\

Search for Variation information by Variation ID:

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

Detailed information for vg1104448944:

Variant ID: vg1104448944 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4448944
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCACCAACGACCAGGGCAACCGCATCACCCCCTCCTGCGTCGCCTTCACCGCCGACGACAGGTTCGTCGGCGACGCCGCCGAGAATCAGGCCGCCCT[C/T]
AACCCCACCAACACCATCTTCGGTCATAAAACACACTCACTCGTTTATACTGCTATGCTAGCTTCTTGTTATTTTTCTTCCATCTTCCAAGGACCAGCAT

Reverse complement sequence

ATGCTGGTCCTTGGAAGATGGAAGAAAAATAACAAGAAGCTAGCATAGCAGTATAAACGAGTGAGTGTGTTTTATGACCGAAGATGGTGTTGGTGGGGTT[G/A]
AGGGCGGCCTGATTCTCGGCGGCGTCGCCGACGAACCTGTCGTCGGCGGTGAAGGCGACGCAGGAGGGGGTGATGCGGTTGCCCTGGTCGTTGGTGATGA

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 66.80% 23.50% 7.81% 1.93% NA
All Indica  2759 67.00% 25.50% 6.09% 1.41% NA
All Japonica  1512 71.60% 15.30% 10.45% 2.58% NA
Aus  269 33.50% 48.70% 13.75% 4.09% NA
Indica I  595 45.90% 27.20% 22.02% 4.87% NA
Indica II  465 91.60% 8.00% 0.43% 0.00% NA
Indica III  913 61.00% 37.20% 1.31% 0.44% NA
Indica Intermediate  786 75.30% 21.00% 2.93% 0.76% NA
Temperate Japonica  767 54.20% 24.90% 16.43% 4.43% NA
Tropical Japonica  504 94.80% 4.20% 0.79% 0.20% NA
Japonica Intermediate  241 78.40% 8.30% 11.62% 1.66% NA
VI/Aromatic  96 66.70% 31.20% 1.04% 1.04% NA
Intermediate  90 77.80% 15.60% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1104448944 C -> T LOC_Os11g08445.1 synonymous_variant ; p.Leu101Leu; LOW synonymous_codon Average:68.6; most accessible tissue: Minghui63 root, score: 84.069 N N N N
vg1104448944 C -> DEL LOC_Os11g08445.1 N frameshift_variant Average:68.6; most accessible tissue: Minghui63 root, score: 84.069 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104448944 NA 8.70E-06 mr1075 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
vg1104448944 NA 2.03E-06 mr1201 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
vg1104448944 NA 3.66E-06 mr1274 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
vg1104448944 NA 2.57E-09 mr1274 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
vg1104448944 9.07E-06 NA mr1841 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
vg1104448944 NA 2.60E-06 mr1933 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
vg1104448944 4.81E-06 4.81E-06 mr1312_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
vg1104448944 7.04E-08 2.60E-09 mr1397_2 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
vg1104448944 NA 3.85E-06 mr1508_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
vg1104448944 NA 9.51E-06 mr1766_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
vg1104448944 1.87E-06 3.03E-06 mr1843_2 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
vg1104448944 7.04E-06 7.04E-06 mr1843_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