| Variant ID: vg0512020664 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 12020664 |
| Reference Allele: CA | Alternative Allele: C |
| Primary Allele: CA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCATCTCTTCCTGAAGTTTCTTCCAAAAATTTGAAGTAAACTGACTGCCTCGATCAGACACTATCTTCTTAGGGACGCCATGCAAACACACAATCCTTGC[CA/C]
TATACAATTCCGCCAAGCGACTTCCGGAATAGGTTGTCTTTACCGGAATAAAATGAGCCACTTTGGTAAGTCTGTCGACTATCACCCAAATAGAATCATG
CATGATTCTATTTGGGTGATAGTCGACAGACTTACCAAAGTGGCTCATTTTATTCCGGTAAAGACAACCTATTCCGGAAGTCGCTTGGCGGAATTGTATA[TG/G]
GCAAGGATTGTGTGTTTGCATGGCGTCCCTAAGAAGATAGTGTCTGATCGAGGCAGTCAGTTTACTTCAAATTTTTGGAAGAAACTTCAGGAAGAGATGG
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.60% | 0.10% | 3.96% | 9.35% | NA |
| All Indica | 2759 | 85.30% | 0.20% | 5.04% | 9.50% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.26% | NA |
| Aus | 269 | 21.90% | 0.00% | 14.50% | 63.57% | NA |
| Indica I | 595 | 91.60% | 0.00% | 2.86% | 5.55% | NA |
| Indica II | 465 | 92.70% | 0.00% | 1.08% | 6.24% | NA |
| Indica III | 913 | 78.20% | 0.50% | 9.31% | 11.94% | NA |
| Indica Intermediate | 786 | 84.40% | 0.00% | 4.07% | 11.58% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 5.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512020664 | CA -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:8.295; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0512020664 | CA -> C | LOC_Os05g20480.1 | N | frameshift_variant | Average:8.295; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |