Search for Variation information by Variation ID:
Detailed information for vg0219830859:
| Variant ID: vg0219830859 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19830859 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )
Flanking Sequence (100 bp) in Reference Genome:
CCAATCTCGTCCCAGTGAACTTTCTTGCTAGTAGGGCTGTCAACGAGCTGAGCTCGAGCGAGTTTGGCTATGTAGGCTTGAGCTTGACATGAACTCGAGC[T/C]
GAGCCTGGATATTGATCGAGCTTGGGAGTGAGCTCGAGTTCGAGCTCGAGCGAGCTTCGAGCCTACTCGAGCTTGGCAGCTTGACTTGGTGAAACTCCAA
Reverse complement sequence
TTGGAGTTTCACCAAGTCAAGCTGCCAAGCTCGAGTAGGCTCGAAGCTCGCTCGAGCTCGAACTCGAGCTCACTCCCAAGCTCGATCAATATCCAGGCTC[A/G]
GCTCGAGTTCATGTCAAGCTCAAGCCTACATAGCCAAACTCGCTCGAGCTCAGCTCGTTGACAGCCCTACTAGCAAGAAAGTTCACTGGGACGAGATTGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.10% | 24.50% | 3.09% | 1.27% | NA |
| All Indica | 2759 | 91.10% | 7.90% | 0.47% | 0.47% | NA |
| All Japonica | 1512 | 34.70% | 54.00% | 8.33% | 2.91% | NA |
| Aus | 269 | 65.40% | 34.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 89.90% | 8.20% | 1.18% | 0.67% | NA |
| Indica II | 465 | 84.90% | 14.20% | 0.22% | 0.65% | NA |
| Indica III | 913 | 95.70% | 3.80% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 90.30% | 8.80% | 0.51% | 0.38% | NA |
| Temperate Japonica | 767 | 32.20% | 46.70% | 15.38% | 5.74% | NA |
| Tropical Japonica | 504 | 26.00% | 74.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 61.00% | 35.70% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 31.10% | 6.67% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0219830859 | T -> DEL | LOC_Os02g33370.1 | N | frameshift_variant | Average:45.644; most accessible tissue: Minghui63 flag leaf, score: 64.867 | N | N | N | N |
| vg0219830859 | T -> C | LOC_Os02g33370.1 | missense_variant ; p.Ser91Gly; MODERATE | nonsynonymous_codon ; S91G | Average:45.644; most accessible tissue: Minghui63 flag leaf, score: 64.867 | benign  |
0.198 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0219830859 | NA | 1.56E-07 | mr1093 | 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 |
| vg0219830859 | NA | 8.32E-09 | mr1354 | 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 |
| vg0219830859 | NA | 5.91E-12 | mr1379 | 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 |
| vg0219830859 | NA | 5.09E-09 | mr1559 | 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 |
| vg0219830859 | NA | 6.35E-06 | mr1553_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 |
| vg0219830859 | NA | 1.28E-08 | mr1559_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 |