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Detailed information for vg1219269007:

Variant ID: vg1219269007 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19269007
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.30, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGAGAATGCAAATGTAAGTTGTTACGCATGAACAGGTCCAGTGGCAGACACAACTTTAAAAAAAGATGGGGCGGAGATGCTAACTTCATAAGAAGAAC[T/C]
GAACGCAACATATATCATATTTATATTTCAATCGTATAAAAATATAGTATAATTAATAAATCAAGGCAAACAAGAACATTCAAGATAATACCTTTTATTT

Reverse complement sequence

AAATAAAAGGTATTATCTTGAATGTTCTTGTTTGCCTTGATTTATTAATTATACTATATTTTTATACGATTGAAATATAAATATGATATATGTTGCGTTC[A/G]
GTTCTTCTTATGAAGTTAGCATCTCCGCCCCATCTTTTTTTAAAGTTGTGTCTGCCACTGGACCTGTTCATGCGTAACAACTTACATTTGCATTCTCTCT

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	37.20%	37.10%	0.44%	25.29%	NA
All Indica	2759	57.40%	5.20%	0.58%	36.86%	NA
All Japonica	1512	2.40%	96.60%	0.00%	0.99%	NA
Aus	269	42.40%	3.70%	1.12%	52.79%	NA
Indica I	595	54.10%	2.90%	0.84%	42.18%	NA
Indica II	465	27.50%	10.50%	0.43%	61.51%	NA
Indica III	913	73.20%	1.90%	0.11%	24.86%	NA
Indica Intermediate	786	59.20%	7.60%	1.02%	32.19%	NA
Temperate Japonica	767	1.20%	98.40%	0.00%	0.39%	NA
Tropical Japonica	504	1.80%	97.60%	0.00%	0.60%	NA
Japonica Intermediate	241	7.50%	88.80%	0.00%	3.73%	NA
VI/Aromatic	96	10.40%	82.30%	0.00%	7.29%	NA
Intermediate	90	17.80%	64.40%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219269007	T -> C	LOC_Os12g31960.1	downstream_gene_variant ; 4765.0bp to feature; MODIFIER	silent_mutation	Average:21.887; most accessible tissue: Callus, score: 68.509	N	N	N	N
vg1219269007	T -> C	LOC_Os12g31960-LOC_Os12g31980	intergenic_region ; MODIFIER	silent_mutation	Average:21.887; most accessible tissue: Callus, score: 68.509	N	N	N	N
vg1219269007	T -> DEL	N	N	silent_mutation	Average:21.887; most accessible tissue: Callus, score: 68.509	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219269007	4.61E-06	NA	mr1116	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