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Detailed information for vg1119521777:

Variant ID: vg1119521777 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19521777
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.13, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TCATCTGTAACGGGCTATAGTTTGACTGGTCGTCTGGGTCAAAGCTATCGGTGACGGGCTTTACTTAGGGCCCGATTGAGATATATTCATTCGTGACGGC[T/C]
GTTTGCCCGATTGAGATAACTCTTCACATCAGTGACTTCTAGCCTGTGACGGACGCTGTGCCCGATTGAGATGAGGGTATCCGTTCTAGTGAGTGTCTTT

Reverse complement sequence

AAAGACACTCACTAGAACGGATACCCTCATCTCAATCGGGCACAGCGTCCGTCACAGGCTAGAAGTCACTGATGTGAAGAGTTATCTCAATCGGGCAAAC[A/G]
GCCGTCACGAATGAATATATCTCAATCGGGCCCTAAGTAAAGCCCGTCACCGATAGCTTTGACCCAGACGACCAGTCAAACTATAGCCCGTTACAGATGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.70%	13.30%	2.71%	49.26%	NA
All Indica	2759	6.00%	11.30%	4.10%	78.54%	NA
All Japonica	1512	89.00%	8.00%	0.20%	2.84%	NA
Aus	269	7.40%	64.30%	4.09%	24.16%	NA
Indica I	595	7.70%	7.70%	2.69%	81.85%	NA
Indica II	465	5.60%	23.00%	3.23%	68.17%	NA
Indica III	913	3.90%	6.40%	5.59%	84.12%	NA
Indica Intermediate	786	7.40%	13.00%	3.94%	75.70%	NA
Temperate Japonica	767	94.00%	2.60%	0.00%	3.39%	NA
Tropical Japonica	504	87.30%	9.70%	0.40%	2.58%	NA
Japonica Intermediate	241	76.30%	21.60%	0.41%	1.66%	NA
VI/Aromatic	96	76.00%	1.00%	1.04%	21.88%	NA
Intermediate	90	41.10%	23.30%	0.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119521777	T -> DEL	N	N	silent_mutation	Average:23.476; most accessible tissue: Callus, score: 50.178	N	N	N	N
vg1119521777	T -> C	LOC_Os11g33030.1	upstream_gene_variant ; 2005.0bp to feature; MODIFIER	silent_mutation	Average:23.476; most accessible tissue: Callus, score: 50.178	N	N	N	N
vg1119521777	T -> C	LOC_Os11g33020.1	downstream_gene_variant ; 745.0bp to feature; MODIFIER	silent_mutation	Average:23.476; most accessible tissue: Callus, score: 50.178	N	N	N	N
vg1119521777	T -> C	LOC_Os11g33020-LOC_Os11g33030	intergenic_region ; MODIFIER	silent_mutation	Average:23.476; most accessible tissue: Callus, score: 50.178	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119521777	NA	9.29E-06	mr1231	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
vg1119521777	6.23E-06	3.10E-07	mr1984	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