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Detailed information for vg0910719137:

Variant ID: vg0910719137 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10719137
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.19, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTCATACTAGAAGTCCTAATCCTCCTAGGAAACCTTCTCATACAAGAAATAATCTTTACATAACCAATCATACCAAATTTGGACTCTTTTCCAAATT[C/T]
GACTCCGTATCCCATACGCACACAATACCTCCATCGTATGCCATATGGAATCTTCACCAACCACGTATATTGAACTCTAGCCTAAGTATCCCGTATGATA

Reverse complement sequence

TATCATACGGGATACTTAGGCTAGAGTTCAATATACGTGGTTGGTGAAGATTCCATATGGCATACGATGGAGGTATTGTGTGCGTATGGGATACGGAGTC[G/A]
AATTTGGAAAAGAGTCCAAATTTGGTATGATTGGTTATGTAAAGATTATTTCTTGTATGAGAAGGTTTCCTAGGAGGATTAGGACTTCTAGTATGAGTTT

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	15.20%	12.50%	1.54%	70.76%	NA
All Indica	2759	9.90%	13.10%	2.07%	74.88%	NA
All Japonica	1512	27.40%	0.50%	0.60%	71.56%	NA
Aus	269	0.70%	74.00%	1.49%	23.79%	NA
Indica I	595	9.40%	1.80%	1.51%	87.23%	NA
Indica II	465	7.10%	18.30%	2.15%	72.47%	NA
Indica III	913	14.60%	17.70%	2.08%	65.61%	NA
Indica Intermediate	786	6.60%	13.20%	2.42%	77.74%	NA
Temperate Japonica	767	47.20%	0.10%	0.78%	51.89%	NA
Tropical Japonica	504	5.40%	0.60%	0.60%	93.45%	NA
Japonica Intermediate	241	10.40%	1.20%	0.00%	88.38%	NA
VI/Aromatic	96	6.20%	19.80%	1.04%	72.92%	NA
Intermediate	90	23.30%	5.60%	2.22%	68.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910719137	C -> DEL	N	N	silent_mutation	Average:9.253; most accessible tissue: Callus, score: 24.272	N	N	N	N
vg0910719137	C -> T	LOC_Os09g17520.1	intron_variant ; MODIFIER	silent_mutation	Average:9.253; most accessible tissue: Callus, score: 24.272	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910719137	6.95E-06	6.95E-06	mr1562	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
vg0910719137	6.50E-06	NA	mr1606	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
vg0910719137	NA	2.25E-06	mr1895	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