Search for Variation information by Variation ID:

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

Detailed information for vg1217858893:

Variant ID: vg1217858893 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17858893
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGCCACATCTCTGGGGTGAGAGCCGCCGCCGCCTCCCTCTCTCTCTCGATGAACTTAACGTACATTAACGTGAACGAACGAACGTTGGTGAACGAAAC[G/A]
TGAACTTAACGAGAACGCAAACGTGAACGATCGTGAACGAAACGTGAACGTAACGAGAACGCGAACGTGAACGAACGTGAATGAAACGCGAACGGACGTG

Reverse complement sequence

CACGTCCGTTCGCGTTTCATTCACGTTCGTTCACGTTCGCGTTCTCGTTACGTTCACGTTTCGTTCACGATCGTTCACGTTTGCGTTCTCGTTAAGTTCA[C/T]
GTTTCGTTCACCAACGTTCGTTCGTTCACGTTAATGTACGTTAAGTTCATCGAGAGAGAGAGGGAGGCGGCGGCGGCTCTCACCCCAGAGATGTGGCGGC

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	72.90%	2.10%	1.33%	23.70%	NA
All Indica	2759	71.80%	1.20%	0.69%	26.31%	NA
All Japonica	1512	75.80%	0.10%	2.78%	21.30%	NA
Aus	269	70.60%	23.80%	0.74%	4.83%	NA
Indica I	595	92.10%	0.20%	0.17%	7.56%	NA
Indica II	465	68.00%	3.00%	0.43%	28.60%	NA
Indica III	913	59.90%	0.90%	0.99%	38.23%	NA
Indica Intermediate	786	72.60%	1.10%	0.89%	25.32%	NA
Temperate Japonica	767	94.40%	0.30%	3.52%	1.83%	NA
Tropical Japonica	504	51.60%	0.00%	2.18%	46.23%	NA
Japonica Intermediate	241	67.20%	0.00%	1.66%	31.12%	NA
VI/Aromatic	96	50.00%	0.00%	0.00%	50.00%	NA
Intermediate	90	87.80%	0.00%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217858893	G -> DEL	N	N	silent_mutation	Average:25.232; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N
vg1217858893	G -> A	LOC_Os12g29860.1	intron_variant ; MODIFIER	silent_mutation	Average:25.232; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217858893	1.04E-11	4.63E-22	Awn_length	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1217858893	3.95E-08	3.89E-16	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652