Search for Variation information by Variation ID:

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

Detailed information for vg0710267058:

Variant ID: vg0710267058 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10267058
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAACAAAAATAATTCATAAAACTAATGTGAAAAACAAAGCTGCACAACAAGACCGTTTTGCCCCCCTCCCTACCCCTCTCGCACGCAGAAGCCCCCAT[C/A]
TCCCAGAAAGGCAGGTCCCGATTGGCCGATTCCCTTCCCTATCCTCGAACCCTACTACATCCCCAAATCCTCTCATCTCTTCTTTCAAATCAAGAGCAAA

Reverse complement sequence

TTTGCTCTTGATTTGAAAGAAGAGATGAGAGGATTTGGGGATGTAGTAGGGTTCGAGGATAGGGAAGGGAATCGGCCAATCGGGACCTGCCTTTCTGGGA[G/T]
ATGGGGGCTTCTGCGTGCGAGAGGGGTAGGGAGGGGGGCAAAACGGTCTTGTTGTGCAGCTTTGTTTTTCACATTAGTTTTATGAATTATTTTTGTTTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.40%	1.60%	2.60%	2.35%	NA
All Indica	2759	88.80%	2.80%	4.46%	3.95%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	68.70%	6.60%	14.45%	10.25%	NA
Indica II	465	94.40%	1.30%	1.29%	3.01%	NA
Indica III	913	99.70%	0.10%	0.11%	0.11%	NA
Indica Intermediate	786	88.20%	3.80%	3.82%	4.20%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710267058	C -> DEL	N	N	silent_mutation	Average:51.044; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N
vg0710267058	C -> A	LOC_Os07g17390.1	downstream_gene_variant ; 1180.0bp to feature; MODIFIER	silent_mutation	Average:51.044; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N
vg0710267058	C -> A	LOC_Os07g17390-LOC_Os07g17400	intergenic_region ; MODIFIER	silent_mutation	Average:51.044; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710267058	7.61E-06	7.61E-06	mr1575	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
vg0710267058	4.37E-06	NA	mr1913	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