| Variant ID: vg0415575753 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 15575753 |
| Reference Allele: CATCCCCGGCCCTCT | Alternative Allele: C,CCCCCGGCCCTCT |
| Primary Allele: CATCCCCGGCCCTCT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCC[CATCCCCGGCCCTCT/C,CCCCCGGCCCTCT]
CCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTC
GAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGG[AGAGGGCCGGGGATG/G,AGAGGGCCGGGGG]
GGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCG
| Populations | Population Size | Frequency of CATCCCCGGCCCTCT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.60% | 0.10% | 2.62% | 17.60% | CCCCCGGCCCTCT: 0.02% |
| All Indica | 2759 | 86.60% | 0.10% | 3.77% | 9.46% | CCCCCGGCCCTCT: 0.04% |
| All Japonica | 1512 | 78.40% | 0.30% | 0.66% | 20.70% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.97% | 88.48% | NA |
| Indica I | 595 | 92.10% | 0.20% | 6.22% | 1.51% | NA |
| Indica II | 465 | 75.70% | 0.00% | 1.94% | 22.37% | NA |
| Indica III | 913 | 88.60% | 0.00% | 3.83% | 7.56% | NA |
| Indica Intermediate | 786 | 86.60% | 0.30% | 2.93% | 10.05% | CCCCCGGCCCTCT: 0.13% |
| Temperate Japonica | 767 | 59.80% | 0.30% | 1.30% | 38.59% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.80% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 1.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575753 | CATCCCCGGCCCTCT -> CCCCCGGCCCTCT | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
| vg0415575753 | CATCCCCGGCCCTCT -> DEL | N | N | silent_mutation | Average:44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
| vg0415575753 | CATCCCCGGCCCTCT -> C | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |