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Detailed information for vg0907952012:

Variant ID: vg0907952012 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7952012
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AATATTTAAGAATAGTAAAACAGTAGAGTAATTAATCATCAATTTTAATCAACACTGAACAGCACACCCATGATGCTCAGGCCCAACCATTCTGAACAAC[C/T]
AAACCCGGCTGCACAGATCTAACTCTAAACCAGGAGCTAAGCAAATTATTACCAATTATAGCATCAATAATTATTGTGAGAGGTATGAGACTAATCACGA

Reverse complement sequence

TCGTGATTAGTCTCATACCTCTCACAATAATTATTGATGCTATAATTGGTAATAATTTGCTTAGCTCCTGGTTTAGAGTTAGATCTGTGCAGCCGGGTTT[G/A]
GTTGTTCAGAATGGTTGGGCCTGAGCATCATGGGTGTGCTGTTCAGTGTTGATTAAAATTGATGATTAATTACTCTACTGTTTTACTATTCTTAAATATT

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	77.30%	19.50%	2.05%	1.12%	NA
All Indica	2759	90.00%	7.90%	0.22%	1.88%	NA
All Japonica	1512	56.50%	37.50%	5.95%	0.00%	NA
Aus	269	92.90%	6.70%	0.00%	0.37%	NA
Indica I	595	97.10%	0.20%	0.17%	2.52%	NA
Indica II	465	97.20%	2.60%	0.00%	0.22%	NA
Indica III	913	79.60%	18.20%	0.22%	1.97%	NA
Indica Intermediate	786	92.50%	4.80%	0.38%	2.29%	NA
Temperate Japonica	767	70.50%	18.80%	10.69%	0.00%	NA
Tropical Japonica	504	25.00%	74.60%	0.40%	0.00%	NA
Japonica Intermediate	241	78.00%	19.50%	2.49%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	67.80%	31.10%	1.11%	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
vg0907952012	C -> DEL	N	N	silent_mutation	Average:52.616; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0907952012	C -> T	LOC_Os09g13640.1	downstream_gene_variant ; 811.0bp to feature; MODIFIER	silent_mutation	Average:52.616; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0907952012	C -> T	LOC_Os09g13630-LOC_Os09g13640	intergenic_region ; MODIFIER	silent_mutation	Average:52.616; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907952012	2.54E-07	NA	mr1002	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
vg0907952012	NA	3.15E-09	mr1002	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
vg0907952012	NA	2.43E-06	mr1330_2	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
vg0907952012	NA	2.22E-09	mr1379_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
vg0907952012	NA	3.61E-07	mr1548_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
vg0907952012	NA	5.09E-07	mr1559_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