Search for Variation information by Variation ID:

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

Detailed information for vg0121868877:

Variant ID: vg0121868877 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21868877
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCACAGTGCAACCACAAGGTGGAATGGGACACCCTGGCTAAGTAACTAGTCGGTTCAGGGAAACCTCGCATGCCAATAGTTGGGAACACCGGGGCAGGG[T/A]
CGGTTGGAGCCAAACTGGGTTCCTGGTAAGCAAGAAAGAGAAGCTTGCAGAATTACCGATCGAGGTGGTTGGAGTTTGATTTGTGAAAACTAAAATGGCC

Reverse complement sequence

GGCCATTTTAGTTTTCACAAATCAAACTCCAACCACCTCGATCGGTAATTCTGCAAGCTTCTCTTTCTTGCTTACCAGGAACCCAGTTTGGCTCCAACCG[A/T]
CCCTGCCCCGGTGTTCCCAACTATTGGCATGCGAGGTTTCCCTGAACCGACTAGTTACTTAGCCAGGGTGTCCCATTCCACCTTGTGGTTGCACTGTGAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	0.50%	1.69%	47.91%	NA
All Indica	2759	20.80%	0.40%	1.27%	77.53%	NA
All Japonica	1512	99.50%	0.00%	0.07%	0.46%	NA
Aus	269	55.00%	3.70%	13.38%	27.88%	NA
Indica I	595	4.00%	0.20%	1.34%	94.45%	NA
Indica II	465	28.00%	0.20%	0.65%	71.18%	NA
Indica III	913	16.90%	0.90%	1.31%	80.94%	NA
Indica Intermediate	786	33.80%	0.10%	1.53%	64.50%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	69.80%	2.10%	7.29%	20.83%	NA
Intermediate	90	73.30%	0.00%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121868877	T -> A	LOC_Os01g38930.1	downstream_gene_variant ; 1071.0bp to feature; MODIFIER	silent_mutation	Average:5.941; most accessible tissue: Callus, score: 14.008	N	N	N	N
vg0121868877	T -> A	LOC_Os01g38920-LOC_Os01g38930	intergenic_region ; MODIFIER	silent_mutation	Average:5.941; most accessible tissue: Callus, score: 14.008	N	N	N	N
vg0121868877	T -> DEL	N	N	silent_mutation	Average:5.941; most accessible tissue: Callus, score: 14.008	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121868877	2.81E-07	NA	Yield	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0121868877	8.98E-07	8.55E-06	Yield	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652