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Detailed information for vg1221714747:

Variant ID: vg1221714747 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21714747
Reference Allele: C	Alternative Allele: T
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: 241. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGTACAACTAACACTGTATAAATTTAGATGACGCCTCCTCGTGCTCTCTCAAACACAACACAACACATGTTCTCAAATCTATCGTCTTTGACAACTTA[C/T]
GATGTAGGAGTGATAGAAACTAGGAATAGAAAAACAAGCCTTCTCGACCACCCTGCCTTTATTAAGATAATAATGCTTACAAGGTAGTCTCTCCGTTCCA

Reverse complement sequence

TGGAACGGAGAGACTACCTTGTAAGCATTATTATCTTAATAAAGGCAGGGTGGTCGAGAAGGCTTGTTTTTCTATTCCTAGTTTCTATCACTCCTACATC[G/A]
TAAGTTGTCAAAGACGATAGATTTGAGAACATGTGTTGTGTTGTGTTTGAGAGAGCACGAGGAGGCGTCATCTAAATTTATACAGTGTTAGTTGTACTGT

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	76.00%	24.00%	0.06%	0.00%	NA
All Indica	2759	96.80%	3.10%	0.04%	0.00%	NA
All Japonica	1512	39.20%	60.80%	0.00%	0.00%	NA
Aus	269	88.50%	11.20%	0.37%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	4.10%	0.13%	0.00%	NA
Temperate Japonica	767	29.30%	70.70%	0.00%	0.00%	NA
Tropical Japonica	504	40.10%	59.90%	0.00%	0.00%	NA
Japonica Intermediate	241	68.90%	31.10%	0.00%	0.00%	NA
VI/Aromatic	96	43.80%	56.20%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	1.11%	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
vg1221714747	C -> T	LOC_Os12g35710.1	upstream_gene_variant ; 888.0bp to feature; MODIFIER	silent_mutation	Average:39.359; most accessible tissue: Callus, score: 76.03	N	N	N	N
vg1221714747	C -> T	LOC_Os12g35710-LOC_Os12g35720	intergenic_region ; MODIFIER	silent_mutation	Average:39.359; most accessible tissue: Callus, score: 76.03	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221714747	NA	3.84E-10	mr1050_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
vg1221714747	NA	1.16E-06	mr1227_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
vg1221714747	NA	9.32E-07	mr1272_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
vg1221714747	NA	2.76E-07	mr1275_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
vg1221714747	NA	1.46E-10	mr1349_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
vg1221714747	NA	9.09E-15	mr1575_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
vg1221714747	NA	2.00E-07	mr1607_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
vg1221714747	NA	9.35E-08	mr1765_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
vg1221714747	4.96E-06	NA	mr1907_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
vg1221714747	NA	1.48E-07	mr1909_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
vg1221714747	NA	2.27E-07	mr1921_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
vg1221714747	3.82E-06	NA	mr1934_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
vg1221714747	NA	1.07E-09	mr1940_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