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Detailed information for vg1128224267:

Variant ID: vg1128224267 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28224267
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, C: 0.37, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTGTCAAATTTACCTTATTCGCTCTAGTGCAGACGCCATGGATCGAACTGTAGAGCAGCTTGTCAACAAGTTAACTCAGGTGGTTTTACCAACCAAC[C/G]
CAAAGCAAGTGAATATTCCAGTGCTGTAACTGATCTCAATCAGACAGAACGGTTCATTTTTGCCATTCTAATTCCACCAGCGGATTGTGACGATATTTTG

Reverse complement sequence

CAAAATATCGTCACAATCCGCTGGTGGAATTAGAATGGCAAAAATGAACCGTTCTGTCTGATTGAGATCAGTTACAGCACTGGAATATTCACTTGCTTTG[G/C]
GTTGGTTGGTAAAACCACCTGAGTTAACTTGTTGACAAGCTGCTCTACAGTTCGATCCATGGCGTCTGCACTAGAGCGAATAAGGTAAATTTGACAGTGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	19.60%	9.70%	1.76%	68.98%	NA
All Indica	2759	26.30%	9.70%	1.92%	62.09%	NA
All Japonica	1512	8.20%	10.80%	0.60%	80.42%	NA
Aus	269	16.40%	2.20%	2.23%	79.18%	NA
Indica I	595	42.70%	22.90%	0.67%	33.78%	NA
Indica II	465	2.40%	15.10%	0.22%	82.37%	NA
Indica III	913	33.20%	0.20%	3.29%	63.31%	NA
Indica Intermediate	786	20.00%	7.60%	2.29%	70.10%	NA
Temperate Japonica	767	12.50%	17.60%	0.52%	69.36%	NA
Tropical Japonica	504	3.40%	0.80%	0.20%	95.63%	NA
Japonica Intermediate	241	4.60%	10.00%	1.66%	83.82%	NA
VI/Aromatic	96	15.60%	3.10%	13.54%	67.71%	NA
Intermediate	90	17.80%	21.10%	2.22%	58.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128224267	C -> DEL	N	N	silent_mutation	Average:56.944; most accessible tissue: Callus, score: 83.014	N	N	N	N
vg1128224267	C -> G	LOC_Os11g46960.1	upstream_gene_variant ; 67.0bp to feature; MODIFIER	silent_mutation	Average:56.944; most accessible tissue: Callus, score: 83.014	N	N	N	N
vg1128224267	C -> G	LOC_Os11g46970.1	upstream_gene_variant ; 4646.0bp to feature; MODIFIER	silent_mutation	Average:56.944; most accessible tissue: Callus, score: 83.014	N	N	N	N
vg1128224267	C -> G	LOC_Os11g46950.1	downstream_gene_variant ; 1003.0bp to feature; MODIFIER	silent_mutation	Average:56.944; most accessible tissue: Callus, score: 83.014	N	N	N	N
vg1128224267	C -> G	LOC_Os11g46950-LOC_Os11g46960	intergenic_region ; MODIFIER	silent_mutation	Average:56.944; most accessible tissue: Callus, score: 83.014	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128224267	NA	2.16E-06	mr1295	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
vg1128224267	4.19E-07	NA	mr1548	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
vg1128224267	NA	1.98E-06	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
vg1128224267	5.58E-06	NA	mr1662	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
vg1128224267	NA	1.36E-06	mr1662	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
vg1128224267	NA	1.36E-08	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
vg1128224267	NA	2.03E-06	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