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Detailed information for vg1119865643:

Variant ID: vg1119865643 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19865643
Reference Allele: G	Alternative Allele: A,C,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGTTGTCTATATTGCTAGATGAATACCTATTATGATTAGTTATTTCATAGATCATTCGTGTAATTCGGAAGCTATGATCATTTTTCTTAAAAATATTT[G/A,C,T]
TTTATCTCCTAGAAAGATCATTTTAAAAGTATCAAGGTCAATTTGTATAGGTACGTAGCTCTCATATGCATGTTAAGAGAAATTAATTAAGTTGGCAGAA

Reverse complement sequence

TTCTGCCAACTTAATTAATTTCTCTTAACATGCATATGAGAGCTACGTACCTATACAAATTGACCTTGATACTTTTAAAATGATCTTTCTAGGAGATAAA[C/T,G,A]
AAATATTTTTAAGAAAAATGATCATAGCTTCCGAATTACACGAATGATCTATGAAATAACTAATCATAATAGGTATTCATCTAGCAATATAGACAACAGG

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	55.70%	6.30%	5.25%	30.36%	C: 1.93%; T: 0.53%
All Indica	2759	46.80%	9.00%	7.72%	32.69%	C: 3.19%; T: 0.62%
All Japonica	1512	61.40%	3.00%	2.18%	32.80%	T: 0.46%; C: 0.07%
Aus	269	95.20%	0.00%	0.00%	4.46%	T: 0.37%
Indica I	595	28.20%	17.00%	9.92%	42.18%	T: 2.69%
Indica II	465	71.40%	4.70%	5.81%	18.06%	NA
Indica III	913	47.20%	7.10%	8.11%	29.90%	C: 7.67%
Indica Intermediate	786	45.80%	7.60%	6.74%	37.40%	C: 2.29%; T: 0.13%
Temperate Japonica	767	84.50%	1.00%	0.26%	14.21%	NA
Tropical Japonica	504	34.70%	6.00%	4.17%	53.57%	T: 1.39%; C: 0.20%
Japonica Intermediate	241	44.00%	3.30%	4.15%	48.55%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	2.20%	2.22%	27.78%	C: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119865643	G -> T	LOC_Os11g33990.1	downstream_gene_variant ; 4680.0bp to feature; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> T	LOC_Os11g33970.1	intron_variant ; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> A	LOC_Os11g33990.1	downstream_gene_variant ; 4680.0bp to feature; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> A	LOC_Os11g33970.1	intron_variant ; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> DEL	N	N	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> C	LOC_Os11g33990.1	downstream_gene_variant ; 4680.0bp to feature; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1119865643	G -> C	LOC_Os11g33970.1	intron_variant ; MODIFIER	silent_mutation	Average:32.083; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119865643	NA	2.74E-06	mr1519	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
vg1119865643	5.42E-07	NA	mr1519_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
vg1119865643	2.28E-07	1.58E-10	mr1519_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