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Detailed information for vg1003099410:

Variant ID: vg1003099410 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3099410
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGGTGATTTTTTTGGATAATGGATTAAATTCCTGCCTTTACTTCAAATAAGCTACAATCACTTATTACAAAATTCTCTCAAAGAGAGCAAACATTCA[G/T]
ACCACTTCATAGCGACGGGCACGTCCAGCAAGAACAGATCCAATATACATCATCACCATGGAGACCAATACCATGTAGACTTCTCACAGCATGACTGCCA

Reverse complement sequence

TGGCAGTCATGCTGTGAGAAGTCTACATGGTATTGGTCTCCATGGTGATGATGTATATTGGATCTGTTCTTGCTGGACGTGCCCGTCGCTATGAAGTGGT[C/A]
TGAATGTTTGCTCTCTTTGAGAGAATTTTGTAATAAGTGATTGTAGCTTATTTGAAGTAAAGGCAGGAATTTAATCCATTATCCAAAAAAATCACCTTAT

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	82.20%	0.40%	8.04%	9.31%	NA
All Indica	2759	87.50%	0.00%	1.74%	10.76%	NA
All Japonica	1512	76.30%	1.30%	20.83%	1.65%	NA
Aus	269	56.90%	0.00%	1.86%	41.26%	NA
Indica I	595	88.70%	0.00%	2.18%	9.08%	NA
Indica II	465	77.80%	0.00%	1.29%	20.86%	NA
Indica III	913	91.10%	0.00%	1.64%	7.23%	NA
Indica Intermediate	786	88.00%	0.00%	1.78%	10.18%	NA
Temperate Japonica	767	64.30%	1.80%	33.77%	0.13%	NA
Tropical Japonica	504	93.30%	0.00%	2.38%	4.37%	NA
Japonica Intermediate	241	78.80%	2.10%	18.26%	0.83%	NA
VI/Aromatic	96	91.70%	0.00%	7.29%	1.04%	NA
Intermediate	90	87.80%	0.00%	5.56%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003099410	G -> T	LOC_Os10g06090.1	downstream_gene_variant ; 1965.0bp to feature; MODIFIER	silent_mutation	Average:23.042; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg1003099410	G -> T	LOC_Os10g06090-LOC_Os10g06100	intergenic_region ; MODIFIER	silent_mutation	Average:23.042; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg1003099410	G -> DEL	N	N	silent_mutation	Average:23.042; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003099410	NA	9.32E-07	mr1585	Jap_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
vg1003099410	1.59E-06	1.59E-06	mr1360_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
vg1003099410	2.61E-09	7.57E-16	mr1709_2	Jap_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