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Detailed information for vg0909000770:

Variant ID: vg0909000770 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9000770
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCTATATAATCTATATTCACGATCAATACAATTCAGCGCATCGCCACCTTTTACCTTTTCTACTTTATTTTATCATCCGGCGGGACTTGGCACCTGACG[C/T]
GGGGCTGCATCGGTGTTCGATCTCCGGCTAAGGTTTAAGTCCAATGTTCCGTCGGCCCAGGCAATTGTATCGTTTACGTCAGCGTCGTTCAAGGCTGCAT

Reverse complement sequence

ATGCAGCCTTGAACGACGCTGACGTAAACGATACAATTGCCTGGGCCGACGGAACATTGGACTTAAACCTTAGCCGGAGATCGAACACCGATGCAGCCCC[G/A]
CGTCAGGTGCCAAGTCCCGCCGGATGATAAAATAAAGTAGAAAAGGTAAAAGGTGGCGATGCGCTGAATTGTATTGATCGTGAATATAGATTATATAGAC

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	87.10%	5.10%	0.61%	7.24%	NA
All Indica	2759	94.10%	2.50%	0.47%	2.86%	NA
All Japonica	1512	75.80%	6.90%	0.66%	16.60%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	0.00%	0.00%	1.51%	NA
Indica II	465	97.80%	1.70%	0.22%	0.22%	NA
Indica III	913	91.00%	3.10%	0.55%	5.37%	NA
Indica Intermediate	786	92.20%	4.30%	0.89%	2.54%	NA
Temperate Japonica	767	69.60%	6.10%	0.65%	23.60%	NA
Tropical Japonica	504	90.30%	1.00%	0.60%	8.13%	NA
Japonica Intermediate	241	65.10%	22.00%	0.83%	12.03%	NA
VI/Aromatic	96	29.20%	57.30%	4.17%	9.38%	NA
Intermediate	90	85.60%	8.90%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909000770	C -> DEL	N	N	silent_mutation	Average:22.914; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0909000770	C -> T	LOC_Os09g14990.1	downstream_gene_variant ; 2516.0bp to feature; MODIFIER	silent_mutation	Average:22.914; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0909000770	C -> T	LOC_Os09g14990-LOC_Os09g15000	intergenic_region ; MODIFIER	silent_mutation	Average:22.914; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909000770	2.48E-06	8.12E-08	mr1004	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
vg0909000770	NA	2.98E-07	mr1280	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