Search for Variation information by Variation ID:

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

Detailed information for vg0202071611:

Variant ID: vg0202071611 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2071611
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTTTACCCCTGTGAAAGAGCTATCTCTCATCTCCTCTCGCTGCACAGTCAAACCTTCCTGATTATGTTGTCATGCTTTGTGATACTTGTGAGGTACAA[T/A]
ATGACTTCATATGATTGTGTAAAATGTTGTTGAAATTTTGTCAAAATTTTTGTTCGATTTCTGTCAAAATGCTGCCGAGATTTTGTCAAAATTCCATCAA

Reverse complement sequence

TTGATGGAATTTTGACAAAATCTCGGCAGCATTTTGACAGAAATCGAACAAAAATTTTGACAAAATTTCAACAACATTTTACACAATCATATGAAGTCAT[A/T]
TTGTACCTCACAAGTATCACAAAGCATGACAACATAATCAGGAAGGTTTGACTGTGCAGCGAGAGGAGATGAGAGATAGCTCTTTCACAGGGGTAAAAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	7.60%	0.23%	0.00%	NA
All Indica	2759	86.70%	12.90%	0.40%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.20%	0.17%	0.00%	NA
Indica II	465	87.70%	11.80%	0.43%	0.00%	NA
Indica III	913	80.30%	19.10%	0.66%	0.00%	NA
Indica Intermediate	786	85.90%	13.90%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0202071611	T -> A	LOC_Os02g04640.1	downstream_gene_variant ; 3885.0bp to feature; MODIFIER	silent_mutation	Average:54.84; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0202071611	T -> A	LOC_Os02g04630.1	intron_variant ; MODIFIER	silent_mutation	Average:54.84; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202071611	NA	1.30E-09	mr1697	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