Search for Variation information by Variation ID:

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

Detailed information for vg1216994127:

Variant ID: vg1216994127 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16994127
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCGTGTTTATGACAGGTGGGACCAGGTATTAATAGTGTAGTACTCCCTCCATCTACTTTTGATAGTCATATTTCCAAATCTGAAAATTTTATTTTTGA[T/G]
AGGCATATTTCAATCCAACAACCTATCATCTTAATGACTTTCTCGAATTTAATGCATGACTCTCTATTCTTTCACACATGATTGGCTACATGGGCATTGA

Reverse complement sequence

TCAATGCCCATGTAGCCAATCATGTGTGAAAGAATAGAGAGTCATGCATTAAATTCGAGAAAGTCATTAAGATGATAGGTTGTTGGATTGAAATATGCCT[A/C]
TCAAAAATAAAATTTTCAGATTTGGAAATATGACTATCAAAAGTAGATGGAGGGAGTACTACACTATTAATACCTGGTCCCACCTGTCATAAACACGCTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.40%	1.10%	1.08%	42.45%	NA
All Indica	2759	36.40%	0.00%	1.59%	61.94%	NA
All Japonica	1512	95.70%	3.40%	0.00%	0.93%	NA
Aus	269	22.30%	0.00%	1.49%	76.21%	NA
Indica I	595	24.20%	0.00%	1.85%	73.95%	NA
Indica II	465	64.50%	0.00%	1.29%	34.19%	NA
Indica III	913	27.20%	0.00%	1.31%	71.52%	NA
Indica Intermediate	786	39.80%	0.10%	1.91%	58.14%	NA
Temperate Japonica	767	93.70%	5.70%	0.00%	0.52%	NA
Tropical Japonica	504	98.80%	0.20%	0.00%	0.99%	NA
Japonica Intermediate	241	95.40%	2.50%	0.00%	2.07%	NA
VI/Aromatic	96	39.60%	0.00%	3.12%	57.29%	NA
Intermediate	90	73.30%	1.10%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216994127	T -> DEL	N	N	silent_mutation	Average:30.529; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1216994127	T -> G	LOC_Os12g28750.1	downstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:30.529; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1216994127	T -> G	LOC_Os12g28750-LOC_Os12g28760	intergenic_region ; MODIFIER	silent_mutation	Average:30.529; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216994127	2.98E-10	2.98E-10	mr1750	Jap_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