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Detailed information for vg1122183720:

Variant ID: vg1122183720 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22183720
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTAGATCTATCTTTAAAAGAAAATCCCAAAACCCCCTCCCGTTCCTCCCATTCCTCCGATTCCTCTCTCCCTACCATTCCTTCTCTGTTCTTTCTTTA[C/T]
CTCCATAGAAACTAAATCCAACATTATCTTTGTGATAAAAAAAACTCCCACAAATGGATTCCGCCTAACAAGTCTAACCAGTTTCCCCTGTGTCATGTGC

Reverse complement sequence

GCACATGACACAGGGGAAACTGGTTAGACTTGTTAGGCGGAATCCATTTGTGGGAGTTTTTTTTATCACAAAGATAATGTTGGATTTAGTTTCTATGGAG[G/A]
TAAAGAAAGAACAGAGAAGGAATGGTAGGGAGAGAGGAATCGGAGGAATGGGAGGAACGGGAGGGGGTTTTGGGATTTTCTTTTAAAGATAGATCTAACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.00%	0.20%	20.42%	28.33%	NA
All Indica	2759	28.30%	0.40%	29.03%	42.26%	NA
All Japonica	1512	92.70%	0.00%	1.65%	5.69%	NA
Aus	269	61.70%	0.00%	32.34%	5.95%	NA
Indica I	595	37.60%	0.50%	23.53%	38.32%	NA
Indica II	465	4.70%	0.40%	27.96%	66.88%	NA
Indica III	913	35.90%	0.10%	32.42%	31.54%	NA
Indica Intermediate	786	26.50%	0.50%	29.90%	43.13%	NA
Temperate Japonica	767	94.40%	0.00%	0.65%	4.95%	NA
Tropical Japonica	504	92.90%	0.00%	1.98%	5.16%	NA
Japonica Intermediate	241	86.70%	0.00%	4.15%	9.13%	NA
VI/Aromatic	96	18.80%	0.00%	38.54%	42.71%	NA
Intermediate	90	50.00%	0.00%	16.67%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122183720	C -> T	LOC_Os11g37560.1	upstream_gene_variant ; 4837.0bp to feature; MODIFIER	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N
vg1122183720	C -> T	LOC_Os11g37570.1	upstream_gene_variant ; 2164.0bp to feature; MODIFIER	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N
vg1122183720	C -> T	LOC_Os11g37560.2	upstream_gene_variant ; 4837.0bp to feature; MODIFIER	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N
vg1122183720	C -> T	LOC_Os11g37580.1	downstream_gene_variant ; 2744.0bp to feature; MODIFIER	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N
vg1122183720	C -> T	LOC_Os11g37570-LOC_Os11g37580	intergenic_region ; MODIFIER	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N
vg1122183720	C -> DEL	N	N	silent_mutation	Average:20.253; most accessible tissue: Callus, score: 35.147	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122183720	NA	2.29E-08	mr1990	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
vg1122183720	4.01E-06	2.89E-06	mr1990	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