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Detailed information for vg0529417221:

Variant ID: vg0529417221 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 29417221
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


GAACATTAGCCAAGCAATGTCCTTCTCTGCGGCCGGCACGAGCTTGATGTCGTCTTCCAGAATACTGAATTTCTGCCTTCCTATGACCCCGCAGATAGAC[C/G]
TAAATCGGCTTAATATTTTCCTTGGAGATGTCGGCAACCCTACAGCGTCCACCGCTGTTATGCGGAACCGTTCCTTAGGGATTTTGTTCCTTGTCCTAGT

Reverse complement sequence

ACTAGGACAAGGAACAAAATCCCTAAGGAACGGTTCCGCATAACAGCGGTGGACGCTGTAGGGTTGCCGACATCTCCAAGGAAAATATTAAGCCGATTTA[G/C]
GTCTATCTGCGGGGTCATAGGAAGGCAGAAATTCAGTATTCTGGAAGACGACATCAAGCTCGTGCCGGCCGCAGAGAAGGACATTGCTTGGCTAATGTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.20% 10.70% 0.11% 0.00% NA
All Indica  2759 82.00% 17.80% 0.18% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 92.00% 7.70% 0.22% 0.00% NA
Indica III  913 67.30% 32.50% 0.22% 0.00% NA
Indica Intermediate  786 81.40% 18.30% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0529417221 C -> G LOC_Os05g51280.1 missense_variant ; p.Arg54Thr; MODERATE nonsynonymous_codon ; R54T Average:27.483; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 benign 1.433 TOLERATED 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0529417221 1.42E-06 NA mr1989 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