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Detailed information for vg0522745422:

Variant ID: vg0522745422 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22745422
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCTCGCTTCCACAATAATATCATTTGACAAAGTTTCCCTTATTATTGCTCCTCTGCATCTTCTTCCTCCTCTTCCTCCCCTTCCTCTTCTTCGTTGTC[G/A]
TTGTCGTCGTCGTCGTCGTCCGAGGAAGACGACGACGAGCTATCAGAGTGATCTGATTTTGGTGCAGGGGAGGCAGATGGAGCTGGGGCTGGGACGCTGG

Reverse complement sequence

CCAGCGTCCCAGCCCCAGCTCCATCTGCCTCCCCTGCACCAAAATCAGATCACTCTGATAGCTCGTCGTCGTCTTCCTCGGACGACGACGACGACGACAA[C/T]
GACAACGAAGAAGAGGAAGGGGAGGAAGAGGAGGAAGAAGATGCAGAGGAGCAATAATAAGGGAAACTTTGTCAAATGATATTATTGTGGAAGCGAGAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.50% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 66.20% 33.50% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0522745422 G -> A LOC_Os05g38770.1 synonymous_variant ; p.Asn399Asn; LOW synonymous_codon Average:43.526; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522745422 NA 5.67E-06 mr1052 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
vg0522745422 NA 6.52E-11 mr1499 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
vg0522745422 NA 4.84E-06 mr1633 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
vg0522745422 NA 1.31E-08 mr1989 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
vg0522745422 NA 1.64E-06 mr1465_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
vg0522745422 NA 3.01E-10 mr1612_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