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Detailed information for vg1120560286:

Variant ID: vg1120560286 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20560286
Reference Allele: A	Alternative Allele: G,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTCCGTGCGTACGTGATCAATCAATAAAAATATAAAATCGTCATAGTGTAAACCAATTCTCTCGGAGATACACTTCGACAGTGCATGTTTCAACCCC[A/G,C]
AAATTCCGTGTTCAATTTCTAATATGCTCATGATTTATTCTTAAAAAAATGTTCAGAGGGGCGTATATCACTTCAAATCTATTTTTTTTAAACCAATTCT

Reverse complement sequence

AGAATTGGTTTAAAAAAAATAGATTTGAAGTGATATACGCCCCTCTGAACATTTTTTTAAGAATAAATCATGAGCATATTAGAAATTGAACACGGAATTT[T/C,G]
GGGGTTGAAACATGCACTGTCGAAGTGTATCTCCGAGAGAATTGGTTTACACTATGACGATTTTATATTTTTATTGATTGATCACGTACGCACGGAATAG

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	67.00%	32.50%	0.30%	0.13%	C: 0.02%
All Indica	2759	89.10%	10.50%	0.25%	0.11%	C: 0.04%
All Japonica	1512	35.60%	64.00%	0.26%	0.13%	NA
Aus	269	41.60%	57.60%	0.74%	0.00%	NA
Indica I	595	68.70%	30.80%	0.50%	0.00%	NA
Indica II	465	96.30%	3.40%	0.00%	0.22%	NA
Indica III	913	95.90%	3.80%	0.22%	0.00%	NA
Indica Intermediate	786	92.40%	7.00%	0.25%	0.25%	C: 0.13%
Temperate Japonica	767	18.50%	81.50%	0.00%	0.00%	NA
Tropical Japonica	504	49.40%	49.80%	0.60%	0.20%	NA
Japonica Intermediate	241	61.00%	38.20%	0.41%	0.41%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	56.70%	41.10%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120560286	A -> DEL	N	N	silent_mutation	Average:51.881; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1120560286	A -> G	LOC_Os11g35070.1	downstream_gene_variant ; 872.0bp to feature; MODIFIER	silent_mutation	Average:51.881; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1120560286	A -> G	LOC_Os11g35070-LOC_Os11g35080	intergenic_region ; MODIFIER	silent_mutation	Average:51.881; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1120560286	A -> C	LOC_Os11g35070.1	downstream_gene_variant ; 872.0bp to feature; MODIFIER	silent_mutation	Average:51.881; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1120560286	A -> C	LOC_Os11g35070-LOC_Os11g35080	intergenic_region ; MODIFIER	silent_mutation	Average:51.881; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120560286	NA	2.43E-07	mr1298	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
vg1120560286	NA	2.92E-06	mr1621	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