Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1116469864:

Variant ID: vg1116469864 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16469864
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTACTAATCACAACCTTTTTGGTTTCAGGACACCATAACTTATAGCCTTTCACACTAGACGGATAACCAAGAAAAATGCACTTATTAGCTCTAGGCTC[C/T]
AATTTACCATTATCAACATGAGCATAAGCAGTACAACCAAATACTCTTAAGTCTGAATAATTTGCTGGGGAACCAGACCATACCTCAATTGGAGTCTTCT

Reverse complement sequence

AGAAGACTCCAATTGAGGTATGGTCTGGTTCCCCAGCAAATTATTCAGACTTAAGAGTATTTGGTTGTACTGCTTATGCTCATGTTGATAATGGTAAATT[G/A]
GAGCCTAGAGCTAATAAGTGCATTTTTCTTGGTTATCCGTCTAGTGTGAAAGGCTATAAGTTATGGTGTCCTGAAACCAAAAAGGTTGTGATTAGTAGAA

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	61.80%	35.80%	0.89%	1.52%	NA
All Indica	2759	93.50%	3.30%	0.72%	2.43%	NA
All Japonica	1512	3.80%	95.80%	0.13%	0.26%	NA
Aus	269	84.40%	9.70%	5.95%	0.00%	NA
Indica I	595	97.60%	1.50%	0.84%	0.00%	NA
Indica II	465	95.50%	0.40%	0.22%	3.87%	NA
Indica III	913	91.20%	3.60%	0.88%	4.27%	NA
Indica Intermediate	786	92.00%	6.00%	0.76%	1.27%	NA
Temperate Japonica	767	3.00%	97.00%	0.00%	0.00%	NA
Tropical Japonica	504	5.00%	93.80%	0.40%	0.79%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	52.20%	42.20%	4.44%	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
vg1116469864	C -> T	LOC_Os11g28550.1	synonymous_variant ; p.Leu284Leu; LOW	synonymous_codon	Average:16.877; most accessible tissue: Zhenshan97 flag leaf, score: 24.112	N	N	N	N
vg1116469864	C -> DEL	LOC_Os11g28550.1	N	frameshift_variant	Average:16.877; most accessible tissue: Zhenshan97 flag leaf, score: 24.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116469864	NA	2.98E-14	mr1376	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
vg1116469864	NA	2.98E-14	mr1431	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
vg1116469864	NA	2.37E-10	mr1595	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
vg1116469864	NA	8.66E-09	mr1600_2	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
vg1116469864	3.94E-06	5.81E-09	mr1672_2	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