\

Search for Variation information by Variation ID:

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

Detailed information for vg0417375976:

Variant ID: vg0417375976 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17375976
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:


TATTTGCTGATCCTTTGGGTTATGCATTAGTCGAGGAGTTCATGATACATGGCCCGTGTGGTGTAGACAATAAAACTTGCCCATGTATGAAAAAAGGTTC[G/C]
TGCTCTAAACATTTCCCTAAAACATTCCAAGCTGAAACAATACTTGATGAGTTTGGGTTAACTGTGTACAAGAGACGAGACGATGGTCGCTATGTAATTA

Reverse complement sequence

TAATTACATAGCGACCATCGTCTCGTCTCTTGTACACAGTTAACCCAAACTCATCAAGTATTGTTTCAGCTTGGAATGTTTTAGGGAAATGTTTAGAGCA[C/G]
GAACCTTTTTTCATACATGGGCAAGTTTTATTGTCTACACCACACGGGCCATGTATCATGAACTCCTCGACTAATGCATAACCCAAAGGATCAGCAAATA

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 83.70% 3.30% 4.97% 7.98% NA
All Indica  2759 88.90% 5.60% 1.63% 3.81% NA
All Japonica  1512 79.00% 0.10% 4.37% 16.53% NA
Aus  269 59.10% 0.00% 37.92% 2.97% NA
Indica I  595 70.90% 11.10% 3.03% 14.96% NA
Indica II  465 97.60% 1.50% 0.65% 0.22% NA
Indica III  913 92.40% 5.60% 1.20% 0.77% NA
Indica Intermediate  786 93.40% 3.90% 1.65% 1.02% NA
Temperate Japonica  767 65.10% 0.00% 6.78% 28.16% NA
Tropical Japonica  504 99.20% 0.00% 0.40% 0.40% NA
Japonica Intermediate  241 81.30% 0.40% 4.98% 13.28% NA
VI/Aromatic  96 69.80% 0.00% 19.79% 10.42% NA
Intermediate  90 92.20% 0.00% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0417375976 G -> C LOC_Os04g29310.1 synonymous_variant ; p.Ser145Ser; LOW synonymous_codon Average:25.707; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0417375976 G -> DEL LOC_Os04g29310.1 N frameshift_variant Average:25.707; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417375976 NA 2.13E-07 mr1038 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
vg0417375976 NA 2.59E-09 mr1389 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
vg0417375976 NA 4.73E-06 mr1020_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
vg0417375976 5.05E-07 1.97E-14 mr1038_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
vg0417375976 9.19E-08 1.59E-14 mr1389_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
vg0417375976 NA 7.57E-06 mr1452_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
vg0417375976 NA 3.64E-06 mr1478_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
vg0417375976 4.55E-06 6.99E-08 mr1576_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
vg0417375976 NA 4.73E-09 mr1627_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
vg0417375976 NA 2.89E-06 mr1851_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
vg0417375976 NA 6.11E-10 mr1864_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
vg0417375976 NA 9.67E-06 mr1875_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