Search for Variation information by Variation ID:

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

Detailed information for vg1220271697:

Variant ID: vg1220271697 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20271697
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGAGAAGTATTTCTGGCTCAAGGTTCCCCTCAGTTGAAATCCGGCTCCCCCAACTACGCATGGTTTGCTTTTGTTTGGCTGAGGTTTGAGGAAGAAGAT[G/C]
CGGCGGAATAGAGCGAAATGCGGCCTAATCCCCAGAAAAGCTTCGCAAGCATGGATGAAGTTGGCGATGTGGACTATGGAATTGGGATTTAGGTGATGCA

Reverse complement sequence

TGCATCACCTAAATCCCAATTCCATAGTCCACATCGCCAACTTCATCCATGCTTGCGAAGCTTTTCTGGGGATTAGGCCGCATTTCGCTCTATTCCGCCG[C/G]
ATCTTCTTCCTCAAACCTCAGCCAAACAAAAGCAAACCATGCGTAGTTGGGGGAGCCGGATTTCAACTGAGGGGAACCTTGAGCCAGAAATACTTCTCCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.40%	0.10%	1.48%	30.98%	NA
All Indica	2759	62.60%	0.00%	1.27%	36.06%	NA
All Japonica	1512	73.90%	0.30%	0.86%	24.93%	NA
Aus	269	69.50%	0.00%	6.69%	23.79%	NA
Indica I	595	82.50%	0.00%	0.50%	16.97%	NA
Indica II	465	46.50%	0.00%	1.51%	52.04%	NA
Indica III	913	56.30%	0.00%	1.53%	42.17%	NA
Indica Intermediate	786	64.50%	0.10%	1.40%	33.97%	NA
Temperate Japonica	767	94.80%	0.70%	0.26%	4.30%	NA
Tropical Japonica	504	41.70%	0.00%	1.98%	56.35%	NA
Japonica Intermediate	241	74.70%	0.00%	0.41%	24.90%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	70.00%	0.00%	4.44%	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
vg1220271697	G -> C	LOC_Os12g33560.1	synonymous_variant ; p.Arg118Arg; LOW	synonymous_codon	Average:16.519; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1220271697	G -> DEL	LOC_Os12g33560.1	N	frameshift_variant	Average:16.519; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220271697	6.76E-07	6.75E-07	mr1664	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