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Detailed information for vg1010276752:

Variant ID: vg1010276752 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10276752
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTTGAAGCTTGCTCGGGCTGGAGGAGGAAGAAGACATATATATATAGGGGTGGGACTTTAGTCCCGGTTGGTGTTATGAACCGGTGCTAAAGATCGC[C/T]
GGGATCTTTAGTCCCGGTTGGTAAAGATCCCGGGGGAGCCTGACAAGCCCTGACAGCATTTGAACCGGGACTAAAGACGGTTGGTGTTACCAACCAGGTC

Reverse complement sequence

GACCTGGTTGGTAACACCAACCGTCTTTAGTCCCGGTTCAAATGCTGTCAGGGCTTGTCAGGCTCCCCCGGGATCTTTACCAACCGGGACTAAAGATCCC[G/A]
GCGATCTTTAGCACCGGTTCATAACACCAACCGGGACTAAAGTCCCACCCCTATATATATATGTCTTCTTCCTCCTCCAGCCCGAGCAAGCTTCAAAATT

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	54.10%	24.30%	17.69%	3.91%	NA
All Indica	2759	39.20%	25.20%	29.07%	6.56%	NA
All Japonica	1512	86.00%	12.80%	1.12%	0.07%	NA
Aus	269	23.00%	74.30%	2.60%	0.00%	NA
Indica I	595	23.50%	29.10%	40.50%	6.89%	NA
Indica II	465	51.60%	17.80%	25.16%	5.38%	NA
Indica III	913	47.00%	23.90%	22.34%	6.79%	NA
Indica Intermediate	786	34.70%	28.00%	30.53%	6.74%	NA
Temperate Japonica	767	90.70%	7.80%	1.30%	0.13%	NA
Tropical Japonica	504	79.60%	19.60%	0.79%	0.00%	NA
Japonica Intermediate	241	84.20%	14.50%	1.24%	0.00%	NA
VI/Aromatic	96	62.50%	35.40%	1.04%	1.04%	NA
Intermediate	90	56.70%	31.10%	10.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010276752	C -> T	LOC_Os10g20430.1	intron_variant ; MODIFIER	silent_mutation	Average:32.218; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg1010276752	C -> DEL	N	N	silent_mutation	Average:32.218; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010276752	3.73E-06	3.73E-06	mr1162_2	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