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Detailed information for vg1009564247:

Variant ID: vg1009564247 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9564247
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCGCTGTTGCAGTAGGCGATGTGCCTCGCTTGATACCACACCACCTTTGCTGGGCCTCCCCTCTTTGACTTACTTCCTTCACAATTCACTCTTTGCTC[T/G]
TTTGTATCTTGATGCCTCACAGATAGGGCAGACATCCAAGTTAGCGTATTCCTTGTAATACAAAATGCAGTCGTTCGGACATGCATGAATTCTTCTGACC

Reverse complement sequence

GGTCAGAAGAATTCATGCATGTCCGAACGACTGCATTTTGTATTACAAGGAATACGCTAACTTGGATGTCTGCCCTATCTGTGAGGCATCAAGATACAAA[A/C]
GAGCAAAGAGTGAATTGTGAAGGAAGTAAGTCAAAGAGGGGAGGCCCAGCAAAGGTGGTGTGGTATCAAGCGAGGCACATCGCCTACTGCAACAGCGGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.60%	12.20%	0.23%	8.95%	NA
All Indica	2759	98.40%	1.00%	0.07%	0.51%	NA
All Japonica	1512	38.10%	35.10%	0.46%	26.39%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	97.50%	1.10%	0.11%	1.31%	NA
Indica Intermediate	786	98.30%	1.40%	0.13%	0.13%	NA
Temperate Japonica	767	18.80%	54.00%	0.52%	26.73%	NA
Tropical Japonica	504	58.30%	6.90%	0.40%	34.33%	NA
Japonica Intermediate	241	57.30%	33.60%	0.41%	8.71%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	15.60%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009564247	T -> G	LOC_Os10g18800.1	upstream_gene_variant ; 3226.0bp to feature; MODIFIER	silent_mutation	Average:22.944; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1009564247	T -> G	LOC_Os10g18790.1	intron_variant ; MODIFIER	silent_mutation	Average:22.944; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1009564247	T -> DEL	N	N	silent_mutation	Average:22.944; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009564247	3.24E-06	NA	mr1305	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
vg1009564247	5.02E-06	NA	mr1586	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