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Detailed information for vg1216422627:

Variant ID: vg1216422627 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16422627
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGTAAAGTGGCAAATCTTGCGAAGTAGAGGCAATAGAGTTTGCCGGTGCAGAAGACAATGAAGATAAAGTCGCTCCACCATGGTGACAAAGTTGCATA[G/A]
CCGTGATGAAGTGAAGACACCATTGGCGGCGGCGAAGCCAACAGGCAATGACGATTACGCCAGTCAATGATGATGAAGACGCGCAGCTGTGGAGGCGAAC

Reverse complement sequence

GTTCGCCTCCACAGCTGCGCGTCTTCATCATCATTGACTGGCGTAATCGTCATTGCCTGTTGGCTTCGCCGCCGCCAATGGTGTCTTCACTTCATCACGG[C/T]
TATGCAACTTTGTCACCATGGTGGAGCGACTTTATCTTCATTGTCTTCTGCACCGGCAAACTCTATTGCCTCTACTTCGCAAGATTTGCCACTTTACTAA

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	46.60%	34.20%	13.61%	5.63%	NA
All Indica	2759	64.20%	12.80%	19.32%	3.70%	NA
All Japonica	1512	10.00%	76.60%	4.37%	9.06%	NA
Aus	269	77.00%	10.80%	7.06%	5.20%	NA
Indica I	595	58.50%	3.00%	36.81%	1.68%	NA
Indica II	465	47.30%	32.90%	15.27%	4.52%	NA
Indica III	913	79.60%	6.50%	9.75%	4.16%	NA
Indica Intermediate	786	60.60%	15.60%	19.59%	4.20%	NA
Temperate Japonica	767	2.10%	89.00%	1.04%	7.82%	NA
Tropical Japonica	504	22.60%	59.10%	9.13%	9.13%	NA
Japonica Intermediate	241	8.70%	73.40%	4.98%	12.86%	NA
VI/Aromatic	96	51.00%	26.00%	14.58%	8.33%	NA
Intermediate	90	24.40%	57.80%	12.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216422627	G -> DEL	N	N	silent_mutation	Average:33.092; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg1216422627	G -> A	LOC_Os12g27860.1	upstream_gene_variant ; 268.0bp to feature; MODIFIER	silent_mutation	Average:33.092; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg1216422627	G -> A	LOC_Os12g27850-LOC_Os12g27860	intergenic_region ; MODIFIER	silent_mutation	Average:33.092; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216422627	NA	4.07E-10	mr1017	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
vg1216422627	NA	1.88E-28	mr1022	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
vg1216422627	2.77E-07	NA	mr1055	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
vg1216422627	5.21E-08	NA	mr1390	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
vg1216422627	NA	3.60E-12	mr1390	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
vg1216422627	2.00E-08	NA	mr1490	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
vg1216422627	NA	4.09E-11	mr1490	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
vg1216422627	NA	5.38E-37	mr1022_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
vg1216422627	6.88E-07	2.33E-13	mr1023_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
vg1216422627	2.63E-06	NA	mr1055_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
vg1216422627	NA	1.56E-13	mr1055_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
vg1216422627	1.09E-06	NA	mr1079_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
vg1216422627	NA	7.52E-14	mr1079_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
vg1216422627	NA	8.37E-13	mr1132_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
vg1216422627	1.38E-06	NA	mr1390_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
vg1216422627	NA	3.87E-13	mr1390_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
vg1216422627	NA	7.50E-12	mr1490_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