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Detailed information for vg0704638070:

Variant ID: vg0704638070 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4638070
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TCGTCTTCCTTCGGCAGGTAGTCTTCGCCTTGCACCCTTCGCCTGAAACGCCTCTGGCCTGGCAAGGCACTCGTACGACTCTTCGCCTCACGCCGTTCTT[A/G]
CTCCATAGCCTTCGCCACGGGTTTCGGCAGATTTAGTCGAAGGGCCTCATGCCATCCGCCAACAATGATGTTAATATGCACGATTCTAATCTATCAACTT

Reverse complement sequence

AAGTTGATAGATTAGAATCGTGCATATTAACATCATTGTTGGCGGATGGCATGAGGCCCTTCGACTAAATCTGCCGAAACCCGTGGCGAAGGCTATGGAG[T/C]
AAGAACGGCGTGAGGCGAAGAGTCGTACGAGTGCCTTGCCAGGCCAGAGGCGTTTCAGGCGAAGGGTGCAAGGCGAAGACTACCTGCCGAAGGAAGACGA

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	32.40%	10.50%	15.83%	41.28%	NA
All Indica	2759	2.00%	3.60%	25.66%	68.76%	NA
All Japonica	1512	75.40%	24.00%	0.26%	0.33%	NA
Aus	269	74.00%	6.30%	8.18%	11.52%	NA
Indica I	595	0.50%	3.00%	20.34%	76.13%	NA
Indica II	465	2.60%	3.20%	18.28%	75.91%	NA
Indica III	913	1.60%	3.00%	32.64%	62.76%	NA
Indica Intermediate	786	3.30%	4.80%	25.95%	65.90%	NA
Temperate Japonica	767	64.40%	34.90%	0.26%	0.39%	NA
Tropical Japonica	504	91.70%	7.70%	0.40%	0.20%	NA
Japonica Intermediate	241	76.30%	23.20%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	46.70%	18.90%	15.56%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0704638070	A -> DEL	N	N	silent_mutation	Average:19.585; most accessible tissue: Callus, score: 47.155	N	N	N	N
vg0704638070	A -> G	LOC_Os07g08910.1	upstream_gene_variant ; 3324.0bp to feature; MODIFIER	silent_mutation	Average:19.585; most accessible tissue: Callus, score: 47.155	N	N	N	N
vg0704638070	A -> G	LOC_Os07g08920.1	upstream_gene_variant ; 559.0bp to feature; MODIFIER	silent_mutation	Average:19.585; most accessible tissue: Callus, score: 47.155	N	N	N	N
vg0704638070	A -> G	LOC_Os07g08930.1	upstream_gene_variant ; 4439.0bp to feature; MODIFIER	silent_mutation	Average:19.585; most accessible tissue: Callus, score: 47.155	N	N	N	N
vg0704638070	A -> G	LOC_Os07g08920-LOC_Os07g08930	intergenic_region ; MODIFIER	silent_mutation	Average:19.585; most accessible tissue: Callus, score: 47.155	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704638070	NA	2.07E-08	mr1756	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
vg0704638070	NA	5.60E-15	mr1883	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