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Detailed information for vg0120024417:

Variant ID: vg0120024417 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 20024417
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATAATTAAGGCTTTTTCTTTTATAGTAAAAACACAGAGAATCTTCTAAAATCATAAGTAATTCATCCGAGCTCTGATTAAGTCCATTCAAGTCTCA[G/A]
TAAATTCATAAAAACGTATAGAATCCATTAAAAATGGTTTTGTTTCCTGTTTCAGTAGTCTTATAGCATGTTTTGCTTGTGTGCTTTGTTTGTCGCGTAG

Reverse complement sequence

CTACGCGACAAACAAAGCACACAAGCAAAACATGCTATAAGACTACTGAAACAGGAAACAAAACCATTTTTAATGGATTCTATACGTTTTTATGAATTTA[C/T]
TGAGACTTGAATGGACTTAATCAGAGCTCGGATGAATTACTTATGATTTTAGAAGATTCTCTGTGTTTTTACTATAAAAGAAAAAGCCTTAATTATTTAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	6.90%	0.47%	0.00%	NA
All Indica	2759	87.70%	11.70%	0.65%	0.00%	NA
All Japonica	1512	99.80%	0.00%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	56.60%	40.90%	2.58%	0.00%	NA
Indica III	913	98.40%	1.60%	0.00%	0.00%	NA
Indica Intermediate	786	84.90%	14.50%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0120024417	G -> A	LOC_Os01g36200.1	upstream_gene_variant ; 977.0bp to feature; MODIFIER	silent_mutation	Average:50.707; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0120024417	G -> A	LOC_Os01g36200-LOC_Os01g36220	intergenic_region ; MODIFIER	silent_mutation	Average:50.707; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0120024417	NA	2.97E-08	mr1174	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
vg0120024417	NA	6.74E-07	mr1231	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
vg0120024417	1.76E-06	1.76E-06	mr1362	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
vg0120024417	NA	1.15E-07	mr1557	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
vg0120024417	NA	8.38E-14	mr1565	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
vg0120024417	NA	8.08E-12	mr1565	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
vg0120024417	NA	3.15E-06	mr1771	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
vg0120024417	NA	8.68E-10	mr1327_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
vg0120024417	NA	1.15E-07	mr1557_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
vg0120024417	NA	4.76E-13	mr1565_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
vg0120024417	NA	5.72E-11	mr1565_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
vg0120024417	NA	4.57E-11	mr1598_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