Search for Variation information by Variation ID:

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

Detailed information for vg0321043305:

Variant ID: vg0321043305 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21043305
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 368. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCTCCTCGTGTTCCTCAACAAAACGGTGTTGTTGAAAGGAAAAATCGTGTTTTGGTTGAGATGGCTAGAACGATGTTGGATGAATATAAAACTCCTA[G/A]
AAAATTTTGGGCTGAGGCGATTAACACTGCTTGCTATATTTCAAATCAAGTTTTCTTGATATCTAAACTTGGAAAAACTTCTTATGAACTTCGATTTGGA

Reverse complement sequence

TCCAAATCGAAGTTCATAAGAAGTTTTTCCAAGTTTAGATATCAAGAAAACTTGATTTGAAATATAGCAAGCAGTGTTAATCGCCTCAGCCCAAAATTTT[C/T]
TAGGAGTTTTATATTCATCCAACATCGTTCTAGCCATCTCAACCAAAACACGATTTTTCCTTTCAACAACACCGTTTTGTTGAGGAACACGAGGAGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.80%	36.90%	0.34%	0.00%	NA
All Indica	2759	95.80%	3.80%	0.43%	0.00%	NA
All Japonica	1512	3.20%	96.80%	0.07%	0.00%	NA
Aus	269	87.70%	11.90%	0.37%	0.00%	NA
Indica I	595	98.20%	1.70%	0.17%	0.00%	NA
Indica II	465	92.70%	6.20%	1.08%	0.00%	NA
Indica III	913	97.50%	2.40%	0.11%	0.00%	NA
Indica Intermediate	786	93.90%	5.50%	0.64%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	8.90%	91.10%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.20%	0.41%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	42.20%	55.60%	2.22%	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
vg0321043305	G -> A	LOC_Os03g37890.1	intron_variant ; MODIFIER	silent_mutation	Average:20.482; most accessible tissue: Minghui63 flag leaf, score: 28.142	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321043305	NA	1.83E-06	mr1184_2	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
vg0321043305	2.97E-06	NA	mr1184_2	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