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Detailed information for vg1216720660:

Variant ID: vg1216720660 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16720660
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCAATCCATCCTCCAAAACTCCGCGAAATCCTTCTGCGCACCCACCGCACCGATTCCCCATCCCCTTCCAGCCATATCTCAGACCAAATTAAACCATC[T/C]
AGTTCACATTCATGGCGGAAGAGAGAGAAAGCTTCGAGAGTCAGTGGGCGCCCTCCGATGTGACGGAGGAGAATCTGAAAGAGATGGTGGCGCACGGCGT

Reverse complement sequence

ACGCCGTGCGCCACCATCTCTTTCAGATTCTCCTCCGTCACATCGGAGGGCGCCCACTGACTCTCGAAGCTTTCTCTCTCTTCCGCCATGAATGTGAACT[A/G]
GATGGTTTAATTTGGTCTGAGATATGGCTGGAAGGGGATGGGGAATCGGTGCGGTGGGTGCGCAGAAGGATTTCGCGGAGTTTTGGAGGATGGATTGGAG

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	63.80%	15.60%	2.67%	17.90%	NA
All Indica	2759	75.10%	3.20%	2.43%	19.28%	NA
All Japonica	1512	51.90%	41.70%	1.92%	4.50%	NA
Aus	269	18.20%	1.50%	5.95%	74.35%	NA
Indica I	595	49.20%	4.90%	4.37%	41.51%	NA
Indica II	465	82.60%	4.10%	3.87%	9.46%	NA
Indica III	913	88.10%	0.50%	0.66%	10.73%	NA
Indica Intermediate	786	75.20%	4.50%	2.16%	18.19%	NA
Temperate Japonica	767	17.90%	75.60%	1.30%	5.22%	NA
Tropical Japonica	504	93.50%	1.40%	2.58%	2.58%	NA
Japonica Intermediate	241	73.40%	17.80%	2.49%	6.22%	NA
VI/Aromatic	96	59.40%	0.00%	7.29%	33.33%	NA
Intermediate	90	57.80%	18.90%	7.78%	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
vg1216720660	T -> C	LOC_Os12g28280.1	upstream_gene_variant ; 12.0bp to feature; MODIFIER	silent_mutation	Average:18.021; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1216720660	T -> C	LOC_Os12g28270-LOC_Os12g28280	intergenic_region ; MODIFIER	silent_mutation	Average:18.021; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1216720660	T -> DEL	N	N	silent_mutation	Average:18.021; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216720660	NA	2.08E-08	mr1084_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
vg1216720660	NA	2.80E-07	mr1205_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
vg1216720660	NA	7.52E-07	mr1302_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
vg1216720660	NA	1.99E-07	mr1418_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
vg1216720660	NA	2.13E-06	mr1419_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
vg1216720660	NA	8.82E-07	mr1488_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
vg1216720660	4.40E-06	4.39E-06	mr1777_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
vg1216720660	NA	3.66E-07	mr1824_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