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Detailed information for vg0301900951:

Variant ID: vg0301900951 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1900951
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCCCTTTCAGCCACCCAAGCTTGAGATGCCATCTTCCCAAGAACTCTGCTTCTTGAAGCACAATGATGATCCTCCTCATTTATTTGGATCTGCACAAG[T/C]
AAACCATATTAGCAACTTATTAGGTAAACAAAATCAATGCATACAGCATAATGTACAATTTAACAACAATTAAATAGTTAGTATAATACCCTGACACTTT

Reverse complement sequence

AAAGTGTCAGGGTATTATACTAACTATTTAATTGTTGTTAAATTGTACATTATGCTGTATGCATTGATTTTGTTTACCTAATAAGTTGCTAATATGGTTT[A/G]
CTTGTGCAGATCCAAATAAATGAGGAGGATCATCATTGTGCTTCAAGAAGCAGAGTTCTTGGGAAGATGGCATCTCAAGCTTGGGTGGCTGAAAGGGCTA

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	77.30%	6.60%	5.95%	10.20%	NA
All Indica	2759	77.90%	0.30%	7.94%	13.88%	NA
All Japonica	1512	73.50%	17.00%	3.37%	6.15%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.80%	0.00%	3.70%	3.53%	NA
Indica II	465	56.80%	0.90%	16.56%	25.81%	NA
Indica III	913	73.80%	0.10%	8.32%	17.74%	NA
Indica Intermediate	786	84.00%	0.30%	5.60%	10.18%	NA
Temperate Japonica	767	95.00%	0.30%	1.69%	3.00%	NA
Tropical Japonica	504	49.80%	44.60%	3.57%	1.98%	NA
Japonica Intermediate	241	54.40%	12.40%	8.30%	24.90%	NA
VI/Aromatic	96	50.00%	41.70%	6.25%	2.08%	NA
Intermediate	90	83.30%	6.70%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301900951	T -> C	LOC_Os03g04140.1	upstream_gene_variant ; 3642.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301900951	T -> C	LOC_Os03g04140.2	upstream_gene_variant ; 3642.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301900951	T -> C	LOC_Os03g04150.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301900951	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301900951	NA	1.27E-07	mr1042_2	Jap_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
vg0301900951	NA	2.57E-08	mr1871_2	Jap_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
vg0301900951	7.01E-07	9.91E-09	mr1929_2	Jap_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