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Detailed information for vg0318764893:

Variant ID: vg0318764893 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18764893
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGGAATTCTCATATCATTTGGACACTATGGAATGGTTGGCTTATGTTGGAATTGGACACACACCTCCCCCTCTATTCAAAACCCCCAAAATGGTTTTA[G/T]
GCTGGGCTCGAGGTGCGTGGTTGGGTTTTGTTAGTCGTACCTTGGGTACTATAAGGATTAAGCTCGGGCCTCTGTTGCAAAGCACTACCGTACTTCCACA

Reverse complement sequence

TGTGGAAGTACGGTAGTGCTTTGCAACAGAGGCCCGAGCTTAATCCTTATAGTACCCAAGGTACGACTAACAAAACCCAACCACGCACCTCGAGCCCAGC[C/A]
TAAAACCATTTTGGGGGTTTTGAATAGAGGGGGAGGTGTGTGTCCAATTCCAACATAAGCCAACCATTCCATAGTGTCCAAATGATATGAGAATTCCCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.70%	1.00%	4.85%	12.48%	NA
All Indica	2759	72.10%	1.40%	7.97%	18.56%	NA
All Japonica	1512	99.50%	0.00%	0.07%	0.46%	NA
Aus	269	73.20%	2.20%	1.12%	23.42%	NA
Indica I	595	55.50%	1.80%	17.48%	25.21%	NA
Indica II	465	69.20%	1.10%	4.52%	25.16%	NA
Indica III	913	86.20%	0.90%	5.04%	7.89%	NA
Indica Intermediate	786	69.80%	1.90%	6.23%	22.01%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	84.40%	2.20%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318764893	G -> T	LOC_Os03g32780.1	upstream_gene_variant ; 1495.0bp to feature; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> T	LOC_Os03g32790.1	upstream_gene_variant ; 3717.0bp to feature; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> T	LOC_Os03g32790.2	upstream_gene_variant ; 3717.0bp to feature; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> T	LOC_Os03g32790.3	upstream_gene_variant ; 3717.0bp to feature; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> T	LOC_Os03g32770.1	downstream_gene_variant ; 4451.0bp to feature; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> T	LOC_Os03g32780-LOC_Os03g32790	intergenic_region ; MODIFIER	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0318764893	G -> DEL	N	N	silent_mutation	Average:16.644; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318764893	7.30E-07	7.30E-07	mr1102	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
vg0318764893	7.84E-06	5.11E-06	mr1704	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