Search for Variation information by Variation ID:

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

Detailed information for vg0717478015:

Variant ID: vg0717478015 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17478015
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACCATGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATATGGAAAGTCGAAAGATACAGTGGAAGCA[C/T]
GTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCTGGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCTAGCCAGCTACACTCTTAGCAA

Reverse complement sequence

TTGCTAAGAGTGTAGCTGGCTAGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCCAGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTAC[G/A]
TGCTTCCACTGTATCTTTCGACTTTCCATATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCATGGTGG

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	49.30%	12.10%	38.57%	0.00%	NA
All Indica	2759	22.50%	19.40%	58.06%	0.00%	NA
All Japonica	1512	88.70%	1.50%	9.85%	0.00%	NA
Aus	269	82.50%	3.00%	14.50%	0.00%	NA
Indica I	595	14.50%	12.60%	72.94%	0.00%	NA
Indica II	465	28.40%	11.80%	59.78%	0.00%	NA
Indica III	913	20.90%	33.10%	46.00%	0.00%	NA
Indica Intermediate	786	27.00%	13.20%	59.80%	0.00%	NA
Temperate Japonica	767	98.80%	0.30%	0.91%	0.00%	NA
Tropical Japonica	504	74.20%	4.00%	21.83%	0.00%	NA
Japonica Intermediate	241	86.70%	0.00%	13.28%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	60.00%	8.90%	31.11%	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
vg0717478015	C -> T	LOC_Os07g29730.1	missense_variant ; p.Arg476Cys; MODERATE	nonsynonymous_codon ; R476C	Average:18.809; most accessible tissue: Callus, score: 43.192	benign	0.915	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717478015	4.34E-06	4.32E-06	mr1429	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
vg0717478015	NA	7.61E-07	mr1748	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