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Detailed information for vg1216930812:

Variant ID: vg1216930812 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16930812
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGTAGTTCAGGTGGGTTGGTTGGGCCTGTTCAACGTGGTGTAGCGTTGATCAGTGGAGATTTAATGTTACTTTAATTACTCAATTGTTTTACTGTTTG[C/T]
TCAATAAAATGTTTTACAGCCGCCTTTATGCAAATAGCCACAAACTGTCCTTGTGTTCCCCTTGCACGTCTGCATCGTTGGTGTGGCTTGCTGAGTACGG

Reverse complement sequence

CCGTACTCAGCAAGCCACACCAACGATGCAGACGTGCAAGGGGAACACAAGGACAGTTTGTGGCTATTTGCATAAAGGCGGCTGTAAAACATTTTATTGA[G/A]
CAAACAGTAAAACAATTGAGTAATTAAAGTAACATTAAATCTCCACTGATCAACGCTACACCACGTTGAACAGGCCCAACCAACCCACCTGAACTACAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.00%	2.20%	44.88%	12.93%	NA
All Indica	2759	22.90%	2.90%	55.27%	18.92%	NA
All Japonica	1512	75.30%	0.10%	19.97%	4.70%	NA
Aus	269	22.70%	5.90%	69.52%	1.86%	NA
Indica I	595	36.60%	2.50%	31.76%	29.08%	NA
Indica II	465	15.30%	0.00%	68.82%	15.91%	NA
Indica III	913	17.50%	4.30%	62.54%	15.66%	NA
Indica Intermediate	786	23.20%	3.40%	56.62%	16.79%	NA
Temperate Japonica	767	94.00%	0.00%	3.39%	2.61%	NA
Tropical Japonica	504	45.00%	0.00%	48.81%	6.15%	NA
Japonica Intermediate	241	78.80%	0.40%	12.45%	8.30%	NA
VI/Aromatic	96	16.70%	3.10%	78.12%	2.08%	NA
Intermediate	90	50.00%	2.20%	35.56%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216930812	C -> DEL	N	N	silent_mutation	Average:20.277; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930812	C -> T	LOC_Os12g28630.1	upstream_gene_variant ; 1753.0bp to feature; MODIFIER	silent_mutation	Average:20.277; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930812	C -> T	LOC_Os12g28620.1	downstream_gene_variant ; 3860.0bp to feature; MODIFIER	silent_mutation	Average:20.277; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930812	C -> T	LOC_Os12g28640.1	downstream_gene_variant ; 551.0bp to feature; MODIFIER	silent_mutation	Average:20.277; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1216930812	C -> T	LOC_Os12g28630-LOC_Os12g28640	intergenic_region ; MODIFIER	silent_mutation	Average:20.277; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216930812	3.47E-06	NA	mr1993_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
vg1216930812	3.39E-06	NA	mr1993_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