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Detailed information for vg0213031762:

Variant ID: vg0213031762 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 13031762
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGGGAGAATTTTTTTTTAATTCTCTTTGCTTTAAATCATTAACAGGACATTCAGAGGAATATTCAGAGCAGATAAAGTAATAATGTTAAGTTAAAATG[C/A]
CAGGAATTGAATTAATAATTTTTTCCTCTCCCTCCTTTGGTCGAGAACCATCCCCGGCTCACTCTCCCCGTTCGTGGTTCGTCGTAAACGCCAACCCCTT

Reverse complement sequence

AAGGGGTTGGCGTTTACGACGAACCACGAACGGGGAGAGTGAGCCGGGGATGGTTCTCGACCAAAGGAGGGAGAGGAAAAAATTATTAATTCAATTCCTG[G/T]
CATTTTAACTTAACATTATTACTTTATCTGCTCTGAATATTCCTCTGAATGTCCTGTTAATGATTTAAAGCAAAGAGAATTAAAAAAAAATTCTCCCTGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.30%	37.60%	0.08%	0.00%	NA
All Indica	2759	96.90%	3.00%	0.11%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	75.50%	24.50%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	97.30%	2.60%	0.11%	0.00%	NA
Indica Intermediate	786	94.40%	5.50%	0.13%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	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
vg0213031762	C -> A	LOC_Os02g21910.1	upstream_gene_variant ; 1714.0bp to feature; MODIFIER	silent_mutation	Average:72.603; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0213031762	C -> A	LOC_Os02g21910-LOC_Os02g21920	intergenic_region ; MODIFIER	silent_mutation	Average:72.603; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0213031762	NA	8.95E-38	mr1064	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
vg0213031762	NA	5.65E-40	mr1534	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
vg0213031762	NA	5.01E-75	mr1536	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
vg0213031762	NA	5.97E-66	mr1538	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
vg0213031762	NA	1.50E-33	mr1733	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
vg0213031762	NA	2.56E-52	mr1795	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
vg0213031762	NA	4.81E-39	mr1890	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
vg0213031762	NA	1.35E-38	mr1264_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
vg0213031762	NA	2.78E-94	mr1536_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
vg0213031762	NA	1.28E-06	mr1727_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
vg0213031762	NA	1.57E-61	mr1733_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
vg0213031762	NA	3.04E-35	mr1888_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