Search for Variation information by Variation ID:

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

Detailed information for vg0710962546:

Variant ID: vg0710962546 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10962546
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAATGCACCACATTCCATCTATTCATCATCATGTCATCAATCAAAAAAATCATTCCTTTACCATATATCATCAATCCCTAAATTCATCCCAACATCCA[C/T]
ATTTCATCCCAACATCCACATTTTCATTATCAACCACATGCAGGTAGCAGAGGGAGGCGCGATGGAGGACTCACATGAGGTCGGCCGGGGGGGCTCGGTG

Reverse complement sequence

CACCGAGCCCCCCCGGCCGACCTCATGTGAGTCCTCCATCGCGCCTCCCTCTGCTACCTGCATGTGGTTGATAATGAAAATGTGGATGTTGGGATGAAAT[G/A]
TGGATGTTGGGATGAATTTAGGGATTGATGATATATGGTAAAGGAATGATTTTTTTGATTGATGACATGATGATGAATAGATGGAATGTGGTGCATTAAT

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	65.30%	25.40%	0.17%	9.12%	NA
All Indica	2759	96.90%	1.00%	0.04%	2.07%	NA
All Japonica	1512	6.30%	74.30%	0.20%	19.18%	NA
Aus	269	90.70%	4.50%	0.00%	4.83%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	91.50%	1.40%	0.13%	7.00%	NA
Temperate Japonica	767	2.00%	65.20%	0.39%	32.46%	NA
Tropical Japonica	504	13.70%	85.70%	0.00%	0.60%	NA
Japonica Intermediate	241	5.00%	79.30%	0.00%	15.77%	NA
VI/Aromatic	96	25.00%	2.10%	3.12%	69.79%	NA
Intermediate	90	56.70%	37.80%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710962546	C -> DEL	N	N	silent_mutation	Average:49.117; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0710962546	C -> T	LOC_Os07g18520.1	upstream_gene_variant ; 364.0bp to feature; MODIFIER	silent_mutation	Average:49.117; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0710962546	C -> T	LOC_Os07g18530.1	downstream_gene_variant ; 2242.0bp to feature; MODIFIER	silent_mutation	Average:49.117; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0710962546	C -> T	LOC_Os07g18520-LOC_Os07g18530	intergenic_region ; MODIFIER	silent_mutation	Average:49.117; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710962546	7.52E-06	NA	mr1829_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
vg0710962546	9.63E-08	NA	mr1842_2	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