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Detailed information for vg1218085065:

Variant ID: vg1218085065 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18085065
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, G: 0.16, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTCCGGTACCAAACATGATAACCCATAGGTATTATCAGCCTCATTGGATGGCATATTATATGAATATGCCAAATGGCATACTTATAAACGAAAATCAA[G/T]
TTGTGAATAAAACTTTTATATATGTGTTTTTAGCGATCCAAAAGTAAAGGCTGAAAAATAAACTTCGATGAAAAAACCCCAAAATCAGCTCCAAATTTAA

Reverse complement sequence

TTAAATTTGGAGCTGATTTTGGGGTTTTTTCATCGAAGTTTATTTTTCAGCCTTTACTTTTGGATCGCTAAAAACACATATATAAAAGTTTTATTCACAA[C/A]
TTGATTTTCGTTTATAAGTATGCCATTTGGCATATTCATATAATATGCCATCCAATGAGGCTGATAATACCTATGGGTTATCATGTTTGGTACCGGAGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.20% 47.60% 0.08% 4.15% NA
All Indica  2759 46.40% 52.00% 0.00% 1.59% NA
All Japonica  1512 54.70% 45.20% 0.00% 0.13% NA
Aus  269 23.80% 30.10% 0.37% 45.72% NA
Indica I  595 5.40% 94.50% 0.00% 0.17% NA
Indica II  465 68.60% 30.30% 0.00% 1.08% NA
Indica III  913 64.30% 33.40% 0.00% 2.30% NA
Indica Intermediate  786 43.50% 54.30% 0.00% 2.16% NA
Temperate Japonica  767 35.20% 64.80% 0.00% 0.00% NA
Tropical Japonica  504 77.60% 22.40% 0.00% 0.00% NA
Japonica Intermediate  241 68.90% 30.30% 0.00% 0.83% NA
VI/Aromatic  96 72.90% 8.30% 0.00% 18.75% NA
Intermediate  90 40.00% 46.70% 3.33% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218085065 G -> DEL N N silent_mutation Average:45.629; most accessible tissue: Callus, score: 70.699 N N N N
vg1218085065 G -> T LOC_Os12g30130-LOC_Os12g30140 intergenic_region ; MODIFIER silent_mutation Average:45.629; most accessible tissue: Callus, score: 70.699 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218085065 NA 8.74E-06 mr1010 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
vg1218085065 NA 4.58E-06 mr1060 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
vg1218085065 NA 2.88E-08 mr1163 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
vg1218085065 NA 5.33E-06 mr1170 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
vg1218085065 NA 6.59E-06 mr1188 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
vg1218085065 NA 7.49E-07 mr1192 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
vg1218085065 NA 6.74E-06 mr1280 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
vg1218085065 NA 7.76E-06 mr1353 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
vg1218085065 NA 9.36E-06 mr1359 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
vg1218085065 NA 1.70E-07 mr1397 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
vg1218085065 NA 5.21E-09 mr1486 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
vg1218085065 NA 3.46E-06 mr1548 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
vg1218085065 NA 1.11E-07 mr1557 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
vg1218085065 NA 8.77E-09 mr1857 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
vg1218085065 NA 5.63E-06 mr1857 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
vg1218085065 NA 8.86E-06 mr1232_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
vg1218085065 NA 8.03E-09 mr1557_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
vg1218085065 NA 4.24E-09 mr1565_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
vg1218085065 NA 1.22E-09 mr1598_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