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Detailed information for vg1119865923:

Variant ID: vg1119865923 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19865923
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAATTGTTAAGGAGATAAAAAAAATAGAGAGAAGAATGGCGCACATTGTACATGGCAGGGAGGAAGGGAGGGTTGGGATATTTTTCTAAATGATTAAT[C/T]
TAACAATCTAAAATAGTGTGTCAAATGTTTATATTGAAACCGATGGTTGGATGTTTTTTTTTAAGAATTCGGATTAGAGTGTTACTTGGTGACCTAGGAG

Reverse complement sequence

CTCCTAGGTCACCAAGTAACACTCTAATCCGAATTCTTAAAAAAAAACATCCAACCATCGGTTTCAATATAAACATTTGACACACTATTTTAGATTGTTA[G/A]
ATTAATCATTTAGAAAAATATCCCAACCCTCCCTTCCTCCCTGCCATGTACAATGTGCGCCATTCTTCTCTCTATTTTTTTTATCTCCTTAACAATTAAA

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	59.00%	4.00%	3.47%	33.50%	NA
All Indica	2759	51.40%	6.70%	5.58%	36.28%	NA
All Japonica	1512	63.50%	0.10%	0.40%	35.98%	NA
Aus	269	94.80%	0.00%	0.37%	4.83%	NA
Indica I	595	31.30%	15.50%	8.07%	45.21%	NA
Indica II	465	72.70%	4.10%	3.23%	20.00%	NA
Indica III	913	55.90%	2.80%	4.38%	36.91%	NA
Indica Intermediate	786	49.00%	6.10%	6.49%	38.42%	NA
Temperate Japonica	767	84.90%	0.10%	0.26%	14.73%	NA
Tropical Japonica	504	39.10%	0.20%	0.40%	60.32%	NA
Japonica Intermediate	241	46.50%	0.00%	0.83%	52.70%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	2.20%	3.33%	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
vg1119865923	C -> T	LOC_Os11g33990.1	downstream_gene_variant ; 4400.0bp to feature; MODIFIER	silent_mutation	Average:29.975; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg1119865923	C -> T	LOC_Os11g33970.1	intron_variant ; MODIFIER	silent_mutation	Average:29.975; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg1119865923	C -> DEL	N	N	silent_mutation	Average:29.975; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119865923	5.73E-06	4.87E-07	mr1519	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
vg1119865923	6.32E-07	NA	mr1519_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
vg1119865923	9.93E-08	1.51E-10	mr1519_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