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Detailed information for vg0816750102:

Variant ID: vg0816750102 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16750102
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGGCGGCGTACTCACCTCCCAGATCCGGACGCGACCCTTCCCTCCCCTCACCCCCCGGATCCAGCAGCTCCCCTCTCCACCCTCTCCCTTCCAAAACC[C/A]
TAACCGAGAGGGGAGGGCGGCGGTGGGTTGGGCTGGGGCGCCGAATTTTTATACGCTTAAAAATATTTTCGCAAGCAGGTGGATTTAGCCGCCTGCAATA

Reverse complement sequence

TATTGCAGGCGGCTAAATCCACCTGCTTGCGAAAATATTTTTAAGCGTATAAAAATTCGGCGCCCCAGCCCAACCCACCGCCGCCCTCCCCTCTCGGTTA[G/T]
GGTTTTGGAAGGGAGAGGGTGGAGAGGGGAGCTGCTGGATCCGGGGGGTGAGGGGAGGGAAGGGTCGCGTCCGGATCTGGGAGGTGAGTACGCCGCCGCC

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	42.70%	28.70%	3.39%	25.22%	NA
All Indica	2759	16.80%	35.70%	5.65%	41.83%	NA
All Japonica	1512	88.20%	10.40%	0.07%	1.32%	NA
Aus	269	28.30%	69.90%	0.74%	1.12%	NA
Indica I	595	13.90%	68.60%	2.52%	14.96%	NA
Indica II	465	28.40%	11.20%	9.03%	51.40%	NA
Indica III	913	9.40%	26.40%	5.37%	58.82%	NA
Indica Intermediate	786	20.70%	36.10%	6.36%	36.77%	NA
Temperate Japonica	767	98.60%	0.30%	0.13%	1.04%	NA
Tropical Japonica	504	69.80%	28.20%	0.00%	1.98%	NA
Japonica Intermediate	241	93.80%	5.40%	0.00%	0.83%	NA
VI/Aromatic	96	94.80%	4.20%	0.00%	1.04%	NA
Intermediate	90	61.10%	22.20%	1.11%	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
vg0816750102	C -> A	LOC_Os08g27430.1	downstream_gene_variant ; 3760.0bp to feature; MODIFIER	silent_mutation	Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg0816750102	C -> A	LOC_Os08g27440.1	intron_variant ; MODIFIER	silent_mutation	Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N
vg0816750102	C -> DEL	N	N	silent_mutation	Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816750102	NA	1.21E-06	mr1071	Ind_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
vg0816750102	NA	4.27E-06	mr1080	Ind_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
vg0816750102	NA	3.09E-06	mr1203	Ind_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
vg0816750102	8.28E-06	7.81E-08	mr1395	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
vg0816750102	NA	6.34E-06	mr1618	Ind_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
vg0816750102	NA	1.67E-08	mr1613_2	Ind_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