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Detailed information for vg1218022863:

Variant ID: vg1218022863 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18022863
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAAATTGTTATCTGCATCTATATATAGTTGGTGGAGACGCCAGAATTATCTAAAGAAAATCAGAATGCCTTGAAAAAAAAAGAGAGGTACACGAGGGT[G/A]
GGAATGAGATGTATTCAGGAAACAGGTGACAAGAACAAGATTCATTGTGGATCAAGTAGGATCGGAAGGTCAACATGACCTGATTGATTGCCAACATATG

Reverse complement sequence

CATATGTTGGCAATCAATCAGGTCATGTTGACCTTCCGATCCTACTTGATCCACAATGAATCTTGTTCTTGTCACCTGTTTCCTGAATACATCTCATTCC[C/T]
ACCCTCGTGTACCTCTCTTTTTTTTTCAAGGCATTCTGATTTTCTTTAGATAATTCTGGCGTCTCCACCAACTATATATAGATGCAGATAACAATTTGAT

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	81.90%	18.00%	0.08%	0.00%	NA
All Indica	2759	71.90%	28.00%	0.14%	0.00%	NA
All Japonica	1512	95.20%	4.80%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	41.00%	58.80%	0.17%	0.00%	NA
Indica II	465	85.80%	14.00%	0.22%	0.00%	NA
Indica III	913	85.30%	14.70%	0.00%	0.00%	NA
Indica Intermediate	786	71.40%	28.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	95.80%	4.20%	0.00%	0.00%	NA
Japonica Intermediate	241	79.30%	20.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg1218022863	G -> A	LOC_Os12g30080-LOC_Os12g30100	intergenic_region ; MODIFIER	silent_mutation	Average:60.599; most accessible tissue: Zhenshan97 flower, score: 86.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218022863	NA	2.93E-06	mr1029	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
vg1218022863	NA	4.20E-06	mr1189	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
vg1218022863	2.72E-06	2.94E-06	mr1471	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
vg1218022863	NA	2.66E-06	mr1502	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
vg1218022863	NA	7.34E-06	mr1502	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
vg1218022863	NA	1.75E-06	mr1625	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
vg1218022863	1.92E-08	NA	mr1645	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
vg1218022863	2.99E-06	5.73E-06	mr1645	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
vg1218022863	1.80E-08	NA	mr1647	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
vg1218022863	2.63E-06	1.73E-06	mr1647	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
vg1218022863	9.96E-07	NA	mr1682	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
vg1218022863	4.55E-06	NA	mr1722	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
vg1218022863	NA	8.90E-07	mr1734	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
vg1218022863	1.32E-06	NA	mr1815	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
vg1218022863	4.12E-06	2.62E-06	mr1815	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