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Detailed information for vg1009887667:

Variant ID: vg1009887667 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9887667
Reference Allele: C	Alternative Allele: A,T
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTCAATACACCACTTTAGCCGGTCAATTTTGTTTTGATCTGTCAAGTGGGGATCAAATGAGCTAGATACATGATTTATAGCACCTTATTTTTTCATT[C/A,T]
TGTAGACCTTGCTTGTGCTAACACCAAATTGAGTAGCTACATCCTGTATTGTGGTACGGCTCAATATTGAAATATCTTCGAGACGGGACACATCCACCAC

Reverse complement sequence

GTGGTGGATGTGTCCCGTCTCGAAGATATTTCAATATTGAGCCGTACCACAATACAGGATGTAGCTACTCAATTTGGTGTTAGCACAAGCAAGGTCTACA[G/T,A]
AATGAAAAAATAAGGTGCTATAAATCATGTATCTAGCTCATTTGATCCCCACTTGACAGATCAAAACAAAATTGACCGGCTAAAGTGGTGTATTGAAATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.00%	20.80%	0.63%	12.46%	T: 0.06%
All Indica	2759	96.30%	2.10%	0.58%	0.94%	T: 0.11%
All Japonica	1512	8.00%	55.80%	0.40%	35.78%	NA
Aus	269	94.40%	1.50%	1.12%	2.97%	NA
Indica I	595	98.20%	1.20%	0.34%	0.34%	NA
Indica II	465	97.60%	1.10%	0.65%	0.65%	NA
Indica III	913	96.20%	2.10%	0.55%	0.99%	T: 0.22%
Indica Intermediate	786	94.30%	3.30%	0.76%	1.53%	T: 0.13%
Temperate Japonica	767	1.00%	86.80%	0.13%	11.99%	NA
Tropical Japonica	504	18.10%	10.90%	0.79%	70.24%	NA
Japonica Intermediate	241	9.10%	51.00%	0.41%	39.42%	NA
VI/Aromatic	96	44.80%	54.20%	1.04%	0.00%	NA
Intermediate	90	48.90%	31.10%	4.44%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009887667	C -> T	LOC_Os10g19820.1	downstream_gene_variant ; 2056.0bp to feature; MODIFIER	silent_mutation	Average:28.972; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg1009887667	C -> T	LOC_Os10g19830.1	intron_variant ; MODIFIER	silent_mutation	Average:28.972; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg1009887667	C -> A	LOC_Os10g19820.1	downstream_gene_variant ; 2056.0bp to feature; MODIFIER	silent_mutation	Average:28.972; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg1009887667	C -> A	LOC_Os10g19830.1	intron_variant ; MODIFIER	silent_mutation	Average:28.972; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg1009887667	C -> DEL	N	N	silent_mutation	Average:28.972; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009887667	NA	5.78E-13	mr1010	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
vg1009887667	NA	1.35E-13	mr1034	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