\

Search for Variation information by Variation ID:

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

Detailed information for vg0222033395:

Variant ID: vg0222033395 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22033395
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAGGGGCAGCAGTATAAGGTCTCTATGGCACAGTTTGCTGCAGCTTTGGGGTTAGATGATGATGACCTGAGTCGTCCACATATCTTTATAGAGGATGCT[C/T]
TGTCACCGACTAGCACTACCTTAATGTATGAGAAGGATGCTCCCAAGGATTGTTTGGGGACTACTCGTGGGTTGCGTCCATACTATAGAGTGTTGTACTC

Reverse complement sequence

GAGTACAACACTCTATAGTATGGACGCAACCCACGAGTAGTCCCCAAACAATCCTTGGGAGCATCCTTCTCATACATTAAGGTAGTGCTAGTCGGTGACA[G/A]
AGCATCCTCTATAAAGATATGTGGACGACTCAGGTCATCATCATCTAACCCCAAAGCTGCAGCAAACTGTGCCATAGAGACCTTATACTGCTGCCCCTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.20% 36.50% 0.30% 0.00% NA
All Indica  2759 92.00% 7.60% 0.36% 0.00% NA
All Japonica  1512 9.00% 91.00% 0.00% 0.00% NA
Aus  269 95.20% 3.30% 1.49% 0.00% NA
Indica I  595 95.30% 4.00% 0.67% 0.00% NA
Indica II  465 97.80% 1.70% 0.43% 0.00% NA
Indica III  913 90.80% 9.10% 0.11% 0.00% NA
Indica Intermediate  786 87.40% 12.20% 0.38% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 19.80% 80.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0222033395 C -> T LOC_Os02g36480.1 synonymous_variant ; p.Leu205Leu; LOW synonymous_codon Average:12.469; most accessible tissue: Callus, score: 16.517 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222033395 NA 9.77E-08 Awn_length Ind_All Not 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
vg0222033395 4.19E-06 4.19E-06 mr1025 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
vg0222033395 NA 1.59E-11 mr1188_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
vg0222033395 NA 2.99E-08 mr1600_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
vg0222033395 NA 1.67E-07 mr1783_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