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Detailed information for vg1216463200:

Variant ID: vg1216463200 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16463200
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.13, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TCGTTCGTTGTAATTATTGTGCTCCTCATGGCTGTCCAAGGTAACAATTTATTTCTGCAATTTTTTATGTTGGTAACTACTTCCCTCTCCGTCAAAGGCT[A/G]
CAGTTTTAACCCAAAAATTTGTTCCATGAAGATTGTAATTTTAGAGTGACCTAATTCTTTTCTCTCTAATACTATCTCATCATTTCTTCTCGTTTTAACC

Reverse complement sequence

GGTTAAAACGAGAAGAAATGATGAGATAGTATTAGAGAGAAAAGAATTAGGTCACTCTAAAATTACAATCTTCATGGAACAAATTTTTGGGTTAAAACTG[T/C]
AGCCTTTGACGGAGAGGGAAGTAGTTACCAACATAAAAAATTGCAGAAATAAATTGTTACCTTGGACAGCCATGAGGAGCACAATAATTACAACGAACGA

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	50.00%	36.60%	0.34%	13.14%	NA
All Indica	2759	32.80%	53.60%	0.29%	13.30%	NA
All Japonica	1512	79.40%	11.80%	0.40%	8.40%	NA
Aus	269	62.80%	10.80%	0.37%	26.02%	NA
Indica I	595	21.80%	73.80%	0.34%	4.03%	NA
Indica II	465	70.50%	20.00%	0.22%	9.25%	NA
Indica III	913	16.00%	61.90%	0.11%	22.02%	NA
Indica Intermediate	786	38.40%	48.50%	0.51%	12.60%	NA
Temperate Japonica	767	91.10%	2.10%	0.52%	6.26%	NA
Tropical Japonica	504	62.70%	27.60%	0.20%	9.52%	NA
Japonica Intermediate	241	76.80%	10.00%	0.41%	12.86%	NA
VI/Aromatic	96	29.20%	15.60%	1.04%	54.17%	NA
Intermediate	90	64.40%	30.00%	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
vg1216463200	A -> DEL	N	N	silent_mutation	Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg1216463200	A -> G	LOC_Os12g27920.1	downstream_gene_variant ; 4812.0bp to feature; MODIFIER	silent_mutation	Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg1216463200	A -> G	LOC_Os12g27930.1	intron_variant ; MODIFIER	silent_mutation	Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216463200	1.33E-07	NA	mr1018	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
vg1216463200	7.79E-06	NA	mr1055	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
vg1216463200	1.90E-07	NA	mr1132	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
vg1216463200	1.83E-07	NA	mr1132	Jap_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
vg1216463200	3.74E-07	NA	mr1178	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
vg1216463200	3.74E-06	NA	mr1178	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
vg1216463200	5.77E-08	NA	mr1390	Jap_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
vg1216463200	2.72E-07	NA	mr1490	Jap_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
vg1216463200	1.08E-06	NA	mr1055_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
vg1216463200	7.42E-06	NA	mr1132_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
vg1216463200	5.84E-06	NA	mr1390_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
vg1216463200	7.31E-06	NA	mr1390_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
vg1216463200	1.58E-06	NA	mr1489_2	Jap_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
vg1216463200	NA	6.72E-06	mr1874_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