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Detailed information for vg0909534950:

Variant ID: vg0909534950 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9534950
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACAACGTCTTTTCTGCAAGATACAAAAAGATGTATTAGGATAAACGCGAAGTAACATATATTGCATTTGACGTTCACGTTTCGTTCACGATATCGTTCA[C/T]
GTTTGCGTTCTCGTTAAGGTCACGTTTCATTCACCTACATTTGTTCGTTCACGTTCATTCACATGCCTATATTGCATTTCACGTTCACGTTCGTTGACGT

Reverse complement sequence

ACGTCAACGAACGTGAACGTGAAATGCAATATAGGCATGTGAATGAACGTGAACGAACAAATGTAGGTGAATGAAACGTGACCTTAACGAGAACGCAAAC[G/A]
TGAACGATATCGTGAACGAAACGTGAACGTCAAATGCAATATATGTTACTTCGCGTTTATCCTAATACATCTTTTTGTATCTTGCAGAAAAGACGTTGTC

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	93.80%	3.60%	1.44%	1.23%	NA
All Indica	2759	98.60%	0.20%	0.54%	0.69%	NA
All Japonica	1512	88.80%	9.70%	1.52%	0.00%	NA
Aus	269	75.10%	0.40%	10.78%	13.75%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	96.80%	0.20%	0.65%	2.37%	NA
Indica III	913	99.60%	0.10%	0.33%	0.00%	NA
Indica Intermediate	786	97.80%	0.40%	0.76%	1.02%	NA
Temperate Japonica	767	89.40%	9.30%	1.30%	0.00%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	70.50%	24.10%	5.39%	0.00%	NA
VI/Aromatic	96	84.40%	14.60%	0.00%	1.04%	NA
Intermediate	90	94.40%	3.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909534950	C -> DEL	N	N	silent_mutation	Average:20.832; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg0909534950	C -> T	LOC_Os09g15610.1	upstream_gene_variant ; 1332.0bp to feature; MODIFIER	silent_mutation	Average:20.832; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg0909534950	C -> T	LOC_Os09g15630.1	downstream_gene_variant ; 1333.0bp to feature; MODIFIER	silent_mutation	Average:20.832; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg0909534950	C -> T	LOC_Os09g15620.1	intron_variant ; MODIFIER	silent_mutation	Average:20.832; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909534950	6.32E-07	NA	mr1712	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
vg0909534950	3.81E-06	NA	mr1712	Jap_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