Search for Variation information by Variation ID:

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

Detailed information for vg0816709248:

Variant ID: vg0816709248 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16709248
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.05, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

CAATCTTCTAGGGAATCACGCCTTTCCCTCGTGTTCATCCTGGATGCTCGGGAGTCTGTAGGGCGAGTGACAGCTCATCCTTCTCTCTGTCGGGTCGGAA[A/T]
GTGCCCTGAGAAGAGGCTACCACTGCGTCCGTTAGTCGACTGGCAGCCTCGCGTATCTGATCGCTGAAGACAAGGGAGCCATCAACTAGGTTAAGCGTTC

Reverse complement sequence

GAACGCTTAACCTAGTTGATGGCTCCCTTGTCTTCAGCGATCAGATACGCGAGGCTGCCAGTCGACTAACGGACGCAGTGGTAGCCTCTTCTCAGGGCAC[T/A]
TTCCGACCCGACAGAGAGAAGGATGAGCTGTCACTCGCCCTACAGACTCCCGAGCATCCAGGATGAACACGAGGGAAAGGCGTGATTCCCTAGAAGATTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.40%	17.60%	29.01%	9.99%	NA
All Indica	2759	15.30%	23.00%	44.87%	16.85%	NA
All Japonica	1512	96.60%	1.10%	2.31%	0.07%	NA
Aus	269	11.20%	61.00%	27.88%	0.00%	NA
Indica I	595	8.20%	22.00%	48.24%	21.51%	NA
Indica II	465	8.60%	35.90%	41.94%	13.55%	NA
Indica III	913	25.00%	16.00%	44.58%	14.46%	NA
Indica Intermediate	786	13.40%	24.20%	44.40%	18.07%	NA
Temperate Japonica	767	99.00%	0.40%	0.52%	0.13%	NA
Tropical Japonica	504	92.50%	2.20%	5.36%	0.00%	NA
Japonica Intermediate	241	97.50%	0.80%	1.66%	0.00%	NA
VI/Aromatic	96	86.50%	7.30%	6.25%	0.00%	NA
Intermediate	90	62.20%	12.20%	18.89%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816709248	A -> T	LOC_Os08g27370.1	upstream_gene_variant ; 4256.0bp to feature; MODIFIER	silent_mutation	Average:9.662; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0816709248	A -> T	LOC_Os08g27360.1	intron_variant ; MODIFIER	silent_mutation	Average:9.662; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0816709248	A -> DEL	N	N	silent_mutation	Average:9.662; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816709248	4.35E-06	NA	mr1911_2	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