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Detailed information for vg1218867681:

Variant ID: vg1218867681 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 18867681
Reference Allele: AAlternative Allele: G,AACAG
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.40, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGCTAGATTACTATAATATAGTAATCCACTCTAAAGGTGCTTTTTATTATTGGGTTGCTAACACCTAACAACCAGCTAATAATCCAGAGAAACAAACA[A/G,AACAG]
CTAACAACTTATATAGTAATCTGTCTCAATAATCAATAATCTAGATTACAATAATCTTAAGCTAAAACAAACAGGGCTTTAATTGAAACACGAAGCGGAT

Reverse complement sequence

ATCCGCTTCGTGTTTCAATTAAAGCCCTGTTTGTTTTAGCTTAAGATTATTGTAATCTAGATTATTGATTATTGAGACAGATTACTATATAAGTTGTTAG[T/C,CTGTT]
TGTTTGTTTCTCTGGATTATTAGCTGGTTGTTAGGTGTTAGCAACCCAATAATAAAAAGCACCTTTAGAGTGGATTACTATATTATAGTAATCTAGCTTA

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 63.00% 34.20% 0.23% 1.35% AACAG: 1.21%
All Indica  2759 93.10% 3.70% 0.33% 0.76% AACAG: 2.07%
All Japonica  1512 7.40% 92.50% 0.07% 0.00% NA
Aus  269 91.80% 0.40% 0.00% 7.81% NA
Indica I  595 93.60% 3.70% 0.50% 0.17% AACAG: 2.02%
Indica II  465 97.00% 2.40% 0.22% 0.43% NA
Indica III  913 93.90% 2.60% 0.11% 1.42% AACAG: 1.97%
Indica Intermediate  786 89.70% 5.70% 0.51% 0.64% AACAG: 3.44%
Temperate Japonica  767 2.20% 97.70% 0.13% 0.00% NA
Tropical Japonica  504 5.80% 94.20% 0.00% 0.00% NA
Japonica Intermediate  241 27.40% 72.60% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 62.50% 0.00% 15.62% NA
Intermediate  90 32.20% 58.90% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218867681 A -> DEL N N silent_mutation Average:31.504; most accessible tissue: Callus, score: 82.635 N N N N
vg1218867681 A -> G LOC_Os12g31350-LOC_Os12g31370 intergenic_region ; MODIFIER silent_mutation Average:31.504; most accessible tissue: Callus, score: 82.635 N N N N
vg1218867681 A -> AACAG LOC_Os12g31350-LOC_Os12g31370 intergenic_region ; MODIFIER silent_mutation Average:31.504; most accessible tissue: Callus, score: 82.635 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218867681 NA 6.84E-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
vg1218867681 NA 5.78E-17 mr1116 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
vg1218867681 NA 7.90E-15 mr1118 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
vg1218867681 NA 2.80E-10 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
vg1218867681 NA 9.84E-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
vg1218867681 NA 3.43E-21 mr1242 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
vg1218867681 NA 4.10E-07 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
vg1218867681 NA 2.78E-08 mr1442 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
vg1218867681 NA 2.25E-37 mr1601 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
vg1218867681 NA 1.27E-13 mr1653 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
vg1218867681 NA 2.18E-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
vg1218867681 NA 7.30E-34 mr1670 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
vg1218867681 NA 5.06E-06 mr1681 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
vg1218867681 NA 6.39E-14 mr1874 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
vg1218867681 NA 4.02E-06 mr1881 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
vg1218867681 NA 1.43E-24 mr1917 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
vg1218867681 NA 5.27E-34 mr1944 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
vg1218867681 4.08E-06 5.14E-07 mr1944 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
vg1218867681 NA 1.80E-24 mr1242_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
vg1218867681 NA 3.54E-13 mr1496_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
vg1218867681 NA 2.32E-29 mr1631_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
vg1218867681 NA 4.84E-20 mr1657_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
vg1218867681 NA 3.47E-24 mr1708_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