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Detailed information for vg1109529985:

Variant ID: vg1109529985 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9529985
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCAGGGACAACAAGGACAGGATCCGAGTTCTCTATCTGAAGATAGAACCATCTTTCCCGCCATTTGCTGCGAGAAGAGGGGCACTGGAAAGGGATGTA[G/T]
CGCAACTTCAGGCGATCCCGAAGTCGAAATCCAACACATCCGGACACCCTATTGGGTTCCATCTAGCGCAACTCATAGTAAAATCGGAAAAGATCAAGGA

Reverse complement sequence

TCCTTGATCTTTTCCGATTTTACTATGAGTTGCGCTAGATGGAACCCAATAGGGTGTCCGGATGTGTTGGATTTCGACTTCGGGATCGCCTGAAGTTGCG[C/A]
TACATCCCTTTCCAGTGCCCCTCTTCTCGCAGCAAATGGCGGGAAAGATGGTTCTATCTTCAGATAGAGAACTCGGATCCTGTCCTTGTTGTCCCTGAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.60%	34.70%	1.74%	6.96%	NA
All Indica	2759	87.40%	4.50%	2.14%	5.98%	NA
All Japonica	1512	2.10%	95.90%	0.13%	1.85%	NA
Aus	269	66.50%	3.30%	5.58%	24.54%	NA
Indica I	595	80.80%	7.70%	3.19%	8.24%	NA
Indica II	465	87.30%	4.10%	2.58%	6.02%	NA
Indica III	913	92.60%	1.20%	1.75%	4.49%	NA
Indica Intermediate	786	86.30%	6.20%	1.53%	5.98%	NA
Temperate Japonica	767	1.00%	97.10%	0.13%	1.69%	NA
Tropical Japonica	504	3.60%	94.40%	0.20%	1.79%	NA
Japonica Intermediate	241	2.50%	95.00%	0.00%	2.49%	NA
VI/Aromatic	96	16.70%	19.80%	2.08%	61.46%	NA
Intermediate	90	42.20%	41.10%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109529985	G -> T	LOC_Os11g17160.1	synonymous_variant ; p.Arg65Arg; LOW	synonymous_codon	Average:21.776; most accessible tissue: Callus, score: 39.317	N	N	N	N
vg1109529985	G -> DEL	LOC_Os11g17160.1	N	frameshift_variant	Average:21.776; most accessible tissue: Callus, score: 39.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109529985	NA	5.35E-19	Yield	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1109529985	NA	3.11E-07	mr1220	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
vg1109529985	NA	1.41E-08	mr1986	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
vg1109529985	NA	5.84E-06	mr1220_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
vg1109529985	1.49E-06	1.49E-06	mr1405_2	Ind_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
vg1109529985	NA	5.42E-13	mr1521_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
vg1109529985	8.08E-06	1.97E-06	mr1554_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
vg1109529985	2.64E-07	NA	mr1558_2	Ind_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
vg1109529985	NA	1.27E-10	mr1646_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
vg1109529985	3.36E-06	2.47E-06	mr1646_2	Ind_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
vg1109529985	NA	1.05E-08	mr1751_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
vg1109529985	NA	5.14E-11	mr1781_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
vg1109529985	NA	5.71E-09	mr1835_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