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Detailed information for vg0218033645:

Variant ID: vg0218033645 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 18033645
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCAGACCAGCGTGTATCGAGCAGTCAGACCGGCTAGCCTATGGTCTGACCGGCTGATTCTGTGTCGGTTTCGGTTTCGGGTTGGTTTGTTGGATATCC[G/A]
TGGATAATTCATGTTTATGACTTCAAGATAGATACTATGCGTATGTAATACTGCTATGTGCTAACAATGAGTCAAGTTGGTAAGAACTTGTACTTGGATA

Reverse complement sequence

TATCCAAGTACAAGTTCTTACCAACTTGACTCATTGTTAGCACATAGCAGTATTACATACGCATAGTATCTATCTTGAAGTCATAAACATGAATTATCCA[C/T]
GGATATCCAACAAACCAACCCGAAACCGAAACCGACACAGAATCAGCCGGTCAGACCATAGGCTAGCCGGTCTGACTGCTCGATACACGCTGGTCTGACC

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	65.80%	34.00%	0.13%	0.15%	NA
All Indica	2759	62.00%	37.60%	0.18%	0.25%	NA
All Japonica	1512	67.80%	32.20%	0.00%	0.00%	NA
Aus	269	81.00%	19.00%	0.00%	0.00%	NA
Indica I	595	79.20%	20.70%	0.17%	0.00%	NA
Indica II	465	80.20%	19.40%	0.00%	0.43%	NA
Indica III	913	31.80%	67.70%	0.33%	0.22%	NA
Indica Intermediate	786	73.30%	26.20%	0.13%	0.38%	NA
Temperate Japonica	767	95.20%	4.80%	0.00%	0.00%	NA
Tropical Japonica	504	28.80%	71.20%	0.00%	0.00%	NA
Japonica Intermediate	241	62.20%	37.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg0218033645	G -> A	LOC_Os02g30300-LOC_Os02g30310	intergenic_region ; MODIFIER	silent_mutation	Average:66.643; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0218033645	G -> DEL	N	N	silent_mutation	Average:66.643; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0218033645	2.52E-06	NA	mr1138	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
vg0218033645	3.50E-06	4.86E-08	mr1138	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
vg0218033645	NA	7.82E-06	mr1169	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
vg0218033645	NA	5.12E-06	mr1295	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
vg0218033645	NA	1.12E-10	mr1563	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
vg0218033645	NA	4.57E-15	mr1769	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
vg0218033645	2.06E-08	1.85E-13	mr1138_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
vg0218033645	1.28E-06	3.66E-09	mr1138_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
vg0218033645	NA	8.74E-06	mr1138_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
vg0218033645	NA	1.78E-11	mr1354_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
vg0218033645	NA	8.96E-08	mr1354_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
vg0218033645	NA	4.11E-14	mr1769_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
vg0218033645	NA	3.84E-09	mr1916_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