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Detailed information for vg0909938033:

Variant ID: vg0909938033 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9938033
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TGAATAAACATTATTACATCATGAGTTTTGTGTGTTCTCGTTTGCAAAGGTACATGCTTGGGTAAAAGGAGAGAGACCAAGCGCAAGGCATAATAAATGG[C/T]
TGATCGAATAAGTTGATTGGGGACCAAACCAAGATCTTTCCCAAGTCTTATCCTACAGTACAACGTCACTTTCTGTCAATGGAAGTCAAGATATAAAGTT

Reverse complement sequence

AACTTTATATCTTGACTTCCATTGACAGAAAGTGACGTTGTACTGTAGGATAAGACTTGGGAAAGATCTTGGTTTGGTCCCCAATCAACTTATTCGATCA[G/A]
CCATTTATTATGCCTTGCGCTTGGTCTCTCTCCTTTTACCCAAGCATGTACCTTTGCAAACGAGAACACACAAAACTCATGATGTAATAATGTTTATTCA

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	54.00%	14.70%	0.63%	30.64%	NA
All Indica	2759	31.80%	22.50%	0.83%	44.84%	NA
All Japonica	1512	89.40%	0.50%	0.33%	9.85%	NA
Aus	269	60.60%	23.40%	0.37%	15.61%	NA
Indica I	595	21.50%	7.20%	1.18%	70.08%	NA
Indica II	465	35.90%	6.90%	1.08%	56.13%	NA
Indica III	913	35.70%	43.60%	0.11%	20.59%	NA
Indica Intermediate	786	32.60%	19.00%	1.27%	47.20%	NA
Temperate Japonica	767	85.90%	0.00%	0.65%	13.43%	NA
Tropical Japonica	504	91.10%	1.40%	0.00%	7.54%	NA
Japonica Intermediate	241	96.70%	0.00%	0.00%	3.32%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	74.40%	3.30%	1.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909938033	C -> DEL	N	N	silent_mutation	Average:35.183; most accessible tissue: Zhenshan97 young leaf, score: 70.625	N	N	N	N
vg0909938033	C -> T	LOC_Os09g16280.1	downstream_gene_variant ; 3794.0bp to feature; MODIFIER	silent_mutation	Average:35.183; most accessible tissue: Zhenshan97 young leaf, score: 70.625	N	N	N	N
vg0909938033	C -> T	LOC_Os09g16280-LOC_Os09g16290	intergenic_region ; MODIFIER	silent_mutation	Average:35.183; most accessible tissue: Zhenshan97 young leaf, score: 70.625	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909938033	NA	8.63E-06	mr1214	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
vg0909938033	NA	6.12E-06	mr1505	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
vg0909938033	NA	2.38E-07	mr1807	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