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Detailed information for vg1221718597:

Variant ID: vg1221718597 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21718597
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCAAACCAAGCACGCTTAACGAGATTGGCTTCCGGAAAAGTAGTTGTAACATGTTGGTATGAGTATTCTATTAATCCTATTAAATCCTAAACCAGGAT[G/A]
TCAAATTGGGGTTATTAAATGATTTCAAATGGAAAAGTCACCAAAACCAAAGTTGTAGAACTCATCGAGGTGCAAAATTTTTATTTTGGTCATTTCTCCA

Reverse complement sequence

TGGAGAAATGACCAAAATAAAAATTTTGCACCTCGATGAGTTCTACAACTTTGGTTTTGGTGACTTTTCCATTTGAAATCATTTAATAACCCCAATTTGA[C/T]
ATCCTGGTTTAGGATTTAATAGGATTAATAGAATACTCATACCAACATGTTACAACTACTTTTCCGGAAGCCAATCTCGTTAAGCGTGCTTGGTTTGGAG

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	78.70%	19.80%	1.52%	0.00%	NA
All Indica	2759	67.60%	29.80%	2.57%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	71.70%	28.30%	0.00%	0.00%	NA
Indica I	595	41.00%	50.60%	8.40%	0.00%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	61.60%	38.20%	0.22%	0.00%	NA
Indica Intermediate	786	76.30%	21.40%	2.29%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	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
vg1221718597	G -> A	LOC_Os12g35710.1	upstream_gene_variant ; 4738.0bp to feature; MODIFIER	silent_mutation	Average:35.199; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg1221718597	G -> A	LOC_Os12g35710-LOC_Os12g35720	intergenic_region ; MODIFIER	silent_mutation	Average:35.199; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221718597	NA	2.91E-06	mr1547	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
vg1221718597	1.30E-06	NA	mr1038_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
vg1221718597	2.62E-07	NA	mr1038_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
vg1221718597	1.70E-06	NA	mr1141_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
vg1221718597	NA	5.40E-06	mr1236_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
vg1221718597	1.87E-07	NA	mr1389_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
vg1221718597	2.37E-06	NA	mr1389_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
vg1221718597	NA	5.06E-07	mr1538_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
vg1221718597	NA	4.05E-07	mr1547_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
vg1221718597	NA	2.27E-09	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
vg1221718597	NA	7.72E-07	mr1641_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
vg1221718597	NA	3.84E-06	mr1659_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
vg1221718597	NA	3.23E-07	mr1838_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