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Detailed information for vg0801635046:

Variant ID: vg0801635046 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1635046
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCCTCATCGTCGAGTGCGTCATCGACGTCGTCGTCGCCAACGGCGGCGACGACGACACGGCGGCCGCGGCGTCCCCCCTCGCCGGCGTGCCGGCGCCG[G/A]
ACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGCGGACGTCACGTTCGACGTCAGGGGGCAACCCTTCGCCGCCCACCGGAT

Reverse complement sequence

ATCCGGTGGGCGGCGAAGGGTTGCCCCCTGACGTCGAACGTGACGTCCGCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGT[C/T]
CGGCGCCGGCACGCCGGCGAGGGGGGACGCCGCGGCCGCCGTGTCGTCGTCGCCGCCGTTGGCGACGACGACGTCGATGACGCACTCGACGATGAGGCGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.30%	19.80%	0.04%	0.78%	NA
All Indica	2759	65.30%	33.20%	0.07%	1.34%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	69.10%	28.20%	0.17%	2.52%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	43.60%	55.50%	0.11%	0.77%	NA
Indica Intermediate	786	72.90%	25.20%	0.00%	1.91%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	0.00%	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
vg0801635046	G -> A	LOC_Os08g03490.1	missense_variant ; p.Asp182Asn; MODERATE	nonsynonymous_codon ; D182N	Average:74.821; most accessible tissue: Zhenshan97 root, score: 83.59	unknown	unknown	TOLERATED	0.25
vg0801635046	G -> DEL	LOC_Os08g03490.1	N	frameshift_variant	Average:74.821; most accessible tissue: Zhenshan97 root, score: 83.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801635046	NA	4.07E-10	mr1739	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
vg0801635046	NA	7.74E-08	mr1739	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