Search for Variation information by Variation ID:

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

Detailed information for vg0207562985:

Variant ID: vg0207562985 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7562985
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGGAAGGAAGCAGTCGTGCGAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGATGCAGGACGTCGAAGGCAGAGGTTCCGAAGACCTGCTCTCC[C/T]
AATCGCCGGTGCACGCTGGCGAGTGGGATGGAGTAGTCTACGAGCGATGGCGCAACACAGAGGAGGAGGCAAACCCTAGATTGATTTCGTGTGTGTTGCG

Reverse complement sequence

CGCAACACACACGAAATCAATCTAGGGTTTGCCTCCTCCTCTGTGTTGCGCCATCGCTCGTAGACTACTCCATCCCACTCGCCAGCGTGCACCGGCGATT[G/A]
GGAGAGCAGGTCTTCGGAACCTCTGCCTTCGACGTCCTGCATCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTCGCACGACTGCTTCCTTCCTG

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	92.20%	7.60%	0.21%	0.00%	NA
All Indica	2759	97.50%	2.30%	0.14%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	18.20%	79.60%	2.23%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	96.50%	3.30%	0.22%	0.00%	NA
Indica Intermediate	786	96.20%	3.60%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	39.60%	60.40%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0207562985	C -> T	LOC_Os02g13910.1	intron_variant ; MODIFIER	silent_mutation	Average:49.659; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207562985	NA	3.98E-11	mr1570	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
vg0207562985	7.52E-07	1.19E-08	mr1697	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