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Detailed information for vg1218766903:

Variant ID: vg1218766903 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18766903
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, G: 0.49, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:


ACACATTTGTATTTTCGTAAAGTTATTGCAAAATTTAAAATTTTGATGTCATTCTAAAAAAATTGAATAATATAATGAGAAAACATATATACTATTATAT[C/G]
AGAGAAAATATAATGATGCTTACCGCGCAATCTGCGCGGGCCACTATGCTAGTTATATTATTAAGACGGCTTTAAAAGAAGGCTTCACGTTCGCTGTGGG

Reverse complement sequence

CCCACAGCGAACGTGAAGCCTTCTTTTAAAGCCGTCTTAATAATATAACTAGCATAGTGGCCCGCGCAGATTGCGCGGTAAGCATCATTATATTTTCTCT[G/C]
ATATAATAGTATATATGTTTTCTCATTATATTATTCAATTTTTTTAGAATGACATCAAAATTTTAAATTTTGCAATAACTTTACGAAAATACAAATGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.70% 35.20% 0.87% 22.24% NA
All Indica  2759 68.30% 7.00% 0.65% 24.03% NA
All Japonica  1512 0.90% 87.90% 0.33% 10.85% NA
Aus  269 18.20% 8.20% 4.83% 68.77% NA
Indica I  595 73.40% 8.90% 0.17% 17.48% NA
Indica II  465 83.20% 4.70% 0.43% 11.61% NA
Indica III  913 64.60% 2.80% 1.10% 31.43% NA
Indica Intermediate  786 59.80% 11.80% 0.64% 27.74% NA
Temperate Japonica  767 1.20% 88.40% 0.39% 10.04% NA
Tropical Japonica  504 0.40% 94.60% 0.40% 4.56% NA
Japonica Intermediate  241 1.20% 72.20% 0.00% 26.56% NA
VI/Aromatic  96 4.20% 65.60% 4.17% 26.04% NA
Intermediate  90 23.30% 60.00% 1.11% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218766903 C -> DEL N N silent_mutation Average:25.41; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1218766903 C -> G LOC_Os12g31160.1 upstream_gene_variant ; 2863.0bp to feature; MODIFIER silent_mutation Average:25.41; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1218766903 C -> G LOC_Os12g31160-LOC_Os12g31180 intergenic_region ; MODIFIER silent_mutation Average:25.41; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218766903 NA 6.26E-06 mr1066 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
vg1218766903 4.28E-06 4.28E-06 mr1066 Jap_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
vg1218766903 NA 1.15E-10 mr1070 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
vg1218766903 NA 2.59E-06 mr1118 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
vg1218766903 NA 2.64E-06 mr1123 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
vg1218766903 NA 1.68E-11 mr1128 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
vg1218766903 NA 9.40E-11 mr1172 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
vg1218766903 NA 1.29E-13 mr1239 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
vg1218766903 NA 5.62E-09 mr1242 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
vg1218766903 NA 2.41E-06 mr1646 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
vg1218766903 NA 1.37E-07 mr1659 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
vg1218766903 NA 6.57E-07 mr1693 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
vg1218766903 NA 1.96E-06 mr1944 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
vg1218766903 NA 6.59E-06 mr1961 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
vg1218766903 NA 2.27E-06 mr1242_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
vg1218766903 NA 2.79E-07 mr1458_2 Ind_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