Search for Variation information by Variation ID:

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

Detailed information for vg0716821119:

Variant ID: vg0716821119 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16821119
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGCGGATGATAGGCAGTACTGAAGTTCAGCTTGGAACCCATCTCCTCCTGAAGTTTCTTCCAAAACTTTGAAGTAAACTGGCTACCTCGATCGGACAC[G/T]
ATCTTCTTAGGAACACCATGCAAACAAACAATCCTTGCCATATACAATTCTGCTAAATGACTTCCGGAATAGGTGATCCTTACTGGGATGAAATGAGCCA

Reverse complement sequence

TGGCTCATTTCATCCCAGTAAGGATCACCTATTCCGGAAGTCATTTAGCAGAATTGTATATGGCAAGGATTGTTTGTTTGCATGGTGTTCCTAAGAAGAT[C/A]
GTGTCCGATCGAGGTAGCCAGTTTACTTCAAAGTTTTGGAAGAAACTTCAGGAGGAGATGGGTTCCAAGCTGAACTTCAGTACTGCCTATCATCCGCAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.90%	0.30%	1.84%	11.98%	NA
All Indica	2759	76.60%	0.50%	3.04%	19.83%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.46%	NA
Aus	269	97.40%	0.40%	0.74%	1.49%	NA
Indica I	595	72.10%	0.20%	2.35%	25.38%	NA
Indica II	465	76.60%	0.40%	2.80%	20.22%	NA
Indica III	913	75.80%	1.10%	3.29%	19.82%	NA
Indica Intermediate	786	81.00%	0.10%	3.44%	15.39%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	0.00%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716821119	G -> DEL	LOC_Os07g28740.1	N	frameshift_variant	Average:22.368; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0716821119	G -> T	LOC_Os07g28740.1	synonymous_variant ; p.Ile335Ile; LOW	synonymous_codon	Average:22.368; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716821119	3.57E-06	3.57E-06	mr1276	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