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Detailed information for vg1218705117:

Variant ID: vg1218705117 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18705117
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAATCTGCGGCACCGCCACGCATGTACGTACGCAAAATCGTATATATAAGCAAACGCATGCACGTACGTAGCTAATCATTGTACGTGCATATACGGAC[A/G]
TACGCACATATAGCATTTGCAAACCCACACGCAAGTAGCATAGTAATCTTTATACACAGATGCATAAGCACATACGTCGGTCTCGCATGGTTCAGCTGCG

Reverse complement sequence

CGCAGCTGAACCATGCGAGACCGACGTATGTGCTTATGCATCTGTGTATAAAGATTACTATGCTACTTGCGTGTGGGTTTGCAAATGCTATATGTGCGTA[T/C]
GTCCGTATATGCACGTACAATGATTAGCTACGTACGTGCATGCGTTTGCTTATATATACGATTTTGCGTACGTACATGCGTGGCGGTGCCGCAGATTGAT

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 63.20% 32.70% 2.75% 1.33% NA
All Indica  2759 69.80% 23.60% 4.31% 2.28% NA
All Japonica  1512 59.40% 40.00% 0.60% 0.00% NA
Aus  269 10.40% 89.60% 0.00% 0.00% NA
Indica I  595 77.00% 18.80% 0.00% 4.20% NA
Indica II  465 67.70% 14.20% 17.42% 0.65% NA
Indica III  913 70.40% 27.50% 0.88% 1.20% NA
Indica Intermediate  786 64.90% 28.20% 3.82% 3.05% NA
Temperate Japonica  767 39.60% 60.10% 0.26% 0.00% NA
Tropical Japonica  504 93.10% 6.70% 0.20% 0.00% NA
Japonica Intermediate  241 51.90% 45.60% 2.49% 0.00% NA
VI/Aromatic  96 88.50% 10.40% 1.04% 0.00% NA
Intermediate  90 57.80% 41.10% 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
vg1218705117 A -> DEL N N silent_mutation Average:76.012; most accessible tissue: Zhenshan97 young leaf, score: 89.875 N N N N
vg1218705117 A -> G LOC_Os12g31110-LOC_Os12g31120 intergenic_region ; MODIFIER silent_mutation Average:76.012; most accessible tissue: Zhenshan97 young leaf, score: 89.875 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218705117 NA 4.52E-08 mr1157 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
vg1218705117 2.71E-06 2.05E-09 mr1171 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
vg1218705117 NA 6.29E-07 mr1229 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
vg1218705117 NA 3.93E-08 mr1403 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
vg1218705117 NA 1.39E-09 mr1446 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
vg1218705117 NA 2.69E-11 mr1457 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
vg1218705117 NA 2.70E-07 mr1458 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
vg1218705117 NA 1.22E-08 mr1539 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
vg1218705117 NA 6.10E-06 mr1614 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
vg1218705117 NA 9.82E-07 mr1621 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
vg1218705117 NA 8.42E-06 mr1742 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
vg1218705117 NA 3.57E-07 mr1748 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
vg1218705117 NA 6.68E-06 mr1851 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
vg1218705117 NA 1.52E-07 mr1310_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
vg1218705117 NA 4.61E-09 mr1364_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
vg1218705117 NA 4.99E-06 mr1458_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
vg1218705117 NA 2.59E-07 mr1959_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