Search for Variation information by Variation ID:

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

Detailed information for vg1002869131:

Variant ID: vg1002869131 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2869131
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATTGTATAAGGGCCTGTACGGCAAGCAGGTGTAGCAGCTGGCTGCAGCCAGCAGCTGCCTTTTTTTTTCTTGCTTCACTGTTCGTACAGGTTGCAGCAG[C/T]
GCTGCAGCCCTTGCAGCCGAGCTCACCCTAAGTTGTCCTAGTTTACAACCAGTTAAGTCTAAAATGGATTAGCGAGAAGTTGAAAGAAAAAAAAACATCA

Reverse complement sequence

TGATGTTTTTTTTTCTTTCAACTTCTCGCTAATCCATTTTAGACTTAACTGGTTGTAAACTAGGACAACTTAGGGTGAGCTCGGCTGCAAGGGCTGCAGC[G/A]
CTGCTGCAACCTGTACGAACAGTGAAGCAAGAAAAAAAAAGGCAGCTGCTGGCTGCAGCCAGCTGCTACACCTGCTTGCCGTACAGGCCCTTATACAATA

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	97.50%	1.40%	0.97%	0.11%	NA
All Indica	2759	99.50%	0.00%	0.40%	0.14%	NA
All Japonica	1512	93.50%	4.20%	2.25%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.17%	0.34%	NA
Indica II	465	99.10%	0.00%	0.86%	0.00%	NA
Indica III	913	99.60%	0.00%	0.33%	0.11%	NA
Indica Intermediate	786	99.50%	0.00%	0.38%	0.13%	NA
Temperate Japonica	767	94.80%	1.30%	3.91%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	80.10%	18.30%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002869131	C -> T	LOC_Os10g05695.1	downstream_gene_variant ; 1316.0bp to feature; MODIFIER	silent_mutation	Average:58.796; most accessible tissue: Callus, score: 82.696	N	N	N	N
vg1002869131	C -> T	LOC_Os10g05695-LOC_Os10g05700	intergenic_region ; MODIFIER	silent_mutation	Average:58.796; most accessible tissue: Callus, score: 82.696	N	N	N	N
vg1002869131	C -> DEL	N	N	silent_mutation	Average:58.796; most accessible tissue: Callus, score: 82.696	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002869131	2.84E-07	2.45E-06	mr1768	Jap_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