Search for Variation information by Variation ID:

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

Detailed information for vg1122571312:

Variant ID: vg1122571312 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22571312
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTCATACTTCCTCCGTACTCGTAAAGGAAGTCGTTTTGGACAGCGACACGGTCTTCAAAACACAACTTTAACTTCTTGTTTCTATAAAAATATTTATT[A/G]
AAAAGTGATATATGTATACTTTTATGAAAGTATTTTTTCAAGGCAAATCTATTTGTATATATTTTACATTTTCAAACTCAACAACTTGAGAGTTATTCAT

Reverse complement sequence

ATGAATAACTCTCAAGTTGTTGAGTTTGAAAATGTAAAATATATACAAATAGATTTGCCTTGAAAAAATACTTTCATAAAAGTATACATATATCACTTTT[T/C]
AATAAATATTTTTATAGAAACAAGAAGTTAAAGTTGTGTTTTGAAGACCGTGTCGCTGTCCAAAACGACTTCCTTTACGAGTACGGAGGAAGTATGAATT

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	43.50%	5.50%	0.78%	50.15%	NA
All Indica	2759	45.80%	0.70%	0.62%	52.95%	NA
All Japonica	1512	45.90%	15.70%	0.40%	38.03%	NA
Aus	269	19.70%	0.00%	4.09%	76.21%	NA
Indica I	595	27.60%	0.30%	0.17%	71.93%	NA
Indica II	465	41.50%	1.50%	0.65%	56.34%	NA
Indica III	913	60.10%	0.40%	0.66%	38.77%	NA
Indica Intermediate	786	45.40%	0.60%	0.89%	53.05%	NA
Temperate Japonica	767	27.90%	28.70%	0.26%	43.16%	NA
Tropical Japonica	504	70.40%	0.20%	0.20%	29.17%	NA
Japonica Intermediate	241	51.90%	6.60%	1.24%	40.25%	NA
VI/Aromatic	96	12.50%	0.00%	2.08%	85.42%	NA
Intermediate	90	40.00%	6.70%	1.11%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122571312	A -> DEL	N	N	silent_mutation	Average:45.338; most accessible tissue: Zhenshan97 root, score: 82.733	N	N	N	N
vg1122571312	A -> G	LOC_Os11g38040.1	upstream_gene_variant ; 2715.0bp to feature; MODIFIER	silent_mutation	Average:45.338; most accessible tissue: Zhenshan97 root, score: 82.733	N	N	N	N
vg1122571312	A -> G	LOC_Os11g38050.1	intron_variant ; MODIFIER	silent_mutation	Average:45.338; most accessible tissue: Zhenshan97 root, score: 82.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122571312	3.91E-07	3.91E-07	mr1273_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