| Variant ID: vg0128509375 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 28509375 |
| Reference Allele: A | Alternative Allele: AGATGG |
| Primary Allele: A | Secondary Allele: AGATGG |
Inferred Ancestral Allele: Not determined.
CTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACAT[A/AGATGG]
TATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGC
GCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATA[T/CCATCT]
ATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AGATGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.50% | 1.40% | 8.00% | 53.20% | NA |
| All Indica | 2759 | 13.50% | 2.20% | 10.95% | 73.32% | NA |
| All Japonica | 1512 | 88.00% | 0.00% | 4.03% | 7.94% | NA |
| Aus | 269 | 4.10% | 0.00% | 2.60% | 93.31% | NA |
| Indica I | 595 | 6.20% | 2.70% | 3.70% | 87.39% | NA |
| Indica II | 465 | 8.20% | 0.00% | 5.38% | 86.45% | NA |
| Indica III | 913 | 25.00% | 4.20% | 19.06% | 51.81% | NA |
| Indica Intermediate | 786 | 8.80% | 1.00% | 10.31% | 79.90% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 6.65% | 0.52% | NA |
| Tropical Japonica | 504 | 77.00% | 0.00% | 1.79% | 21.23% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 2.08% | 83.33% | NA |
| Intermediate | 90 | 46.70% | 2.20% | 6.67% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509375 | A -> AGATGG | LOC_Os01g49570.1 | frameshift_variant ; p.Tyr67fs; HIGH | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509375 | A -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |