Search for Variation information by Variation ID:

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

Detailed information for vg0514678744:

Variant ID: vg0514678744 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14678744
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGACGTTTCGCTGCTCCTCCTGGTCCTCGTCGGAATGCTTCTGTACTCGTGTACTCTGATGTCGTAGCTTGCTGGGAGCATGGCCCCGGAGCTGTACA[C/T]
GAGGAAGAAGGGTGTTTCCTTGTTAGACGTTGTCGGTGTGGTGTGTACGGCCCATTTTTTGTCATGTGACATGAGCCTGTCGTAGATGCGGGTTTTGATC

Reverse complement sequence

GATCAAAACCCGCATCTACGACAGGCTCATGTCACATGACAAAAAATGGGCCGTACACACCACACCGACAACGTCTAACAAGGAAACACCCTTCTTCCTC[G/A]
TGTACAGCTCCGGGGCCATGCTCCCAGCAAGCTACGACATCAGAGTACACGAGTACAGAAGCATTCCGACGAGGACCAGGAGGAGCAGCGAAACGTCGAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.00%	23.30%	3.66%	0.00%	NA
All Indica	2759	54.90%	39.10%	6.05%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.13%	0.00%	NA
Aus	269	97.00%	2.20%	0.74%	0.00%	NA
Indica I	595	71.80%	15.10%	13.11%	0.00%	NA
Indica II	465	52.50%	41.90%	5.59%	0.00%	NA
Indica III	913	46.50%	52.50%	0.99%	0.00%	NA
Indica Intermediate	786	53.20%	39.90%	6.87%	0.00%	NA
Temperate Japonica	767	99.10%	0.70%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	2.22%	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
vg0514678744	C -> T	LOC_Os05g25290.1	missense_variant ; p.Val746Met; MODERATE	nonsynonymous_codon ; V746M	Average:56.887; most accessible tissue: Minghui63 young leaf, score: 79.191	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514678744	2.87E-07	3.64E-33	mr1039	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
vg0514678744	5.77E-06	1.30E-13	mr1039	Ind_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
vg0514678744	8.66E-06	NA	mr1632	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
vg0514678744	NA	1.68E-09	mr1632	Ind_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
vg0514678744	7.28E-11	8.59E-35	mr1039_2	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
vg0514678744	2.14E-08	5.98E-14	mr1039_2	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
vg0514678744	4.34E-07	NA	mr1632_2	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
vg0514678744	2.53E-06	1.22E-10	mr1632_2	Ind_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