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

Detailed information for vg0506835795:

Variant ID: vg0506835795 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6835795
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GCCACCGCGCCATTGCCACCTCAGCGTCAAGTTTGCCGCCGGGTGCCGCCGCTCGACAAACGCACTCCGTCTCCTTGTCCTCCGTCGACCGAACAACGGT[C/T]
GTCGCCGCCTCATCGCGACCCTGTCCGTGCCGCCCCGGTGCCGTGATCATGACCCACGCCCCCGTGCGCCACCGACTCCCACTCACCACCGGATCACCGC

Reverse complement sequence

GCGGTGATCCGGTGGTGAGTGGGAGTCGGTGGCGCACGGGGGCGTGGGTCATGATCACGGCACCGGGGCGGCACGGACAGGGTCGCGATGAGGCGGCGAC[G/A]
ACCGTTGTTCGGTCGACGGAGGACAAGGAGACGGAGTGCGTTTGTCGAGCGGCGGCACCCGGCGGCAAACTTGACGCTGAGGTGGCAATGGCGCGGTGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.10% 41.70% 0.19% 0.08% NA
All Indica  2759 88.60% 11.00% 0.29% 0.11% NA
All Japonica  1512 4.80% 95.20% 0.00% 0.00% NA
Aus  269 70.60% 29.40% 0.00% 0.00% NA
Indica I  595 95.80% 4.00% 0.00% 0.17% NA
Indica II  465 80.00% 19.40% 0.65% 0.00% NA
Indica III  913 89.40% 10.30% 0.22% 0.11% NA
Indica Intermediate  786 87.30% 12.20% 0.38% 0.13% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 40.00% 57.80% 1.11% 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
vg0506835795 C -> T LOC_Os05g11960.1 synonymous_variant ; p.Thr172Thr; LOW synonymous_codon Average:68.936; most accessible tissue: Callus, score: 81.775 N N N N
vg0506835795 C -> DEL LOC_Os05g11960.1 N frameshift_variant Average:68.936; most accessible tissue: Callus, score: 81.775 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506835795 5.43E-11 1.41E-42 mr1039 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
vg0506835795 9.30E-08 8.84E-11 mr1039 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
vg0506835795 NA 2.41E-11 mr1514 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
vg0506835795 NA 1.32E-08 mr1593 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
vg0506835795 5.15E-09 1.24E-42 mr1632 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
vg0506835795 3.60E-06 2.67E-12 mr1632 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
vg0506835795 4.02E-09 1.82E-48 mr1873 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
vg0506835795 NA 1.63E-09 mr1873 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
vg0506835795 NA 4.68E-10 mr1904 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
vg0506835795 3.07E-10 1.73E-43 mr1039_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
vg0506835795 3.50E-06 7.88E-10 mr1039_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
vg0506835795 5.08E-09 1.09E-19 mr1514_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
vg0506835795 NA 1.61E-06 mr1514_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
vg0506835795 NA 1.56E-08 mr1593_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
vg0506835795 3.60E-14 2.22E-56 mr1632_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
vg0506835795 5.59E-09 1.09E-14 mr1632_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
vg0506835795 4.41E-06 1.05E-37 mr1873_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
vg0506835795 NA 2.00E-06 mr1873_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