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Detailed information for vg0712646803:

Variant ID: vg0712646803 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12646803
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGTGGGGGAGATATCCCAGCTTCTGACGTGCACATAATCTGAAAATTGCTGAATATTTGAACACCTAGAAGGCACCAAACTCTGCAGCAATTTGCAGA[A/G]
GGATTGGGCACCAGAGTGGTTCGGCCGAACCAAGTCTGGCCCCAAACCCTCTCAACTTTCAATGGTAAACAGGTGAGCACGTCTTTTATCTGTATATCTC

Reverse complement sequence

GAGATATACAGATAAAAGACGTGCTCACCTGTTTACCATTGAAAGTTGAGAGGGTTTGGGGCCAGACTTGGTTCGGCCGAACCACTCTGGTGCCCAATCC[T/C]
TCTGCAAATTGCTGCAGAGTTTGGTGCCTTCTAGGTGTTCAAATATTCAGCAATTTTCAGATTATGTGCACGTCAGAAGCTGGGATATCTCCCCCACACT

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	41.40%	7.00%	20.93%	30.60%	NA
All Indica	2759	9.40%	11.30%	33.71%	45.63%	NA
All Japonica	1512	96.60%	0.10%	1.65%	1.59%	NA
Aus	269	38.30%	0.40%	9.67%	51.67%	NA
Indica I	595	2.00%	2.70%	22.18%	73.11%	NA
Indica II	465	9.20%	3.90%	29.89%	56.99%	NA
Indica III	913	8.00%	20.90%	50.16%	20.92%	NA
Indica Intermediate	786	16.50%	11.10%	25.57%	46.82%	NA
Temperate Japonica	767	98.40%	0.00%	0.39%	1.17%	NA
Tropical Japonica	504	94.80%	0.40%	3.97%	0.79%	NA
Japonica Intermediate	241	94.60%	0.00%	0.83%	4.56%	NA
VI/Aromatic	96	86.50%	12.50%	1.04%	0.00%	NA
Intermediate	90	58.90%	6.70%	7.78%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712646803	A -> DEL	N	N	silent_mutation	Average:15.69; most accessible tissue: Callus, score: 38.231	N	N	N	N
vg0712646803	A -> G	LOC_Os07g22480.1	downstream_gene_variant ; 259.0bp to feature; MODIFIER	silent_mutation	Average:15.69; most accessible tissue: Callus, score: 38.231	N	N	N	N
vg0712646803	A -> G	LOC_Os07g22480-LOC_Os07g22494	intergenic_region ; MODIFIER	silent_mutation	Average:15.69; most accessible tissue: Callus, score: 38.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712646803	NA	3.36E-07	mr1205_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
vg0712646803	2.51E-06	2.51E-06	mr1643_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
vg0712646803	NA	3.34E-06	mr1954_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