Search for Variation information by Variation ID:

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

Detailed information for vg1121623117:

Variant ID: vg1121623117 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21623117
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGTGGTTGTGATGCGTCTTGTCGCCAACTCCTAGGTAGTGTAGCGATCTCTGACACCGGATTTGAAGGCGCGAATTACAGAAGCGTCGATGATTTCGGG[G/A]
ATTGTATTTCTGCACTCGTTGAAGCGCCGAACATATTCCCTCAATGATTCACCAGAGTTCTGTGTCAACGCATGTAGGTCGTCTTCGATCGCGTGGTGCT

Reverse complement sequence

AGCACCACGCGATCGAAGACGACCTACATGCGTTGACACAGAACTCTGGTGAATCATTGAGGGAATATGTTCGGCGCTTCAACGAGTGCAGAAATACAAT[C/T]
CCCGAAATCATCGACGCTTCTGTAATTCGCGCCTTCAAATCCGGTGTCAGAGATCGCTACACTACCTAGGAGTTGGCGACAAGACGCATCACAACCACTC

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	96.70%	0.90%	0.87%	1.57%	NA
All Indica	2759	97.90%	1.10%	0.87%	0.07%	NA
All Japonica	1512	94.50%	0.60%	0.60%	4.30%	NA
Aus	269	95.90%	0.40%	1.49%	2.23%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	93.10%	3.90%	3.01%	0.00%	NA
Indica III	913	99.00%	0.50%	0.44%	0.00%	NA
Indica Intermediate	786	98.20%	0.90%	0.76%	0.13%	NA
Temperate Japonica	767	92.80%	0.30%	0.65%	6.26%	NA
Tropical Japonica	504	97.60%	1.00%	0.40%	0.99%	NA
Japonica Intermediate	241	93.40%	0.80%	0.83%	4.98%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	96.70%	0.00%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121623117	G -> A	LOC_Os11g36640.1	synonymous_variant ; p.Ile546Ile; LOW	synonymous_codon	Average:12.473; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1121623117	G -> DEL	LOC_Os11g36640.1	N	frameshift_variant	Average:12.473; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121623117	7.53E-08	2.65E-07	mr1913	Jap_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