| Variant ID: vg1128667909 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 28667909 |
| Reference Allele: CG | Alternative Allele: TG,C |
| Primary Allele: CG | Secondary Allele: TG |
Inferred Ancestral Allele: Not determined.
AGTTGACGTCGTCGCTCGCCGAGTTGGTGCAGGCGATGGAGGTGATTCCTCCTCGCCACGCGACCAGGATCGGCGAGGAGACGTCTAACGGGATTTACAC[CG/TG,C]
GGGCGTGCCACATCCTCGCGTGCCTGAGGCTAGCGCATCCCAAGATAGACCTCAAAGAGGTTCTGACTCCTGGAGCTACCAATGACGTGCACAAGGGCGT
ACGCCCTTGTGCACGTCATTGGTAGCTCCAGGAGTCAGAACCTCTTTGAGGTCTATCTTGGGATGCGCTAGCCTCAGGCACGCGAGGATGTGGCACGCCC[CG/CA,G]
GTGTAAATCCCGTTAGACGTCTCCTCGCCGATCCTGGTCGCGTGGCGAGGAGGAATCACCTCCATCGCCTGCACCAACTCGGCGAGCGACGACGTCAACT
| Populations | Population Size | Frequency of CG(primary allele) | Frequency of TG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 3.90% | 0.21% | 3.20% | C: 0.02% |
| All Indica | 2759 | 94.30% | 1.70% | 0.36% | 3.59% | NA |
| All Japonica | 1512 | 92.80% | 4.90% | 0.00% | 2.25% | C: 0.07% |
| Aus | 269 | 73.20% | 22.70% | 0.00% | 4.09% | NA |
| Indica I | 595 | 98.70% | 0.50% | 0.00% | 0.84% | NA |
| Indica II | 465 | 92.90% | 0.20% | 0.65% | 6.24% | NA |
| Indica III | 913 | 92.40% | 3.10% | 0.44% | 4.05% | NA |
| Indica Intermediate | 786 | 94.10% | 1.90% | 0.38% | 3.56% | NA |
| Temperate Japonica | 767 | 97.50% | 1.80% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 90.10% | 5.60% | 0.00% | 4.37% | NA |
| Japonica Intermediate | 241 | 83.40% | 13.30% | 0.00% | 2.90% | C: 0.41% |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128667909 | CG -> TG | LOC_Os11g47449.1 | synonymous_variant ; p.Thr22Thr; LOW | synonymous_codon | Average:58.496; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| vg1128667909 | CG -> DEL | LOC_Os11g47449.1 | N | frameshift_variant | Average:58.496; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| vg1128667909 | CG -> C | LOC_Os11g47449.1 | frameshift_variant ; p.Ala24fs; HIGH | frameshift_variant | Average:58.496; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128667909 | 1.47E-07 | 1.47E-07 | mr1412 | 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 |
| vg1128667909 | 3.97E-06 | 3.97E-06 | mr1417 | 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 |
| vg1128667909 | 3.23E-07 | 3.23E-07 | mr1881 | 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 |