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Detailed information for vg1125600946:

Variant ID: vg1125600946 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25600946
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTTTGTGCAAATATGAAAATATTTATATCATACTTAAAGAACATTTGATGATGAATCTAGTCACAATAAAATAAATGAAAATTACATAAATTTTTT[G/A]
AATAAGACAAATGGTCAAACGTTAGATAAAAAATCAACGGCGTCATAGATTAAAATATGGAGGTAGTACTATGCGATTGCAAGTACAACAGGGCCAGATA

Reverse complement sequence

TATCTGGCCCTGTTGTACTTGCAATCGCATAGTACTACCTCCATATTTTAATCTATGACGCCGTTGATTTTTTATCTAACGTTTGACCATTTGTCTTATT[C/T]
AAAAAATTTATGTAATTTTCATTTATTTTATTGTGACTAGATTCATCATCAAATGTTCTTTAAGTATGATATAAATATTTTCATATTTGCACAAAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	15.60%	0.06%	0.00%	NA
All Indica	2759	94.50%	5.40%	0.04%	0.00%	NA
All Japonica	1512	62.10%	37.80%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	82.20%	17.80%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	92.20%	7.60%	0.13%	0.00%	NA
Temperate Japonica	767	79.70%	20.30%	0.00%	0.00%	NA
Tropical Japonica	504	38.50%	61.30%	0.20%	0.00%	NA
Japonica Intermediate	241	55.60%	44.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg1125600946	G -> A	LOC_Os11g42510.1	intron_variant ; MODIFIER	silent_mutation	Average:49.949; most accessible tissue: Minghui63 flower, score: 75.689	N	N	N	N
vg1125600946	G -> A	LOC_Os11g42510.2	intron_variant ; MODIFIER	silent_mutation	Average:49.949; most accessible tissue: Minghui63 flower, score: 75.689	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125600946	NA	9.33E-06	mr1192	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
vg1125600946	1.50E-10	NA	mr1238	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
vg1125600946	1.98E-13	1.15E-13	mr1238	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
vg1125600946	1.06E-08	NA	mr1309	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
vg1125600946	1.85E-08	5.88E-09	mr1309	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
vg1125600946	NA	6.09E-07	mr1453	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
vg1125600946	2.35E-08	3.60E-17	mr1484	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
vg1125600946	NA	3.86E-06	mr1835	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
vg1125600946	1.31E-06	NA	mr1841	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
vg1125600946	2.95E-07	4.31E-07	mr1841	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
vg1125600946	1.11E-06	3.37E-16	mr1900	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
vg1125600946	5.65E-09	NA	mr1238_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
vg1125600946	7.55E-11	2.79E-11	mr1238_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
vg1125600946	5.99E-09	NA	mr1484_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
vg1125600946	2.68E-10	3.39E-11	mr1484_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
vg1125600946	2.16E-10	NA	mr1841_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
vg1125600946	3.75E-12	6.48E-12	mr1841_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
vg1125600946	4.41E-08	2.30E-20	mr1900_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
vg1125600946	4.51E-07	1.67E-07	mr1900_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
vg1125600946	7.73E-06	NA	mr1945_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
vg1125600946	8.48E-07	8.48E-07	mr1945_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