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Detailed information for vg1013277170:

Variant ID: vg1013277170 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13277170
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, G: 0.41, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GACGACGCCCGAGAGAGAGAGAAGGGGGGAGAGGACAAAGAGGAGGTGAGAGAGAATGACAGGTGGGCCCCCACCATTTAAAAAAAGAAAATGTTGATTA[T/G]
ATCTGCTACTAGTACAAAACCGCTCTAGTTTGGGTTGAGGGGGGTAATTCGTCCGGTCTTGAAAGTTCAGGGTGAGTGATGTCTGGTTTTTGGGTTCATG

Reverse complement sequence

CATGAACCCAAAAACCAGACATCACTCACCCTGAACTTTCAAGACCGGACGAATTACCCCCCTCAACCCAAACTAGAGCGGTTTTGTACTAGTAGCAGAT[A/C]
TAATCAACATTTTCTTTTTTTAAATGGTGGGGGCCCACCTGTCATTCTCTCTCACCTCCTCTTTGTCCTCTCCCCCCTTCTCTCTCTCTCGGGCGTCGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.20%	21.60%	0.21%	0.00%	NA
All Indica	2759	74.60%	25.00%	0.36%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	1.10%	98.90%	0.00%	0.00%	NA
Indica I	595	71.10%	28.20%	0.67%	0.00%	NA
Indica II	465	93.80%	5.40%	0.86%	0.00%	NA
Indica III	913	69.80%	30.10%	0.11%	0.00%	NA
Indica Intermediate	786	71.50%	28.40%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	69.80%	30.20%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg1013277170	T -> G	LOC_Os10g25620.1	upstream_gene_variant ; 4223.0bp to feature; MODIFIER	silent_mutation	Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg1013277170	T -> G	LOC_Os10g25630.1	downstream_gene_variant ; 668.0bp to feature; MODIFIER	silent_mutation	Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg1013277170	T -> G	LOC_Os10g25640.1	downstream_gene_variant ; 2183.0bp to feature; MODIFIER	silent_mutation	Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg1013277170	T -> G	LOC_Os10g25620-LOC_Os10g25630	intergenic_region ; MODIFIER	silent_mutation	Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013277170	1.55E-12	NA	mr1533	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
vg1013277170	2.25E-14	1.98E-20	mr1533	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
vg1013277170	8.99E-13	NA	mr1980	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
vg1013277170	1.15E-14	9.37E-21	mr1980	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
vg1013277170	3.50E-13	NA	mr1533_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
vg1013277170	3.92E-15	1.41E-25	mr1533_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
vg1013277170	5.66E-06	5.97E-10	mr1980_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