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Detailed information for vg1214961636:

Variant ID: vg1214961636 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14961636
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TGCACATGACCTAGGGTATTTTACACATTAAAAATATTGCTTCATATATAGTAGAATGGCAATTCAGTGATCTACATTAAAATCAAAGTAGCAAACAACA[T/C]
CATTGCTCATCGAGATTATCCCAGTCAATGCAGCAAAAAGTGCATTTACTTACCAACAAAGATTGTTTCATCTGTGATTTTACATTGACAACCAAATCCC

Reverse complement sequence

GGGATTTGGTTGTCAATGTAAAATCACAGATGAAACAATCTTTGTTGGTAAGTAAATGCACTTTTTGCTGCATTGACTGGGATAATCTCGATGAGCAATG[A/G]
TGTTGTTTGCTACTTTGATTTTAATGTAGATCACTGAATTGCCATTCTACTATATATGAAGCAATATTTTTAATGTGTAAAATACCCTAGGTCATGTGCA

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	80.30%	11.20%	8.06%	0.40%	NA
All Indica	2759	74.60%	13.90%	10.84%	0.65%	NA
All Japonica	1512	86.00%	9.00%	4.96%	0.00%	NA
Aus	269	98.10%	0.70%	0.74%	0.37%	NA
Indica I	595	91.80%	3.50%	4.71%	0.00%	NA
Indica II	465	66.20%	12.30%	20.22%	1.29%	NA
Indica III	913	70.50%	19.80%	8.98%	0.66%	NA
Indica Intermediate	786	71.40%	15.80%	12.09%	0.76%	NA
Temperate Japonica	767	92.00%	7.60%	0.39%	0.00%	NA
Tropical Japonica	504	80.00%	9.10%	10.91%	0.00%	NA
Japonica Intermediate	241	79.70%	13.30%	7.05%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	10.00%	5.56%	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
vg1214961636	T -> C	LOC_Os12g25800.1	upstream_gene_variant ; 1485.0bp to feature; MODIFIER	silent_mutation	Average:19.715; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1214961636	T -> C	LOC_Os12g25790.1	downstream_gene_variant ; 1790.0bp to feature; MODIFIER	silent_mutation	Average:19.715; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1214961636	T -> C	LOC_Os12g25790-LOC_Os12g25800	intergenic_region ; MODIFIER	silent_mutation	Average:19.715; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1214961636	T -> DEL	N	N	silent_mutation	Average:19.715; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214961636	4.31E-06	1.16E-07	mr1221_2	Jap_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
vg1214961636	5.90E-06	5.90E-06	mr1767_2	Jap_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