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Detailed information for vg0610480987:

Variant ID: vg0610480987 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10480987
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGATATGTTTTAGTGAGTTTAAATCTCTATAAATAGTACTCCCTCCGTTTCAAAATATTTGACACCGTTGACTTTTTAGCACATGTTTAACCATTCGTC[A/T]
AATTCAAAAAAATTTGTGAAATATGTAAAACTATGTGTACATGAAAGTATATTTAACAATGAATCAAATGATATAAAAAAATAAATAATTACTTAAATTT

Reverse complement sequence

AAATTTAAGTAATTATTTATTTTTTTATATCATTTGATTCATTGTTAAATATACTTTCATGTACACATAGTTTTACATATTTCACAAATTTTTTTGAATT[T/A]
GACGAATGGTTAAACATGTGCTAAAAAGTCAACGGTGTCAAATATTTTGAAACGGAGGGAGTACTATTTATAGAGATTTAAACTCACTAAAACATATCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.40%	9.90%	0.17%	42.55%	NA
All Indica	2759	72.00%	0.80%	0.07%	27.18%	NA
All Japonica	1512	9.90%	28.90%	0.26%	60.91%	NA
Aus	269	16.70%	1.50%	0.00%	81.78%	NA
Indica I	595	92.10%	1.20%	0.00%	6.72%	NA
Indica II	465	89.70%	0.90%	0.00%	9.46%	NA
Indica III	913	55.60%	0.10%	0.00%	44.25%	NA
Indica Intermediate	786	65.30%	1.10%	0.25%	33.33%	NA
Temperate Japonica	767	2.90%	51.40%	0.26%	45.50%	NA
Tropical Japonica	504	22.80%	0.80%	0.00%	76.39%	NA
Japonica Intermediate	241	5.40%	16.20%	0.83%	77.59%	NA
VI/Aromatic	96	7.30%	0.00%	1.04%	91.67%	NA
Intermediate	90	56.70%	6.70%	1.11%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610480987	A -> T	LOC_Os06g18010.1	downstream_gene_variant ; 85.0bp to feature; MODIFIER	silent_mutation	Average:54.157; most accessible tissue: Minghui63 flower, score: 72.046	N	N	N	N
vg0610480987	A -> T	LOC_Os06g18010-LOC_Os06g18020	intergenic_region ; MODIFIER	silent_mutation	Average:54.157; most accessible tissue: Minghui63 flower, score: 72.046	N	N	N	N
vg0610480987	A -> DEL	N	N	silent_mutation	Average:54.157; most accessible tissue: Minghui63 flower, score: 72.046	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610480987	3.62E-11	NA	mr1087	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
vg0610480987	2.49E-06	1.42E-09	mr1087	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
vg0610480987	NA	9.11E-06	mr1096	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
vg0610480987	NA	7.10E-13	mr1844	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
vg0610480987	NA	1.13E-06	mr1844	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
vg0610480987	5.23E-19	NA	mr1087_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
vg0610480987	2.29E-11	1.66E-20	mr1087_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
vg0610480987	3.30E-06	NA	mr1091_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
vg0610480987	NA	5.69E-08	mr1091_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
vg0610480987	NA	3.32E-06	mr1094_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
vg0610480987	NA	7.22E-07	mr1096_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
vg0610480987	NA	4.06E-13	mr1844_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
vg0610480987	NA	3.18E-06	mr1844_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