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Detailed information for vg1217810691:

Variant ID: vg1217810691 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17810691
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCGATGCTTGCCTCCGGACGAGCACGGATATGAACATACTTCTTTAGAACGCCCATGTACCTCTCGAAAGGAAACATGTTGTGTAGGTACACAGGCC[T/C]
GAAAATACCGATCTCTTTGACAAGGTGACAAAGCAGATGCGTCATTATATTGAAAAATGAAGGTGGAAATATCAACTCAAAGCTGACAAGACATTACACC

Reverse complement sequence

GGTGTAATGTCTTGTCAGCTTTGAGTTGATATTTCCACCTTCATTTTTCAATATAATGACGCATCTGCTTTGTCACCTTGTCAAAGAGATCGGTATTTTC[A/G]
GGCCTGTGTACCTACACAACATGTTTCCTTTCGAGAGGTACATGGGCGTTCTAAAGAAGTATGTTCATATCCGTGCTCGTCCGGAGGCAAGCATCGCCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.20% 29.50% 0.91% 34.43% NA
All Indica  2759 39.50% 25.20% 1.12% 34.14% NA
All Japonica  1512 25.60% 44.00% 0.66% 29.76% NA
Aus  269 43.10% 1.50% 0.37% 55.02% NA
Indica I  595 46.90% 44.00% 0.34% 8.74% NA
Indica II  465 18.50% 23.00% 2.37% 56.13% NA
Indica III  913 40.00% 17.50% 1.10% 41.40% NA
Indica Intermediate  786 45.90% 21.10% 1.02% 31.93% NA
Temperate Japonica  767 21.80% 74.20% 0.13% 3.91% NA
Tropical Japonica  504 34.90% 4.60% 1.19% 59.33% NA
Japonica Intermediate  241 18.30% 30.30% 1.24% 50.21% NA
VI/Aromatic  96 34.40% 3.10% 0.00% 62.50% NA
Intermediate  90 40.00% 28.90% 1.11% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217810691 T -> C LOC_Os12g29800.1 missense_variant ; p.Arg135Gly; MODERATE nonsynonymous_codon ; R135G Average:23.56; most accessible tissue: Zhenshan97 root, score: 47.644 unknown unknown TOLERATED 1.00
vg1217810691 T -> DEL LOC_Os12g29800.1 N frameshift_variant Average:23.56; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217810691 NA 3.41E-20 Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1217810691 NA 1.81E-06 mr1164 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
vg1217810691 NA 1.84E-06 mr1180 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
vg1217810691 NA 1.71E-08 mr1183 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
vg1217810691 NA 1.03E-07 mr1503 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
vg1217810691 NA 7.75E-06 mr1561 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
vg1217810691 4.37E-06 NA mr1824 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
vg1217810691 NA 6.21E-06 mr1826 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
vg1217810691 NA 5.84E-08 mr1063_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
vg1217810691 NA 1.41E-06 mr1653_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
vg1217810691 NA 6.81E-06 mr1844_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
vg1217810691 NA 2.29E-09 mr1870_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