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Detailed information for vg0910215512:

Variant ID: vg0910215512 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10215512
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CCCGACTGGCTGGCTAACCCAGTCCTGGTTCGGAAGAAGACCGGGCAATGACGTATGTGTGTCGATTACACCGACCTCAACAAGTCTTGCCCTAAAGATC[T/C]
TTTCGGGTTACCTCGCATTGACCAGGTGGTTGACTCAACGGCCGGCTGCGAGCTACTCAGTTTCTTGGACTGCTATTCGGGATATCATCAGATCCGACTA

Reverse complement sequence

TAGTCGGATCTGATGATATCCCGAATAGCAGTCCAAGAAACTGAGTAGCTCGCAGCCGGCCGTTGAGTCAACCACCTGGTCAATGCGAGGTAACCCGAAA[A/G]
GATCTTTAGGGCAAGACTTGTTGAGGTCGGTGTAATCGACACACATACGTCATTGCCCGGTCTTCTTCCGAACCAGGACTGGGTTAGCCAGCCAGTCGGG

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	19.20%	1.70%	35.63%	43.42%	NA
All Indica	2759	4.30%	1.70%	23.67%	70.28%	NA
All Japonica	1512	45.10%	2.00%	50.00%	2.91%	NA
Aus	269	12.30%	0.70%	69.52%	17.47%	NA
Indica I	595	7.20%	0.00%	8.57%	84.20%	NA
Indica II	465	5.20%	0.20%	27.10%	67.53%	NA
Indica III	913	1.30%	3.70%	31.33%	63.64%	NA
Indica Intermediate	786	5.20%	1.50%	24.17%	69.08%	NA
Temperate Japonica	767	69.60%	0.50%	28.42%	1.43%	NA
Tropical Japonica	504	13.10%	4.40%	77.38%	5.16%	NA
Japonica Intermediate	241	34.00%	1.70%	61.41%	2.90%	NA
VI/Aromatic	96	42.70%	2.10%	48.96%	6.25%	NA
Intermediate	90	35.60%	1.10%	45.56%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910215512	T -> DEL	N	N	silent_mutation	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0910215512	T -> C	LOC_Os09g16670.1	upstream_gene_variant ; 1441.0bp to feature; MODIFIER	silent_mutation	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0910215512	T -> C	LOC_Os09g16660.1	downstream_gene_variant ; 3959.0bp to feature; MODIFIER	silent_mutation	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0910215512	T -> C	LOC_Os09g16690.1	downstream_gene_variant ; 2079.0bp to feature; MODIFIER	silent_mutation	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0910215512	T -> C	LOC_Os09g16680.1	intron_variant ; MODIFIER	silent_mutation	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910215512	NA	1.58E-06	mr1031_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