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Detailed information for vg0222645252:

Variant ID: vg0222645252 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22645252
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATGAAGACTGACATATGGTGCAATTCCCGTACGTACGTTTGCAGAGCCCTACGCCGACCCCAGCAACGACGACCCCAACGCCGGCTACGGCAGCAGC[G/A]
GCTACGGCTACCCGTCGCAGCAGGGACAAAACCCAGCGCAGCAGGGACCTAACCCGGCGCAACAGGGACCAAACCCGGCCCAGCAGGGACAGAACCCTGC

Reverse complement sequence

GCAGGGTTCTGTCCCTGCTGGGCCGGGTTTGGTCCCTGTTGCGCCGGGTTAGGTCCCTGCTGCGCTGGGTTTTGTCCCTGCTGCGACGGGTAGCCGTAGC[C/T]
GCTGCTGCCGTAGCCGGCGTTGGGGTCGTCGTTGCTGGGGTCGGCGTAGGGCTCTGCAAACGTACGTACGGGAATTGCACCATATGTCAGTCTTCATTTT

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 85.40% 13.40% 0.76% 0.49% NA
All Indica  2759 97.30% 1.00% 0.91% 0.80% NA
All Japonica  1512 60.60% 38.80% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 94.60% 1.20% 2.19% 1.97% NA
Indica Intermediate  786 97.70% 1.30% 0.51% 0.51% NA
Temperate Japonica  767 81.70% 17.70% 0.52% 0.00% NA
Tropical Japonica  504 27.40% 72.00% 0.60% 0.00% NA
Japonica Intermediate  241 62.70% 36.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 20.00% 2.22% 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
vg0222645252 G -> A LOC_Os02g37520.1 missense_variant ; p.Gly44Ser; MODERATE nonsynonymous_codon ; G44S Average:75.769; most accessible tissue: Minghui63 root, score: 85.142 unknown unknown DELETERIOUS 0.04
vg0222645252 G -> DEL LOC_Os02g37520.1 N frameshift_variant Average:75.769; most accessible tissue: Minghui63 root, score: 85.142 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222645252 NA 9.75E-07 mr1388 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
vg0222645252 NA 2.13E-08 mr1510 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
vg0222645252 NA 1.10E-06 mr1518 Jap_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
vg0222645252 1.66E-06 NA mr1622 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
vg0222645252 NA 1.15E-10 mr1379_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
vg0222645252 NA 1.04E-07 mr1559_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
vg0222645252 NA 5.91E-06 mr1559_2 Jap_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