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Detailed information for vg1005760390:

Variant ID: vg1005760390 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5760390
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GCATTCAAATTTTTCATAAAACGTTTTTGGAATTATTCTCCAGGTAGTTGCATGGCTTGATAACTACTCCCTCCATCCCAAAATGTTTGACACCGTTGAC[T/A]
TTTTAAAAAATATTTGACCATTCATCTTATTCAAAAAATTTAAGTAATTATTAATTTTTTTCCTATCATTTGATTTATTGTTAAATATTTTTATTTATAC

Reverse complement sequence

GTATAAATAAAAATATTTAACAATAAATCAAATGATAGGAAAAAAATTAATAATTACTTAAATTTTTTGAATAAGATGAATGGTCAAATATTTTTTAAAA[A/T]
GTCAACGGTGTCAAACATTTTGGGATGGAGGGAGTAGTTATCAAGCCATGCAACTACCTGGAGAATAATTCCAAAAACGTTTTATGAAAAATTTGAATGC

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	76.90%	23.00%	0.13%	0.00%	NA
All Indica	2759	70.90%	28.90%	0.18%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	3.00%	97.00%	0.00%	0.00%	NA
Indica I	595	89.70%	10.30%	0.00%	0.00%	NA
Indica II	465	70.10%	29.50%	0.43%	0.00%	NA
Indica III	913	66.80%	32.90%	0.33%	0.00%	NA
Indica Intermediate	786	61.80%	38.20%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg1005760390	T -> A	LOC_Os10g10480.1	intron_variant ; MODIFIER	silent_mutation	Average:37.271; most accessible tissue: Zhenshan97 flower, score: 47.586	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005760390	NA	1.01E-06	mr1709	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
vg1005760390	NA	6.27E-12	mr1027_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
vg1005760390	NA	5.67E-08	mr1170_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
vg1005760390	NA	4.69E-07	mr1252_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
vg1005760390	9.47E-06	NA	mr1580_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
vg1005760390	6.26E-06	3.77E-10	mr1580_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
vg1005760390	NA	2.20E-06	mr1691_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
vg1005760390	NA	1.85E-12	mr1709_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
vg1005760390	NA	2.59E-08	mr1709_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
vg1005760390	NA	1.29E-07	mr1743_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
vg1005760390	NA	3.88E-07	mr1792_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
vg1005760390	4.23E-06	NA	mr1825_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
vg1005760390	3.92E-06	2.96E-10	mr1825_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
vg1005760390	NA	1.71E-06	mr1968_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