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Detailed information for vg0724211934:

Variant ID: vg0724211934 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24211934
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAGCTGGGCTCGCCACGTTCATGGGGGTCAGCTTCATGTGCCTCTCATTCGTGACGGTGGGCATGGTTCACCTTGTGCTTGTTCTTCATCTTACGATG[G/A]
TGAGGGGAGTCGGCGGTTTTCCAAGGCTGACGATTCTCTTTCGTTGGTTCATGCCTGCTTGCCTCCTGGCGTCCACCTTTGTATACTTTGTCCAGTCCAT

Reverse complement sequence

ATGGACTGGACAAAGTATACAAAGGTGGACGCCAGGAGGCAAGCAGGCATGAACCAACGAAAGAGAATCGTCAGCCTTGGAAAACCGCCGACTCCCCTCA[C/T]
CATCGTAAGATGAAGAACAAGCACAAGGTGAACCATGCCCACCGTCACGAATGAGAGGCACATGAAGCTGACCCCCATGAACGTGGCGAGCCCAGCTGGA

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 78.40% 21.30% 0.11% 0.19% NA
All Indica  2759 95.00% 4.80% 0.07% 0.14% NA
All Japonica  1512 48.10% 51.70% 0.20% 0.07% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 95.10% 4.70% 0.17% 0.00% NA
Indica II  465 91.00% 8.60% 0.22% 0.22% NA
Indica III  913 97.70% 2.10% 0.00% 0.22% NA
Indica Intermediate  786 94.00% 5.90% 0.00% 0.13% NA
Temperate Japonica  767 83.20% 16.60% 0.26% 0.00% NA
Tropical Japonica  504 6.70% 93.30% 0.00% 0.00% NA
Japonica Intermediate  241 22.80% 76.30% 0.41% 0.41% NA
VI/Aromatic  96 50.00% 49.00% 0.00% 1.04% NA
Intermediate  90 66.70% 30.00% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0724211934 G -> DEL LOC_Os07g40380.1 N frameshift_variant Average:67.045; most accessible tissue: Callus, score: 97.192 N N N N
vg0724211934 G -> A LOC_Os07g40380.1 missense_variant ; p.Val99Met; MODERATE nonsynonymous_codon ; V99M Average:67.045; most accessible tissue: Callus, score: 97.192 unknown unknown TOLERATED 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724211934 NA 6.92E-08 mr1401 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
vg0724211934 NA 2.99E-08 mr1408 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
vg0724211934 NA 8.21E-06 mr1632 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
vg0724211934 NA 7.19E-06 mr1682 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
vg0724211934 NA 3.19E-06 mr1942 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
vg0724211934 NA 5.80E-06 mr1182_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