Search for Variation information by Variation ID:

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

Detailed information for vg0120215560:

Variant ID: vg0120215560 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 20215560
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGCGATGCTTGCCTCTGGACGAGCACGGTTACGAATATACTTCTTCGGAATGCCCATGTACCTCTCGAAAGGAAACATGTTGTGTAGGTACACGGGCC[C/T]
GAGAATACCGATCTCTTTGACAAGGTGACAAAGCAGATGCGTCATTATATTGAAAAATGAAGGTGAAAATATCAACTCAAAGCTGACAAGACATTGCAGT

Reverse complement sequence

ACTGCAATGTCTTGTCAGCTTTGAGTTGATATTTTCACCTTCATTTTTCAATATAATGACGCATCTGCTTTGTCACCTTGTCAAAGAGATCGGTATTCTC[G/A]
GGCCCGTGTACCTACACAACATGTTTCCTTTCGAGAGGTACATGGGCATTCCGAAGAAGTATATTCGTAACCGTGCTCGTCCAGAGGCAAGCATCGCCAA

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	98.70%	0.20%	0.61%	0.51%	NA
All Indica	2759	97.70%	0.40%	1.05%	0.87%	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	96.30%	0.30%	2.18%	1.18%	NA
Indica II	465	98.30%	0.00%	0.43%	1.29%	NA
Indica III	913	99.20%	0.10%	0.11%	0.55%	NA
Indica Intermediate	786	96.70%	0.90%	1.65%	0.76%	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	100.00%	0.00%	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
vg0120215560	C -> T	LOC_Os01g36420.1	missense_variant ; p.Gly655Arg; MODERATE	N	Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0120215560	C -> T	LOC_Os01g36430.1	upstream_gene_variant ; 4907.0bp to feature; MODIFIER	N	Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0120215560	C -> T	LOC_Os01g36410.1	downstream_gene_variant ; 1487.0bp to feature; MODIFIER	N	Average:37.244; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0120215560	5.84E-06	NA	mr1050_2	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