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Detailed information for vg0716242647:

Variant ID: vg0716242647 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16242647
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGGGTCTAGTACCAGGGGGTACCGCCTCGGGTGGACCACTCGGTCGGGATGATCCGAGCGGTCGAACTTAATTGCTATCTCTGACCACCGAAGATATT[A/G]
GGGCGTGTTAGGCTGAACCGCATTGATCTCCCATTCTGTTAGCTTCTGCTTTCTCTTAGATTCATAAGCTAGGGGTCCGCCGAAGATGTGATTGAGTTCT

Reverse complement sequence

AGAACTCAATCACATCTTCGGCGGACCCCTAGCTTATGAATCTAAGAGAAAGCAGAAGCTAACAGAATGGGAGATCAATGCGGTTCAGCCTAACACGCCC[T/C]
AATATCTTCGGTGGTCAGAGATAGCAATTAAGTTCGACCGCTCGGATCATCCCGACCGAGTGGTCCACCCGAGGCGGTACCCCCTGGTACTAGACCCAGT

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	37.90%	22.40%	18.26%	21.46%	NA
All Indica	2759	5.80%	27.60%	30.48%	36.10%	NA
All Japonica	1512	97.60%	1.90%	0.26%	0.26%	NA
Aus	269	8.60%	90.30%	1.12%	0.00%	NA
Indica I	595	3.70%	42.50%	18.32%	35.46%	NA
Indica II	465	6.50%	14.00%	23.23%	56.34%	NA
Indica III	913	2.40%	19.30%	49.62%	28.70%	NA
Indica Intermediate	786	10.90%	34.10%	21.76%	33.21%	NA
Temperate Japonica	767	96.20%	3.10%	0.13%	0.52%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	55.60%	12.20%	16.67%	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
vg0716242647	A -> DEL	N	N	silent_mutation	Average:9.797; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N
vg0716242647	A -> G	LOC_Os07g27820.1	downstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:9.797; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N
vg0716242647	A -> G	LOC_Os07g27834.1	intron_variant ; MODIFIER	silent_mutation	Average:9.797; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716242647	1.88E-06	6.36E-06	mr1528_2	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