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Detailed information for vg0630422705:

Variant ID: vg0630422705 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30422705
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.65, C: 0.35, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AATTACATTGTAAAATACTGGGCGAGCTTCTTCTTCTTGACCTGTACTTGTTTACCGAAGCACGCTGACGTCCGGCGTGCCCACTTTCTGATCTTCTTGT[C/A]
TTCAGCAATGTCGGAAAAATCACAGTGATCATCATCAGCCAATATTGTGTGGGGTTCAATGGACATAAACTCCAGGGCAACGGCATTCTCAAGGATGAAA

Reverse complement sequence

TTTCATCCTTGAGAATGCCGTTGCCCTGGAGTTTATGTCCATTGAACCCCACACAATATTGGCTGATGATGATCACTGTGATTTTTCCGACATTGCTGAA[G/T]
ACAAGAAGATCAGAAAGTGGGCACGCCGGACGTCAGCGTGCTTCGGTAAACAAGTACAGGTCAAGAAGAAGAAGCTCGCCCAGTATTTTACAATGTAATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.00% 18.80% 0.17% 0.00% NA
All Indica  2759 99.30% 0.60% 0.14% 0.00% NA
All Japonica  1512 43.80% 56.00% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 98.60% 1.10% 0.25% 0.00% NA
Temperate Japonica  767 8.60% 91.30% 0.13% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 62.70% 36.90% 0.41% 0.00% NA
VI/Aromatic  96 83.30% 15.60% 1.04% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg0630422705 C -> A LOC_Os06g50250.1 missense_variant ; p.Asp126Tyr; MODERATE nonsynonymous_codon ; D126Y Average:58.331; most accessible tissue: Callus, score: 84.111 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630422705 NA 5.39E-36 mr1533 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
vg0630422705 NA 1.98E-30 mr1980 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
vg0630422705 NA 2.82E-37 mr1533_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
vg0630422705 NA 1.42E-06 mr1582_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
vg0630422705 NA 3.45E-19 mr1980_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