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Detailed information for vg0700645458:

Variant ID: vg0700645458 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 645458
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAAAATTCCTAACCCCAAACCGGGTCCACCATGGACATGTACGTATTACTATATGTATACGTACATTTCTTTAAGGATAGTACGTACGTACGTACTT[G/C]
CACCCCTTCTTCCCTCGATTTCTTATATTTTTGCACACATTTATTCTCCTATTATCATACTTTATTAGCTAGAAAAAAAACTTTTGTGCTGAACAATTCA

Reverse complement sequence

TGAATTGTTCAGCACAAAAGTTTTTTTTCTAGCTAATAAAGTATGATAATAGGAGAATAAATGTGTGCAAAAATATAAGAAATCGAGGGAAGAAGGGGTG[C/G]
AAGTACGTACGTACGTACTATCCTTAAAGAAATGTACGTATACATATAGTAATACGTACATGTCCATGGTGGACCCGGTTTGGGGTTAGGAATTTTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.30%	28.70%	2.22%	9.84%	NA
All Indica	2759	34.90%	44.80%	3.73%	16.56%	NA
All Japonica	1512	99.30%	0.50%	0.07%	0.13%	NA
Aus	269	63.90%	35.70%	0.37%	0.00%	NA
Indica I	595	41.70%	31.10%	2.52%	24.71%	NA
Indica II	465	59.60%	37.60%	0.65%	2.15%	NA
Indica III	913	19.30%	54.00%	6.68%	20.04%	NA
Indica Intermediate	786	33.50%	48.60%	3.05%	14.89%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	1.20%	0.20%	0.40%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	0.00%	1.04%	NA
Intermediate	90	81.10%	13.30%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0700645458	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700645458	G -> C	LOC_Os07g02070.1	downstream_gene_variant ; 762.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700645458	G -> C	LOC_Os07g02060-LOC_Os07g02070	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700645458	NA	3.21E-06	mr1216	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
vg0700645458	NA	2.94E-06	mr1216	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
vg0700645458	8.88E-07	8.88E-07	mr1770	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
vg0700645458	NA	1.23E-06	mr1158_2	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