| Variant ID: vg1215445580 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 15445580 |
| Reference Allele: G | Alternative Allele: A,T,GCAAA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGTGAGGCGAGTGAGGGCGTCGTGGCCAAGGTGACCGAGATGACGATGCCAAAGAACGTCGGAGGTGGTGCTGGCGGCGAGGGTGGTGGCGGTCGGTGG[G/A,T,GCAAA]
GAAGGTAGTGCTTGGTGGAGTGGGTAGAGCGGACCGGAGCTATTGAACCTGGCGATCACGGTCCTGGTGTGAAAATCCTTCACAGAGAAGCCAAAAGGGT
ACCCTTTTGGCTTCTCTGTGAAGGATTTTCACACCAGGACCGTGATCGCCAGGTTCAATAGCTCCGGTCCGCTCTACCCACTCCACCAAGCACTACCTTC[C/T,A,TTTGC]
CCACCGACCGCCACCACCCTCGCCGCCAGCACCACCTCCGACGTTCTTTGGCATCGTCATCTCGGTCACCTTGGCCACGACGCCCTCACTCGCCTCACCG
| 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 | 58.40% | 5.90% | 2.54% | 30.72% | T: 2.39%; GCAAA: 0.02% |
| All Indica | 2759 | 63.30% | 8.20% | 2.65% | 24.68% | T: 1.16%; GCAAA: 0.04% |
| All Japonica | 1512 | 60.30% | 0.20% | 1.79% | 35.78% | T: 1.92% |
| Aus | 269 | 14.50% | 7.80% | 5.58% | 65.43% | T: 6.69% |
| Indica I | 595 | 91.90% | 0.20% | 0.67% | 7.23% | NA |
| Indica II | 465 | 72.50% | 6.20% | 4.95% | 14.84% | T: 1.51% |
| Indica III | 913 | 37.60% | 14.70% | 2.96% | 42.72% | T: 1.97%; GCAAA: 0.11% |
| Indica Intermediate | 786 | 66.00% | 7.90% | 2.42% | 22.77% | T: 0.89% |
| Temperate Japonica | 767 | 91.30% | 0.00% | 0.91% | 7.30% | T: 0.52% |
| Tropical Japonica | 504 | 16.10% | 0.20% | 2.98% | 79.76% | T: 0.99% |
| Japonica Intermediate | 241 | 54.40% | 0.80% | 2.07% | 34.44% | T: 8.30% |
| VI/Aromatic | 96 | 13.50% | 29.20% | 3.12% | 27.08% | T: 27.08% |
| Intermediate | 90 | 57.80% | 0.00% | 2.22% | 31.11% | T: 8.89% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215445580 | G -> A | LOC_Os12g26430.1 | missense_variant ; p.Gly21Arg; MODERATE | nonsynonymous_codon ; G21T | Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1215445580 | G -> A | LOC_Os12g26430.1 | missense_variant ; p.Gly21Arg; MODERATE | nonsynonymous_codon ; G21R | Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1215445580 | G -> DEL | LOC_Os12g26430.1 | N | frameshift_variant | Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| vg1215445580 | G -> GCAAA | LOC_Os12g26430.1 | frameshift_variant ; p.Gly21fs; HIGH | frameshift_variant | Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| vg1215445580 | G -> T | LOC_Os12g26430.1 | stop_gained ; p.Gly21*; HIGH | stop_gained | Average:31.106; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215445580 | 6.11E-10 | 1.92E-10 | mr1350_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 |
| vg1215445580 | NA | 3.31E-06 | mr1865_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 |