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Detailed information for vg1003706835:

Variant ID: vg1003706835 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3706835
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, A: 0.09, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAATTATTCATCTTAGCTCACCATGGATGGTGGACATGTTAATTCGTGCCTCCGGCAGCATGCTCACATCATCATACTTAGAAGAAAAAAAAAGTGCC[C/A,T]
TGCATGTATATATATATGTAACTACCTCATGCCCCTCTTTTCATTAAAGAAAAAAATTCTATACCCATGCATGCACACCGGGATGCACCGGCTAGCCCTC

Reverse complement sequence

GAGGGCTAGCCGGTGCATCCCGGTGTGCATGCATGGGTATAGAATTTTTTTCTTTAATGAAAAGAGGGGCATGAGGTAGTTACATATATATATACATGCA[G/T,A]
GGCACTTTTTTTTTCTTCTAAGTATGATGATGTGAGCATGCTGCCGGAGGCACGAATTAACATGTCCACCATCCATGGTGAGCTAAGATGAATAATTTGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.60%	30.70%	0.97%	23.76%	T: 0.02%
All Indica	2759	15.20%	45.10%	0.91%	38.78%	T: 0.04%
All Japonica	1512	94.60%	1.50%	1.12%	2.84%	NA
Aus	269	41.30%	58.70%	0.00%	0.00%	NA
Indica I	595	3.20%	63.40%	0.34%	33.11%	NA
Indica II	465	30.80%	33.30%	0.65%	35.27%	NA
Indica III	913	16.60%	32.70%	0.99%	49.51%	T: 0.11%
Indica Intermediate	786	13.20%	52.70%	1.40%	32.70%	NA
Temperate Japonica	767	97.90%	0.40%	0.39%	1.30%	NA
Tropical Japonica	504	91.50%	3.20%	1.39%	3.97%	NA
Japonica Intermediate	241	90.50%	1.20%	2.90%	5.39%	NA
VI/Aromatic	96	95.80%	1.00%	2.08%	1.04%	NA
Intermediate	90	62.20%	25.60%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003706835	C -> T	LOC_Os10g07050.1	upstream_gene_variant ; 3470.0bp to feature; MODIFIER	silent_mutation	Average:16.268; most accessible tissue: Callus, score: 29.731	N	N	N	N
vg1003706835	C -> T	LOC_Os10g07050-LOC_Os10g07060	intergenic_region ; MODIFIER	silent_mutation	Average:16.268; most accessible tissue: Callus, score: 29.731	N	N	N	N
vg1003706835	C -> A	LOC_Os10g07050.1	upstream_gene_variant ; 3470.0bp to feature; MODIFIER	silent_mutation	Average:16.268; most accessible tissue: Callus, score: 29.731	N	N	N	N
vg1003706835	C -> A	LOC_Os10g07050-LOC_Os10g07060	intergenic_region ; MODIFIER	silent_mutation	Average:16.268; most accessible tissue: Callus, score: 29.731	N	N	N	N
vg1003706835	C -> DEL	N	N	silent_mutation	Average:16.268; most accessible tissue: Callus, score: 29.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003706835	2.96E-06	1.49E-19	mr1836_2	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
vg1003706835	NA	2.93E-08	mr1836_2	Ind_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