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Detailed information for vg0620734924:

Variant ID: vg0620734924 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20734924
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTCACCAACATTCTATAATAAGCTACAGGGAACTGAAACAAGATACGACCAATTGTTTCCTTCTTTTGACATACTCCAAAACCATCCTAATTTCCAC[A/G]
ACTAAGTGAACTGCGCAAGGTAAACTATCTCTATCTACCATAAACAAAAAAAAGTTTTATCTTTAGAGATCTAGGGTCTGTATTTAGGGACCTTGTGTGA

Reverse complement sequence

TCACACAAGGTCCCTAAATACAGACCCTAGATCTCTAAAGATAAAACTTTTTTTTGTTTATGGTAGATAGAGATAGTTTACCTTGCGCAGTTCACTTAGT[T/C]
GTGGAAATTAGGATGGTTTTGGAGTATGTCAAAAGAAGGAAACAATTGGTCGTATCTTGTTTCAGTTCCCTGTAGCTTATTATAGAATGTTGGTGAGTTG

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	42.80%	15.40%	0.59%	41.18%	NA
All Indica	2759	5.70%	24.90%	0.91%	68.47%	NA
All Japonica	1512	97.40%	0.80%	0.07%	1.79%	NA
Aus	269	92.20%	6.70%	0.00%	1.12%	NA
Indica I	595	3.00%	4.20%	1.34%	91.43%	NA
Indica II	465	6.70%	31.80%	1.08%	60.43%	NA
Indica III	913	3.20%	39.90%	0.11%	56.85%	NA
Indica Intermediate	786	10.20%	19.10%	1.40%	69.34%	NA
Temperate Japonica	767	97.10%	1.30%	0.13%	1.43%	NA
Tropical Japonica	504	97.20%	0.20%	0.00%	2.58%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	94.80%	0.00%	1.04%	4.17%	NA
Intermediate	90	60.00%	13.30%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620734924	A -> G	LOC_Os06g35540.1	upstream_gene_variant ; 3153.0bp to feature; MODIFIER	silent_mutation	Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461	N	N	N	N
vg0620734924	A -> G	LOC_Os06g35550.1	downstream_gene_variant ; 1001.0bp to feature; MODIFIER	silent_mutation	Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461	N	N	N	N
vg0620734924	A -> G	LOC_Os06g35540-LOC_Os06g35550	intergenic_region ; MODIFIER	silent_mutation	Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461	N	N	N	N
vg0620734924	A -> DEL	N	N	silent_mutation	Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620734924	NA	1.83E-06	mr1184_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
vg0620734924	NA	1.53E-06	mr1278_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
vg0620734924	NA	2.17E-07	mr1329_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
vg0620734924	NA	1.30E-06	mr1418_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
vg0620734924	3.23E-07	3.12E-07	mr1471_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
vg0620734924	NA	9.11E-07	mr1488_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
vg0620734924	NA	6.97E-08	mr1524_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
vg0620734924	1.75E-06	1.75E-06	mr1663_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
vg0620734924	NA	7.12E-08	mr1690_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
vg0620734924	NA	1.85E-06	mr1754_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
vg0620734924	NA	9.38E-06	mr1779_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
vg0620734924	1.03E-06	4.35E-07	mr1812_2	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
vg0620734924	3.08E-07	3.08E-07	mr1812_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
vg0620734924	2.91E-06	NA	mr1832_2	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
vg0620734924	2.34E-06	2.34E-06	mr1832_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
vg0620734924	4.40E-06	NA	mr1833_2	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
vg0620734924	1.33E-06	1.33E-06	mr1833_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
vg0620734924	2.18E-06	8.76E-06	mr1834_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
vg0620734924	3.01E-06	NA	mr1843_2	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
vg0620734924	2.58E-06	2.58E-06	mr1843_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
vg0620734924	3.86E-06	3.86E-06	mr1847_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