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Detailed information for vg0912020992:

Variant ID: vg0912020992 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12020992
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAACTATAGCCCGTCACAGATGACTGATGACCTCAATCGGGCCTAAAATAGAGCCCGTCACAGATGACTACTGACCTCAATCGGGCCTAAAATAGAGCC[C/T]
GTCACAGATGACTACTGACCTCAATCGGGCCTAAACTAGAGCCCGTCACAGATGACTACTGATCTCAATCGGGCCTAAACTAGAGCCCGTCACAAATGAC

Reverse complement sequence

GTCATTTGTGACGGGCTCTAGTTTAGGCCCGATTGAGATCAGTAGTCATCTGTGACGGGCTCTAGTTTAGGCCCGATTGAGGTCAGTAGTCATCTGTGAC[G/A]
GGCTCTATTTTAGGCCCGATTGAGGTCAGTAGTCATCTGTGACGGGCTCTATTTTAGGCCCGATTGAGGTCATCAGTCATCTGTGACGGGCTATAGTTTA

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	96.90%	0.80%	2.24%	0.00%	NA
All Indica	2759	95.60%	1.10%	3.33%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	92.20%	2.60%	5.20%	0.00%	NA
Indica I	595	90.40%	1.30%	8.24%	0.00%	NA
Indica II	465	95.90%	1.10%	3.01%	0.00%	NA
Indica III	913	98.90%	0.40%	0.66%	0.00%	NA
Indica Intermediate	786	95.40%	1.70%	2.93%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0912020992	C -> T	LOC_Os09g20050.1	downstream_gene_variant ; 2777.0bp to feature; MODIFIER	silent_mutation	Average:39.596; most accessible tissue: Zhenshan97 flower, score: 52.192	N	N	N	N
vg0912020992	C -> T	LOC_Os09g20060.1	downstream_gene_variant ; 486.0bp to feature; MODIFIER	silent_mutation	Average:39.596; most accessible tissue: Zhenshan97 flower, score: 52.192	N	N	N	N
vg0912020992	C -> T	LOC_Os09g20070.1	downstream_gene_variant ; 2478.0bp to feature; MODIFIER	silent_mutation	Average:39.596; most accessible tissue: Zhenshan97 flower, score: 52.192	N	N	N	N
vg0912020992	C -> T	LOC_Os09g20050-LOC_Os09g20060	intergenic_region ; MODIFIER	silent_mutation	Average:39.596; most accessible tissue: Zhenshan97 flower, score: 52.192	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912020992	1.11E-06	1.55E-06	mr1993	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