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Detailed information for vg1206852097:

Variant ID: vg1206852097 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6852097
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGAGGCAAAACCTAGAAGAAACCCTTCATCACACCGACTTTCAAATTTGGTTAGTCTAACACCCTTTCGGTGAATATAACACTTGCAACCAAAAACTC[A/G]
AAAATAGGCAACATTTGGCTTCCTCCCAACAATTAGCTCATAGGAAGTCTTTTTCAAGAGACGATGCAAATAAAGCCTATTGGTTGCATGGCAAGCGGTG

Reverse complement sequence

CACCGCTTGCCATGCAACCAATAGGCTTTATTTGCATCGTCTCTTGAAAAAGACTTCCTATGAGCTAATTGTTGGGAGGAAGCCAAATGTTGCCTATTTT[T/C]
GAGTTTTTGGTTGCAAGTGTTATATTCACCGAAAGGGTGTTAGACTAACCAAATTTGAAAGTCGGTGTGATGAAGGGTTTCTTCTAGGTTTTGCCTCAAA

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	77.70%	0.80%	0.30%	21.22%	NA
All Indica	2759	98.90%	0.10%	0.25%	0.80%	NA
All Japonica	1512	39.40%	0.30%	0.40%	59.99%	NA
Aus	269	85.90%	1.10%	0.37%	12.64%	NA
Indica I	595	99.20%	0.00%	0.17%	0.67%	NA
Indica II	465	98.30%	0.00%	0.00%	1.72%	NA
Indica III	913	99.20%	0.10%	0.44%	0.22%	NA
Indica Intermediate	786	98.60%	0.10%	0.25%	1.02%	NA
Temperate Japonica	767	44.10%	0.30%	0.39%	55.28%	NA
Tropical Japonica	504	25.20%	0.00%	0.40%	74.40%	NA
Japonica Intermediate	241	53.90%	0.80%	0.41%	44.81%	NA
VI/Aromatic	96	56.20%	22.90%	0.00%	20.83%	NA
Intermediate	90	72.20%	5.60%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206852097	A -> DEL	N	N	silent_mutation	Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1206852097	A -> G	LOC_Os12g12440.1	upstream_gene_variant ; 3765.0bp to feature; MODIFIER	silent_mutation	Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1206852097	A -> G	LOC_Os12g12450.1	intron_variant ; MODIFIER	silent_mutation	Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206852097	NA	4.00E-06	mr1460	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
vg1206852097	4.27E-06	NA	mr1576	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
vg1206852097	7.57E-06	NA	mr1824	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