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Detailed information for vg1126333420:

Variant ID: vg1126333420 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26333420
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CATATATATACAGAACAAACAAGACAAGCCATGACGTACACATGATGCAACCATCATATCACACTGCACATAAATTCAGTCATTAACTTCACCCCGATTT[A/G]
CATTTTTGTAGGCGGCTATTTGGCTCTAAGGGCTATGTCCGCCTGCGAAAATAAATACCCAACGTTGACGAAAATGCTTTTTCTAGTAGTGCCTCTTGGC

Reverse complement sequence

GCCAAGAGGCACTACTAGAAAAAGCATTTTCGTCAACGTTGGGTATTTATTTTCGCAGGCGGACATAGCCCTTAGAGCCAAATAGCCGCCTACAAAAATG[T/C]
AAATCGGGGTGAAGTTAATGACTGAATTTATGTGCAGTGTGATATGATGGTTGCATCATGTGTACGTCATGGCTTGTCTTGTTTGTTCTGTATATATATG

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	83.50%	9.30%	2.43%	4.74%	NA
All Indica	2759	83.50%	4.80%	4.02%	7.72%	NA
All Japonica	1512	81.70%	17.80%	0.20%	0.26%	NA
Aus	269	88.50%	11.50%	0.00%	0.00%	NA
Indica I	595	62.90%	2.20%	10.25%	24.71%	NA
Indica II	465	81.50%	2.40%	6.45%	9.68%	NA
Indica III	913	91.20%	8.20%	0.22%	0.33%	NA
Indica Intermediate	786	91.20%	4.20%	2.29%	2.29%	NA
Temperate Japonica	767	68.60%	30.50%	0.39%	0.52%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	88.40%	11.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	10.00%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126333420	A -> DEL	N	N	silent_mutation	Average:50.585; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1126333420	A -> G	LOC_Os11g43650.1	downstream_gene_variant ; 2963.0bp to feature; MODIFIER	silent_mutation	Average:50.585; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1126333420	A -> G	LOC_Os11g43650-LOC_Os11g43660	intergenic_region ; MODIFIER	silent_mutation	Average:50.585; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126333420	6.30E-07	NA	mr1191	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
vg1126333420	1.39E-09	2.54E-12	mr1191	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
vg1126333420	9.45E-07	9.10E-09	mr1644	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
vg1126333420	1.84E-09	9.53E-13	mr1644	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
vg1126333420	NA	7.23E-06	mr1745	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
vg1126333420	NA	2.76E-08	mr1010_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
vg1126333420	NA	9.19E-06	mr1164_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
vg1126333420	3.84E-11	6.49E-19	mr1191_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
vg1126333420	NA	7.73E-06	mr1206_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
vg1126333420	NA	3.15E-06	mr1332_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
vg1126333420	NA	1.25E-06	mr1530_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
vg1126333420	NA	4.89E-06	mr1576_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
vg1126333420	NA	2.32E-07	mr1662_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
vg1126333420	NA	9.25E-08	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
vg1126333420	NA	1.24E-08	mr1745_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
vg1126333420	NA	9.32E-08	mr1748_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
vg1126333420	NA	4.76E-06	mr1865_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
vg1126333420	NA	8.94E-06	mr1902_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
vg1126333420	2.44E-06	2.44E-06	mr1972_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