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Detailed information for vg1119999188:

Variant ID: vg1119999188 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19999188
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAATGTACAATTATTGCTAGAGCTACCTATTCTAAACAGATGCAAAATAATTTCATATAACCTCTCGCCCACCCACCGGCGATCACTTTCCCCAAAT[C/T]
ATGGGTTCTTCGTCCCTACTCTCCATGTTGTCGATGGAATTGTCGCTATGGATCCAAGCCTCCTCCTCTCCCTCCCCCTTACCATGGTGACACCATTGCC

Reverse complement sequence

GGCAATGGTGTCACCATGGTAAGGGGGAGGGAGAGGAGGAGGCTTGGATCCATAGCGACAATTCCATCGACAACATGGAGAGTAGGGACGAAGAACCCAT[G/A]
ATTTGGGGAAAGTGATCGCCGGTGGGTGGGCGAGAGGTTATATGAAATTATTTTGCATCTGTTTAGAATAGGTAGCTCTAGCAATAATTGTACATTAAAA

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	97.60%	2.10%	0.32%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.60%	6.40%	0.99%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.40%	11.90%	1.69%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119999188	C -> T	LOC_Os11g34150.1	upstream_gene_variant ; 2215.0bp to feature; MODIFIER	silent_mutation	Average:73.727; most accessible tissue: Callus, score: 83.698	N	N	N	N
vg1119999188	C -> T	LOC_Os11g34150.2	upstream_gene_variant ; 2215.0bp to feature; MODIFIER	silent_mutation	Average:73.727; most accessible tissue: Callus, score: 83.698	N	N	N	N
vg1119999188	C -> T	LOC_Os11g34150.3	upstream_gene_variant ; 2215.0bp to feature; MODIFIER	silent_mutation	Average:73.727; most accessible tissue: Callus, score: 83.698	N	N	N	N
vg1119999188	C -> T	LOC_Os11g34160.1	downstream_gene_variant ; 2818.0bp to feature; MODIFIER	silent_mutation	Average:73.727; most accessible tissue: Callus, score: 83.698	N	N	N	N
vg1119999188	C -> T	LOC_Os11g34150-LOC_Os11g34160	intergenic_region ; MODIFIER	silent_mutation	Average:73.727; most accessible tissue: Callus, score: 83.698	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119999188	9.30E-06	5.96E-08	mr1300	Jap_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
vg1119999188	1.13E-06	5.07E-09	mr1310	Jap_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
vg1119999188	1.42E-06	1.42E-06	mr1409	Jap_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
vg1119999188	NA	9.99E-06	mr1765	Jap_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
vg1119999188	5.10E-07	2.94E-09	mr1926	Jap_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
vg1119999188	2.51E-06	3.38E-07	mr1959	Jap_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