Search for Variation information by Variation ID:

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

Detailed information for vg1221792096:

Variant ID: vg1221792096 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21792096
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGAGGAAAGAACATTGAATTGGACTGCTGTAGTCTGGGTCCATGATCTACTTGTTCATTGCGCACAAAGATATTCGATCATGGAGGACAGGTTTTTT[G/A]
TCATTTGTTTTCACTGCATGCATGCTGTACATCTTAGTTACAAGACAGTTGTAGTGTAAATACTTAGTAATATCATTACATGTCTTGTGCCCTCTAGAAC

Reverse complement sequence

GTTCTAGAGGGCACAAGACATGTAATGATATTACTAAGTATTTACACTACAACTGTCTTGTAACTAAGATGTACAGCATGCATGCAGTGAAAACAAATGA[C/T]
AAAAAACCTGTCCTCCATGATCGAATATCTTTGTGCGCAATGAACAAGTAGATCATGGACCCAGACTACAGCAGTCCAATTCAATGTTCTTTCCTCTAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.80%	24.10%	0.06%	0.00%	NA
All Indica	2759	73.60%	26.40%	0.07%	0.00%	NA
All Japonica	1512	74.10%	25.80%	0.07%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	49.90%	49.90%	0.17%	0.00%	NA
Indica II	465	86.90%	13.10%	0.00%	0.00%	NA
Indica III	913	80.20%	19.80%	0.00%	0.00%	NA
Indica Intermediate	786	76.00%	23.90%	0.13%	0.00%	NA
Temperate Japonica	767	85.90%	14.10%	0.00%	0.00%	NA
Tropical Japonica	504	69.80%	30.20%	0.00%	0.00%	NA
Japonica Intermediate	241	45.60%	53.90%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg1221792096	G -> A	LOC_Os12g35770-LOC_Os12g35790	intergenic_region ; MODIFIER	silent_mutation	Average:46.488; most accessible tissue: Zhenshan97 young leaf, score: 71.497	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221792096	1.58E-06	7.33E-08	mr1932	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