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Detailed information for vg0909065655:

Variant ID: vg0909065655 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9065655
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGGAGGCTTGGGCTGTGCACGTGGGGACGCCCGGGGGTGCGGGGACGGAGCCCCCGCAAAACGGATCGTCATCCCTTTTAGGGTTCCACCATATATATA[T/C]
CTTTTGTAAGCCACCATGCGGCAATGTAACCTCACCCCAGATATAGTGAAGATATTTTGCTGGCTGGTGCCCGTGGTTTTTTCTCTCCTGTTTTGGGAGG

Reverse complement sequence

CCTCCCAAAACAGGAGAGAAAAAACCACGGGCACCAGCCAGCAAAATATCTTCACTATATCTGGGGTGAGGTTACATTGCCGCATGGTGGCTTACAAAAG[A/G]
TATATATATGGTGGAACCCTAAAAGGGATGACGATCCGTTTTGCGGGGGCTCCGTCCCCGCACCCCCGGGCGTCCCCACGTGCACAGCCCAAGCCTCCCG

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	34.90%	6.40%	8.38%	50.34%	NA
All Indica	2759	9.30%	4.00%	6.23%	80.50%	NA
All Japonica	1512	86.40%	0.20%	8.00%	5.42%	NA
Aus	269	4.50%	56.10%	19.70%	19.70%	NA
Indica I	595	6.40%	8.20%	8.40%	76.97%	NA
Indica II	465	4.70%	1.70%	8.39%	85.16%	NA
Indica III	913	13.70%	1.10%	3.94%	81.27%	NA
Indica Intermediate	786	9.00%	5.50%	5.98%	79.52%	NA
Temperate Japonica	767	86.70%	0.00%	8.74%	4.56%	NA
Tropical Japonica	504	93.30%	0.20%	4.76%	1.79%	NA
Japonica Intermediate	241	71.00%	0.80%	12.45%	15.77%	NA
VI/Aromatic	96	21.90%	32.30%	41.67%	4.17%	NA
Intermediate	90	61.10%	6.70%	11.11%	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
vg0909065655	T -> DEL	N	N	silent_mutation	Average:40.946; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0909065655	T -> C	LOC_Os09g15030.1	upstream_gene_variant ; 217.0bp to feature; MODIFIER	silent_mutation	Average:40.946; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0909065655	T -> C	LOC_Os09g15020-LOC_Os09g15030	intergenic_region ; MODIFIER	silent_mutation	Average:40.946; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909065655	2.13E-06	2.29E-40	mr1891	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
vg0909065655	NA	1.54E-10	mr1905	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
vg0909065655	NA	3.70E-19	mr1637_2	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