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Detailed information for vg0715576538:

Variant ID: vg0715576538 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15576538
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAAGCAAACCCGAATAAACGGAGTGGGTTTCGATTCAACTCAAGTATCCCAAGGGTCCAAGGAAGGATTGCGACAAATGGCAAGGGTTTCGGGACTTC[A/G]
ATTAGCTTAGCACCGAAATGCTTAACGAAACGGACGGAGAGGGGAGAGGTCAAGGAAGGGACATTACCCTAGGTGGCGATTCTGTAAAAACTACTGGGTT

Reverse complement sequence

AACCCAGTAGTTTTTACAGAATCGCCACCTAGGGTAATGTCCCTTCCTTGACCTCTCCCCTCTCCGTCCGTTTCGTTAAGCATTTCGGTGCTAAGCTAAT[T/C]
GAAGTCCCGAAACCCTTGCCATTTGTCGCAATCCTTCCTTGGACCCTTGGGATACTTGAGTTGAATCGAAACCCACTCCGTTTATTCGGGTTTGCTTTCC

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	72.20%	27.50%	0.23%	0.02%	NA
All Indica	2759	80.60%	19.10%	0.29%	0.04%	NA
All Japonica	1512	61.00%	38.90%	0.13%	0.00%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	88.40%	11.40%	0.17%	0.00%	NA
Indica II	465	95.10%	4.70%	0.22%	0.00%	NA
Indica III	913	71.50%	28.00%	0.44%	0.00%	NA
Indica Intermediate	786	76.70%	22.90%	0.25%	0.13%	NA
Temperate Japonica	767	31.70%	68.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.20%	0.40%	0.00%	NA
Japonica Intermediate	241	78.00%	22.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	20.00%	1.11%	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
vg0715576538	A -> DEL	N	N	silent_mutation	Average:53.607; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0715576538	A -> G	LOC_Os07g26900.1	upstream_gene_variant ; 3415.0bp to feature; MODIFIER	silent_mutation	Average:53.607; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0715576538	A -> G	LOC_Os07g26890.1	downstream_gene_variant ; 4528.0bp to feature; MODIFIER	silent_mutation	Average:53.607; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0715576538	A -> G	LOC_Os07g26890-LOC_Os07g26900	intergenic_region ; MODIFIER	silent_mutation	Average:53.607; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715576538	NA	8.31E-12	mr1229	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
vg0715576538	NA	1.11E-08	mr1539	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
vg0715576538	NA	4.11E-07	mr1621	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
vg0715576538	NA	7.84E-13	mr1732	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
vg0715576538	NA	1.04E-08	mr1763	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
vg0715576538	NA	2.46E-07	mr1880	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
vg0715576538	NA	7.14E-06	mr1975	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
vg0715576538	NA	2.80E-06	mr1582_2	Jap_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