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Detailed information for vg1104747649:

Variant ID: vg1104747649 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4747649
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTGACGCCGCCCTGCCACCTCCCTACATCCTCGACGCTTCCCTCGCTGCCTGGACAGCGGGGACGGAGGAACAGGTAAGATTATTAGTGCAGTACCAT[G/C]
TTTGTGCATTTTTCCCGTTCCCTGTTGTGCTAGCGTACATTAGTTCATCGTTTTTGTGTGAACCATATATCAATCTCATTATATGTTTAATTGTTAGAAC

Reverse complement sequence

GTTCTAACAATTAAACATATAATGAGATTGATATATGGTTCACACAAAAACGATGAACTAATGTACGCTAGCACAACAGGGAACGGGAAAAATGCACAAA[C/G]
ATGGTACTGCACTAATAATCTTACCTGTTCCTCCGTCCCCGCTGTCCAGGCAGCGAGGGAAGCGTCGAGGATGTAGGGAGGTGGCAGGGCGGCGTCAGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.70% 2.10% 1.02% 12.10% NA
All Indica  2759 75.00% 3.60% 1.63% 19.83% NA
All Japonica  1512 99.70% 0.00% 0.00% 0.26% NA
Aus  269 98.50% 0.00% 0.00% 1.49% NA
Indica I  595 73.40% 2.90% 1.51% 22.18% NA
Indica II  465 90.30% 0.60% 0.65% 8.39% NA
Indica III  913 73.80% 0.40% 1.86% 23.88% NA
Indica Intermediate  786 68.40% 9.40% 2.04% 20.10% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 83.30% 2.10% 2.08% 12.50% NA
Intermediate  90 92.20% 1.10% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1104747649 G -> DEL N N silent_mutation Average:22.158; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N
vg1104747649 G -> C LOC_Os11g08950-LOC_Os11g08970 intergenic_region ; MODIFIER silent_mutation Average:22.158; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104747649 NA 5.67E-06 mr1155 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
vg1104747649 NA 2.50E-06 mr1515 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
vg1104747649 NA 8.72E-07 mr1730 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
vg1104747649 4.71E-06 4.70E-06 mr1777 Ind_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
vg1104747649 NA 4.12E-06 mr1981 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
vg1104747649 NA 6.88E-06 mr1092_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
vg1104747649 NA 7.85E-06 mr1097_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
vg1104747649 NA 1.25E-07 mr1533_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
vg1104747649 NA 3.05E-07 mr1980_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