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Detailed information for vg0406620827:

Variant ID: vg0406620827 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6620827
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCAACTGAGCTCCGGTTAGAGTTTTGCTAGCATAGCAGACTGCGTGTTGCTTTTTATCCTTAGTTTGGCCCAAGACCACACCAACAGCGAAATCGCTT[G/A]
CATCACACATGATCTCGAAGGGTAGAGTCCAATCAGGGGGTTGGATGATTGGAGCAGAGACGAGTGCCTTTTTGAGAATCTCAAAGGATTTTAGGCACAC

Reverse complement sequence

GTGTGCCTAAAATCCTTTGAGATTCTCAAAAAGGCACTCGTCTCTGCTCCAATCATCCAACCCCCTGATTGGACTCTACCCTTCGAGATCATGTGTGATG[C/T]
AAGCGATTTCGCTGTTGGTGTGGTCTTGGGCCAAACTAAGGATAAAAAGCAACACGCAGTCTGCTATGCTAGCAAAACTCTAACCGGAGCTCAGTTGAAT

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	43.20%	39.50%	0.78%	16.50%	NA
All Indica	2759	15.70%	58.80%	1.30%	24.14%	NA
All Japonica	1512	99.10%	0.50%	0.00%	0.40%	NA
Aus	269	1.10%	72.10%	0.00%	26.77%	NA
Indica I	595	1.50%	81.50%	1.34%	15.63%	NA
Indica II	465	23.70%	66.90%	0.65%	8.82%	NA
Indica III	913	26.20%	34.80%	1.31%	37.68%	NA
Indica Intermediate	786	9.70%	64.80%	1.65%	23.92%	NA
Temperate Japonica	767	99.30%	0.50%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.60%	0.00%	0.40%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	55.20%	15.60%	1.04%	28.12%	NA
Intermediate	90	57.80%	32.20%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406620827	G -> DEL	N	N	silent_mutation	Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847	N	N	N	N
vg0406620827	G -> A	LOC_Os04g12050.1	downstream_gene_variant ; 1398.0bp to feature; MODIFIER	silent_mutation	Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847	N	N	N	N
vg0406620827	G -> A	LOC_Os04g12040-LOC_Os04g12050	intergenic_region ; MODIFIER	silent_mutation	Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406620827	NA	2.29E-07	mr1071	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
vg0406620827	NA	4.42E-13	mr1239	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
vg0406620827	NA	1.93E-06	mr1613	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
vg0406620827	NA	2.75E-10	mr1071_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
vg0406620827	6.15E-06	4.51E-12	mr1613_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
vg0406620827	NA	1.26E-06	mr1619_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