Search for Variation information by Variation ID:
Detailed information for vg1214642319:
| Variant ID: vg1214642319 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14642319 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
GCAACAAAAGCAGAATTTGCACAAACATCAGGAGCTGTTACCTTAGACCTTGTAGTCCGCTCACCTATATTACCAATAATTTGTTCTGGCGGATGTCGTC[G/C,A]
TTGAATGTGCAAAGGAGCAGCGACTTCTGAAGTTGATCCACGTTCTGTATCAGTACTGGTCGAAGTAGTAATTTCTGGAGGACCATTTCGATCAGCATCA
Reverse complement sequence
TGATGCTGATCGAAATGGTCCTCCAGAAATTACTACTTCGACCAGTACTGATACAGAACGTGGATCAACTTCAGAAGTCGCTGCTCCTTTGCACATTCAA[C/G,T]
GACGACATCCGCCAGAACAAATTATTGGTAATATAGGTGAGCGGACTACAAGGTCTAAGGTAACAGCTCCTGATGTTTGTGCAAATTCTGCTTTTGTTGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.80% | 14.90% | 19.70% | 12.70% | C: 4.85% |
| All Indica | 2759 | 23.80% | 16.40% | 30.70% | 20.99% | C: 8.12% |
| All Japonica | 1512 | 80.80% | 15.70% | 2.58% | 0.79% | C: 0.13% |
| Aus | 269 | 90.70% | 1.10% | 7.06% | 0.37% | C: 0.74% |
| Indica I | 595 | 27.60% | 5.50% | 40.00% | 14.12% | C: 12.77% |
| Indica II | 465 | 17.60% | 25.20% | 27.74% | 23.23% | C: 6.24% |
| Indica III | 913 | 21.60% | 16.40% | 28.59% | 25.08% | C: 8.32% |
| Indica Intermediate | 786 | 27.20% | 19.30% | 27.86% | 20.10% | C: 5.47% |
| Temperate Japonica | 767 | 90.20% | 7.20% | 1.83% | 0.78% | NA |
| Tropical Japonica | 504 | 69.40% | 26.20% | 3.37% | 0.79% | C: 0.20% |
| Japonica Intermediate | 241 | 74.30% | 21.20% | 3.32% | 0.83% | C: 0.41% |
| VI/Aromatic | 96 | 86.50% | 0.00% | 7.29% | 6.25% | NA |
| Intermediate | 90 | 62.20% | 13.30% | 21.11% | 2.22% | C: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214642319 | G -> C | LOC_Os12g25380.1 | N | nonsynonymous_codon ; R618G | Average:19.641; most accessible tissue: Minghui63 young leaf, score: 31.294 | possibly damaging  |
1.64 |
TOLERATED | 0.11 |
| vg1214642319 | G -> DEL | LOC_Os12g25380.1 | N | frameshift_variant | Average:19.641; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
| vg1214642319 | G -> A | LOC_Os12g25380.1 | stop_gained ; p.Arg618*; HIGH | stop_gained | Average:19.641; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214642319 | NA | 4.68E-06 | mr1603 | 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 |
| vg1214642319 | NA | 2.88E-06 | mr1422_2 | Jap_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 |
| vg1214642319 | 5.40E-06 | 5.40E-06 | mr1767_2 | Jap_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 |
| vg1214642319 | 4.92E-06 | 4.92E-06 | mr1960_2 | Jap_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 |