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Detailed information for vg0121835067:

Variant ID: vg0121835067 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21835067
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTTGAAAAGCAATATCTCATAAGATATGTATTATTTTTAAAACCGTTCTCACAATGATGCTATAGTGTTACTGCATGTGGAGGATATATGGGTTAAT[A/G]
TCTCACATGCTAAATATATTTGTTACTACACAAAAGTGGAGTGTTACTGCAAAGGCAGGTACACGTTACCATATGTTTATACAGTAACACTATCCAAAAA

Reverse complement sequence

TTTTTGGATAGTGTTACTGTATAAACATATGGTAACGTGTACCTGCCTTTGCAGTAACACTCCACTTTTGTGTAGTAACAAATATATTTAGCATGTGAGA[T/C]
ATTAACCCATATATCCTCCACATGCAGTAACACTATAGCATCATTGTGAGAACGGTTTTAAAAATAATACATATCTTATGAGATATTGCTTTTCAAATAT

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	40.50%	37.70%	4.61%	17.14%	NA
All Indica	2759	7.70%	60.10%	6.34%	25.88%	NA
All Japonica	1512	99.40%	0.40%	0.00%	0.20%	NA
Aus	269	32.70%	23.40%	14.50%	29.37%	NA
Indica I	595	0.70%	92.30%	1.51%	5.55%	NA
Indica II	465	3.20%	88.80%	2.37%	5.59%	NA
Indica III	913	6.90%	30.10%	10.62%	52.35%	NA
Indica Intermediate	786	16.50%	53.60%	7.38%	22.52%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	1.70%	0.00%	0.41%	NA
VI/Aromatic	96	65.60%	24.00%	3.12%	7.29%	NA
Intermediate	90	54.40%	36.70%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121835067	A -> G	LOC_Os01g38900.1	downstream_gene_variant ; 2559.0bp to feature; MODIFIER	silent_mutation	Average:22.089; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0121835067	A -> G	LOC_Os01g38890-LOC_Os01g38900	intergenic_region ; MODIFIER	silent_mutation	Average:22.089; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0121835067	A -> DEL	N	N	silent_mutation	Average:22.089; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121835067	6.09E-07	7.59E-12	mr1151	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
vg0121835067	NA	1.82E-08	mr1249	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
vg0121835067	NA	5.54E-18	mr1148_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
vg0121835067	NA	8.36E-12	mr1781_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
vg0121835067	NA	6.17E-20	mr1922_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