Search for Variation information by Variation ID:

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

Detailed information for vg1119866382:

Variant ID: vg1119866382 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19866382
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTTTAAGATTTTTTAATACTTTGTCTAATTTAATAGCACCATGTAGCGATTTAGAAGAGTTCGTAAGATTTTAAAGTGACGGAGGAAGAGTTGATAGA[T/C]
CTAGTAGTTGGTCTATTTGTGATTTATTTTGCTAATAAAAGTAATTTTGATTTTATTTTCTCATGAAATAGAAAATAACAAAGAAAGGAACAGAAGGAAC

Reverse complement sequence

GTTCCTTCTGTTCCTTTCTTTGTTATTTTCTATTTCATGAGAAAATAAAATCAAAATTACTTTTATTAGCAAAATAAATCACAAATAGACCAACTACTAG[A/G]
TCTATCAACTCTTCCTCCGTCACTTTAAAATCTTACGAACTCTTCTAAATCGCTACATGGTGCTATTAAATTAGACAAAGTATTAAAAAATCTTAAACAA

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	54.80%	2.40%	1.97%	40.82%	NA
All Indica	2759	47.20%	4.10%	3.01%	45.70%	NA
All Japonica	1512	58.70%	0.00%	0.33%	40.94%	NA
Aus	269	94.40%	0.00%	0.00%	5.58%	NA
Indica I	595	26.90%	12.90%	4.20%	55.97%	NA
Indica II	465	69.90%	1.30%	2.58%	26.24%	NA
Indica III	913	52.40%	0.30%	2.52%	44.80%	NA
Indica Intermediate	786	43.00%	3.60%	2.93%	50.51%	NA
Temperate Japonica	767	82.50%	0.00%	0.00%	17.47%	NA
Tropical Japonica	504	33.70%	0.00%	0.99%	65.28%	NA
Japonica Intermediate	241	35.30%	0.00%	0.00%	64.73%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	56.70%	1.10%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119866382	T -> DEL	N	N	silent_mutation	Average:42.553; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N
vg1119866382	T -> C	LOC_Os11g33990.1	downstream_gene_variant ; 3941.0bp to feature; MODIFIER	silent_mutation	Average:42.553; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N
vg1119866382	T -> C	LOC_Os11g33970.1	intron_variant ; MODIFIER	silent_mutation	Average:42.553; most accessible tissue: Minghui63 young leaf, score: 81.798	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119866382	1.25E-06	7.83E-08	mr1519	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
vg1119866382	8.58E-06	3.60E-09	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