44.07%	NA
All Japonica	1512	99.20%	0.30%	0.07%	0.46%	NA
Aus	269	43.90%	0.40%	1.49%	54.28%	NA
Indica I	595	54.60%	0.50%	1.18%	43.70%	NA
Indica II	465	54.60%	27.10%	1.08%	17.20%	NA
Indica III	913	34.20%	4.30%	2.63%	58.93%	NA
Indica Intermediate	786	47.10%	6.50%	3.44%	43.00%	NA
Temperate Japonica	767	99.00%	0.40%	0.13%	0.52%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	1.00%	2.08%	22.92%	NA
Intermediate	90	81.10%	4.40%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221819145	T -> C	LOC_Os12g35790-LOC_Os12g35810	intergenic_region ; MODIFIER	silent_mutation	Average:41.252; most accessible tissue: Minghui63 young leaf, score: 80.562	N	N	N	N
vg1221819145	T -> DEL	N	N	silent_mutation	Average:41.252; most accessible tissue: Minghui63 young leaf, score: 80.562	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221819145	NA	4.51E-08	mr1268	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
vg1221819145	NA	4.03E-06	mr1268	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
vg1221819145	NA	2.26E-07	mr1498	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
vg1221819145	NA	4.41E-06	mr1679	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
vg1221819145	NA	5.93E-06	mr1693	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
vg1221819145	NA	6.95E-11	mr1769	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
vg1221819145	NA	8.18E-10	mr1769	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
vg1221819145	NA	4.88E-11	mr1951	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
vg1221819145	NA	2.74E-09	mr1951	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