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Detailed information for vg0108450212:

Variant ID: vg0108450212 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 8450212
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCAATTATTTTAAGCTCAATTATATCAAATTGTTTTAGTTTTTAATTAAATTATATTTTATTTGTATATAGTATATGCATCTTAATTTTTTGCAGCAA[C/T]
GCAGCGGGGTATTCGTATATGAATACTAACGAAGTAACGAGTGTGTAACCAAAATGAGTAGCAAAAGTAGGAGTAATTAGCAAAAAGACAAATTAAATCA

Reverse complement sequence

TGATTTAATTTGTCTTTTTGCTAATTACTCCTACTTTTGCTACTCATTTTGGTTACACACTCGTTACTTCGTTAGTATTCATATACGAATACCCCGCTGC[G/A]
TTGCTGCAAAAAATTAAGATGCATATACTATATACAAATAAAATATAATTTAATTAAAAACTAAAACAATTTGATATAATTGAGCTTAAAATAATTGAGA

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	54.50%	31.70%	8.74%	5.01%	NA
All Indica	2759	81.90%	5.60%	9.64%	2.90%	NA
All Japonica	1512	14.90%	81.10%	3.84%	0.13%	NA
Aus	269	11.90%	4.10%	27.88%	56.13%	NA
Indica I	595	67.20%	11.10%	21.68%	0.00%	NA
Indica II	465	84.90%	4.90%	8.39%	1.72%	NA
Indica III	913	92.90%	1.30%	2.08%	3.72%	NA
Indica Intermediate	786	78.40%	6.70%	10.05%	4.83%	NA
Temperate Japonica	767	4.00%	93.70%	2.22%	0.00%	NA
Tropical Japonica	504	27.80%	66.30%	5.56%	0.40%	NA
Japonica Intermediate	241	22.80%	71.80%	5.39%	0.00%	NA
VI/Aromatic	96	12.50%	84.40%	3.12%	0.00%	NA
Intermediate	90	53.30%	30.00%	12.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0108450212	C -> T	LOC_Os01g15029.1	upstream_gene_variant ; 3158.0bp to feature; MODIFIER	silent_mutation	Average:53.474; most accessible tissue: Callus, score: 85.158	N	N	N	N
vg0108450212	C -> T	LOC_Os01g15039.1	intron_variant ; MODIFIER	silent_mutation	Average:53.474; most accessible tissue: Callus, score: 85.158	N	N	N	N
vg0108450212	C -> DEL	N	N	silent_mutation	Average:53.474; most accessible tissue: Callus, score: 85.158	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0108450212	NA	6.86E-19	mr1179	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
vg0108450212	NA	2.65E-08	mr1465	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
vg0108450212	NA	2.16E-13	mr1720	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
vg0108450212	NA	7.60E-09	mr1827	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
vg0108450212	NA	9.13E-18	mr1131_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
vg0108450212	NA	8.09E-08	mr1612_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
vg0108450212	NA	3.51E-19	mr1720_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