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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1218047316:

Variant ID: vg1218047316 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18047316
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CACCTCATTCCCAACTCCCCTTTCCACAATCTCCATTTCAGCCTCACCAACTTTAGTGTGTACCTTGCCCCATTCGACCATACGACTTAATTCAGCTGCA[G/A]
AAGAACGAAAAGTCCCATCACCATTATCATGCACCACCCACTTCCATCTACCAGGTATGAACCTCTCCAACTCAGAAATAATAGAACTTACAGACATCTG

Reverse complement sequence

CAGATGTCTGTAAGTTCTATTATTTCTGAGTTGGAGAGGTTCATACCTGGTAGATGGAAGTGGGTGGTGCATGATAATGGTGATGGGACTTTTCGTTCTT[C/T]
TGCAGCTGAATTAAGTCGTATGGTCGAATGGGGCAAGGTACACACTAAAGTTGGTGAGGCTGAAATGGAGATTGTGGAAAGGGGAGTTGGGAATGAGGTG

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 94.00% 5.60% 0.00% 0.42% NA
All Indica  2759 91.40% 7.90% 0.00% 0.72% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 84.80% 15.20% 0.00% 0.00% NA
Indica I  595 92.90% 7.10% 0.00% 0.00% NA
Indica II  465 94.20% 5.40% 0.00% 0.43% NA
Indica III  913 90.60% 7.60% 0.00% 1.86% NA
Indica Intermediate  786 89.40% 10.40% 0.00% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 96.70% 3.30% 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
vg1218047316 G -> DEL LOC_Os12g30120.1 N frameshift_variant Average:36.108; most accessible tissue: Minghui63 young leaf, score: 53.016 N N N N
vg1218047316 G -> A LOC_Os12g30120.1 missense_variant ; p.Ser182Phe; MODERATE nonsynonymous_codon ; S182F Average:36.108; most accessible tissue: Minghui63 young leaf, score: 53.016 unknown unknown TOLERATED 0.59

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218047316 1.21E-06 NA mr1321 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
vg1218047316 3.86E-08 3.86E-08 mr1321 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
vg1218047316 2.71E-06 2.71E-06 mr1323 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
vg1218047316 2.44E-06 6.46E-07 mr1324 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
vg1218047316 8.15E-06 NA mr1325 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
vg1218047316 5.35E-06 1.14E-06 mr1325 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
vg1218047316 NA 6.54E-06 mr1326 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
vg1218047316 NA 8.47E-06 mr1335 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
vg1218047316 8.96E-06 NA mr1336 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
vg1218047316 NA 1.56E-06 mr1336 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
vg1218047316 2.55E-06 3.03E-06 mr1621 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
vg1218047316 3.80E-06 NA mr1873 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