| Variant ID: vg0118270545 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270545 |
| Reference Allele: GATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACC | Alternative Allele: G |
| Primary Allele: GATTGCTACGTACTGGTTCG AGAACCAGCGAGCAAGTAGA ATCATCTCTCGAACACCAAT GGAGGTTGCGGTGCGGGAGA TTGCTACGTACTGGTTCAAG AACC | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGA[GATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACC/G]
AGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGTGGTGTAGGAGATTGCTACGTACTGGTTCGA
TCGAACCAGTACGTAGCAATCTCCTACACCACAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCT[GGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATC/C]
TCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTG
| Populations | Population Size | Frequency of GATTGCTACGTACTGGTTCG AGAACCAGCGAGCAAGTAGA ATCATCTCTCGAACACCAAT GGAGGTTGCGGTGCGGGAGA TTGCTACGTACTGGTTCAAG AACC(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.00% | 0.68% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 0.00% | 2.18% | 0.00% | NA |
| Indica II | 465 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.00% | 1.27% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270545 | GATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACC -> G | LOC_Os01g33180.1 | frameshift_variant ; p.Ile34fs; HIGH | N | Average:54.798; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |
| vg0118270545 | GATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACC -> G | LOC_Os01g33160.1 | downstream_gene_variant ; 3348.0bp to feature; MODIFIER | N | Average:54.798; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |