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Detailed information for vg0816681021:

Variant ID: vg0816681021 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16681021
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CGCTCGGCCTCGCGTCGTGCTTCGGTTTCCCGGGCTTGGCGTTGCTCCTCCGTCTCGTTATCGGCCATAAAGACGCCGAAATAGAGAGGGGTGTAGTTGT[C/A]
TTCTAGGCTTTCATCGAAATCGTCGAGATCCGGGTCGTTGTTGCGAAAGCCGAACTCATTGTACTCCACGATCTCGGTCGGACGCGAGTCGACGGCGGGA

Reverse complement sequence

TCCCGCCGTCGACTCGCGTCCGACCGAGATCGTGGAGTACAATGAGTTCGGCTTTCGCAACAACGACCCGGATCTCGACGATTTCGATGAAAGCCTAGAA[G/T]
ACAACTACACCCCTCTCTATTTCGGCGTCTTTATGGCCGATAACGAGACGGAGGAGCAACGCCAAGCCCGGGAAACCGAAGCACGACGCGAGGCCGAGCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.90%	14.90%	23.61%	27.59%	NA
All Indica	2759	21.50%	1.20%	32.80%	44.47%	NA
All Japonica	1512	56.50%	36.80%	3.44%	3.24%	NA
Aus	269	42.40%	0.40%	52.04%	5.20%	NA
Indica I	595	11.90%	0.20%	32.94%	54.96%	NA
Indica II	465	18.10%	3.00%	34.62%	44.30%	NA
Indica III	913	31.20%	0.30%	33.19%	35.27%	NA
Indica Intermediate	786	19.60%	1.90%	31.17%	47.33%	NA
Temperate Japonica	767	68.10%	30.60%	0.52%	0.78%	NA
Tropical Japonica	504	38.30%	45.60%	7.94%	8.13%	NA
Japonica Intermediate	241	58.10%	37.80%	3.32%	0.83%	NA
VI/Aromatic	96	7.30%	91.70%	0.00%	1.04%	NA
Intermediate	90	36.70%	27.80%	21.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816681021	C -> A	LOC_Os08g27310.1	upstream_gene_variant ; 3062.0bp to feature; MODIFIER	silent_mutation	Average:47.543; most accessible tissue: Minghui63 young leaf, score: 82.642	N	N	N	N
vg0816681021	C -> A	LOC_Os08g27330.1	upstream_gene_variant ; 4361.0bp to feature; MODIFIER	silent_mutation	Average:47.543; most accessible tissue: Minghui63 young leaf, score: 82.642	N	N	N	N
vg0816681021	C -> A	LOC_Os08g27320.1	intron_variant ; MODIFIER	silent_mutation	Average:47.543; most accessible tissue: Minghui63 young leaf, score: 82.642	N	N	N	N
vg0816681021	C -> DEL	N	N	silent_mutation	Average:47.543; most accessible tissue: Minghui63 young leaf, score: 82.642	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816681021	6.63E-06	NA	mr1037	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
vg0816681021	9.00E-06	NA	mr1080_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