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Detailed information for vg1216679292:

Variant ID: vg1216679292 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16679292
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACCTATTTTTTTCAAATTAGCACAATTTTCACAATCTATCATAACACCTTTGCTTTTACAACATTTGGGGCAAGAAAGCACTTCATTAGTTTTCACAA[C/T]
ATCCTCCATGTACTCAACACGACCTAATGCATCTTTTAGCCTCAACTTGTTTAGTGTGCATGTTGAGCAATTCAAAACACCATGTTGTTCTTTTTAACTT

Reverse complement sequence

AAGTTAAAAAGAACAACATGGTGTTTTGAATTGCTCAACATGCACACTAAACAAGTTGAGGCTAAAAGATGCATTAGGTCGTGTTGAGTACATGGAGGAT[G/A]
TTGTGAAAACTAATGAAGTGCTTTCTTGCCCCAAATGTTGTAAAAGCAAAGGTGTTATGATAGATTGTGAAAATTGTGCTAATTTGAAAAAAATAGGTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	25.40%	0.30%	29.07%	NA
All Indica	2759	73.80%	2.40%	0.40%	23.41%	NA
All Japonica	1512	3.20%	71.60%	0.07%	25.13%	NA
Aus	269	3.00%	8.60%	0.37%	88.10%	NA
Indica I	595	88.60%	1.70%	0.17%	9.58%	NA
Indica II	465	74.20%	3.40%	0.22%	22.15%	NA
Indica III	913	70.50%	0.30%	0.55%	28.59%	NA
Indica Intermediate	786	66.20%	4.70%	0.51%	28.63%	NA
Temperate Japonica	767	1.30%	96.00%	0.13%	2.61%	NA
Tropical Japonica	504	4.20%	31.20%	0.00%	64.68%	NA
Japonica Intermediate	241	7.10%	78.80%	0.00%	14.11%	NA
VI/Aromatic	96	9.40%	1.00%	0.00%	89.58%	NA
Intermediate	90	40.00%	31.10%	1.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216679292	C -> DEL	N	N	silent_mutation	Average:14.621; most accessible tissue: Callus, score: 48.349	N	N	N	N
vg1216679292	C -> T	LOC_Os12g28230.1	downstream_gene_variant ; 3854.0bp to feature; MODIFIER	silent_mutation	Average:14.621; most accessible tissue: Callus, score: 48.349	N	N	N	N
vg1216679292	C -> T	LOC_Os12g28240.1	intron_variant ; MODIFIER	silent_mutation	Average:14.621; most accessible tissue: Callus, score: 48.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216679292	NA	2.95E-35	mr1017	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
vg1216679292	NA	9.47E-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
vg1216679292	3.34E-06	8.65E-12	mr1023	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
vg1216679292	NA	5.04E-34	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
vg1216679292	NA	1.22E-09	mr1132	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
vg1216679292	NA	2.28E-60	mr1142	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
vg1216679292	5.80E-06	1.43E-11	mr1142	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
vg1216679292	7.16E-07	NA	mr1178	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
vg1216679292	NA	3.24E-07	mr1334	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
vg1216679292	2.89E-06	3.84E-09	mr1489	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
vg1216679292	NA	2.22E-52	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
vg1216679292	NA	2.59E-06	mr1792_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
vg1216679292	NA	3.64E-06	mr1803_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