Search for Variation information by Variation ID:

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

Detailed information for vg0710993160:

Variant ID: vg0710993160 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10993160
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAAAACAAGGAAGAATTTTCACCATGATGTACAGCTTCTCCAAGCATGGAAAACATTTAAGGAAGCCAAATTGTGTCCAGATTTGGTCCAGCAGACT[C/T]
AAGAACCAAAACCTTCACTGTGCGCAGCGAGGCTGTCGAACTGACGACCATCGTTTCCTGAAGAAAACCAAGACGTACAGCATGTCAAGATGTCCATGTC

Reverse complement sequence

GACATGGACATCTTGACATGCTGTACGTCTTGGTTTTCTTCAGGAAACGATGGTCGTCAGTTCGACAGCCTCGCTGCGCACAGTGAAGGTTTTGGTTCTT[G/A]
AGTCTGCTGGACCAAATCTGGACACAATTTGGCTTCCTTAAATGTTTTCCATGCTTGGAGAAGCTGTACATCATGGTGAAAATTCTTCCTTGTTTTTTGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.70%	47.20%	0.04%	0.00%	NA
All Indica	2759	80.50%	19.40%	0.07%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	70.60%	29.40%	0.00%	0.00%	NA
Indica I	595	67.20%	32.60%	0.17%	0.00%	NA
Indica II	465	86.90%	13.10%	0.00%	0.00%	NA
Indica III	913	92.70%	7.20%	0.11%	0.00%	NA
Indica Intermediate	786	72.60%	27.40%	0.00%	0.00%	NA
Temperate Japonica	767	1.70%	98.30%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	43.30%	56.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710993160	C -> T	LOC_Os07g18600.1	missense_variant ; p.Glu328Lys; MODERATE	nonsynonymous_codon ; E328K	Average:45.145; most accessible tissue: Zhenshan97 young leaf, score: 71.497	unknown	unknown	TOLERATED	0.39

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710993160	NA	2.14E-20	mr1689	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251