Search for Variation information by Variation ID:

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

Detailed information for vg0321793105:

Variant ID: vg0321793105 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21793105
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, C: 0.10, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAGGACCCCGACCCTCCCTCGCCGGAGCAGGTGGACTGGGCGGAAGGTGCAGTGATCTCCGCCCAGTCGGCGGCGGATAACATGGCGTCCTATGTGCT[G/C]
GATCTCAGGAGGGGCCTGGCCGTGTTCGCCGGGACAGGGAGGCCCGAGGAGGCGGTGCTCAGGAAGCACGTCGCGTGGGCCGACGCGCGCCGCGCGGAGG

Reverse complement sequence

CCTCCGCGCGGCGCGCGTCGGCCCACGCGACGTGCTTCCTGAGCACCGCCTCCTCGGGCCTCCCTGTCCCGGCGAACACGGCCAGGCCCCTCCTGAGATC[C/G]
AGCACATAGGACGCCATGTTATCCGCCGCCGACTGGGCGGAGATCACTGCACCTTCCGCCCAGTCCACCTGCTCCGGCGAGGGAGGGTCGGGGTCCTCAA

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 79.20% 18.80% 1.46% 0.53% NA
All Indica  2759 68.60% 31.20% 0.11% 0.04% NA
All Japonica  1512 93.10% 1.10% 4.30% 1.59% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 29.70% 70.30% 0.00% 0.00% NA
Indica II  465 89.00% 11.00% 0.00% 0.00% NA
Indica III  913 72.90% 27.10% 0.00% 0.00% NA
Indica Intermediate  786 80.90% 18.60% 0.38% 0.13% NA
Temperate Japonica  767 99.30% 0.30% 0.26% 0.13% NA
Tropical Japonica  504 95.00% 1.00% 3.57% 0.40% NA
Japonica Intermediate  241 68.90% 3.70% 18.67% 8.71% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321793105 G -> C LOC_Os03g39240.1 synonymous_variant ; p.Leu82Leu; LOW synonymous_codon Average:67.254; most accessible tissue: Zhenshan97 flower, score: 78.132 N N N N
vg0321793105 G -> DEL LOC_Os03g39240.1 N frameshift_variant Average:67.254; most accessible tissue: Zhenshan97 flower, score: 78.132 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321793105 NA 2.08E-06 mr1029 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
vg0321793105 NA 4.82E-07 mr1074 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
vg0321793105 NA 7.78E-07 mr1081 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
vg0321793105 NA 5.93E-09 mr1130 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
vg0321793105 NA 1.29E-09 mr1148 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
vg0321793105 NA 6.95E-07 mr1254 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
vg0321793105 NA 1.63E-06 mr1272 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
vg0321793105 NA 9.11E-06 mr1531 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
vg0321793105 NA 4.38E-07 mr1680 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
vg0321793105 NA 2.36E-06 mr1734 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
vg0321793105 NA 3.82E-07 mr1857 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
vg0321793105 NA 3.52E-09 mr1857 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
vg0321793105 NA 3.11E-06 mr1928 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
vg0321793105 NA 8.43E-06 mr1974 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
vg0321793105 NA 3.05E-06 mr1558_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
vg0321793105 NA 4.94E-10 mr1565_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