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Detailed information for vg0809709071:

Variant ID: vg0809709071 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9709071
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATACAGTAGCGAAGAGATAAGCAGGAGGCACAGGCGACGCCACCCCTGGCCTCTATAAAAGGAGACGTTGGCCTTCACTCCGGGGAGACAGAACCAC[G/A]
AAGACACCATTCAGAGAAAAGCTTCCAAGCGCGCTCTCACCCTCCATTCCATCTTTCTTAGTAGTAGTTCCTCTAGCCTACCTTGCATAATATATATTGA

Reverse complement sequence

TCAATATATATTATGCAAGGTAGGCTAGAGGAACTACTACTAAGAAAGATGGAATGGAGGGTGAGAGCGCGCTTGGAAGCTTTTCTCTGAATGGTGTCTT[C/T]
GTGGTTCTGTCTCCCCGGAGTGAAGGCCAACGTCTCCTTTTATAGAGGCCAGGGGTGGCGTCGCCTGTGCCTCCTGCTTATCTCTTCGCTACTGTATCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	41.20%	11.47%	4.87%	NA
All Indica	2759	65.70%	22.60%	11.27%	0.40%	NA
All Japonica	1512	2.40%	82.90%	0.99%	13.76%	NA
Aus	269	42.80%	3.70%	53.16%	0.37%	NA
Indica I	595	82.90%	16.80%	0.34%	0.00%	NA
Indica II	465	47.10%	17.40%	34.19%	1.29%	NA
Indica III	913	64.30%	27.70%	7.89%	0.11%	NA
Indica Intermediate	786	65.40%	24.20%	9.92%	0.51%	NA
Temperate Japonica	767	2.00%	94.30%	1.30%	2.48%	NA
Tropical Japonica	504	2.40%	65.70%	0.20%	31.75%	NA
Japonica Intermediate	241	3.70%	82.60%	1.66%	12.03%	NA
VI/Aromatic	96	12.50%	12.50%	66.67%	8.33%	NA
Intermediate	90	33.30%	54.40%	10.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809709071	G -> A	LOC_Os08g15940.1	upstream_gene_variant ; 2852.0bp to feature; MODIFIER	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0809709071	G -> A	LOC_Os08g15960.1	upstream_gene_variant ; 1882.0bp to feature; MODIFIER	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0809709071	G -> A	LOC_Os08g15930.1	downstream_gene_variant ; 4932.0bp to feature; MODIFIER	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0809709071	G -> A	LOC_Os08g15950.1	downstream_gene_variant ; 787.0bp to feature; MODIFIER	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0809709071	G -> A	LOC_Os08g15950-LOC_Os08g15960	intergenic_region ; MODIFIER	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0809709071	G -> DEL	N	N	silent_mutation	Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809709071	NA	1.16E-10	mr1595_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
vg0809709071	NA	8.65E-12	mr1600_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