| Variant ID: vg0118270578 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270578 |
| Reference Allele: A | Alternative Allele: G,AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 295. )
ACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGC[A/G,AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG]
AGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGC
GCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACT[T/C,CGCTCGCTGGTTCTCGAACTAGTACGTAGCAATCTCCCGCACCACAACCTCCATTGGTGTTCGAGGGATGATTCTACT]
GCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.90% | 24.00% | 9.71% | 27.36% | AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG: 0.02% |
| All Indica | 2759 | 5.10% | 39.60% | 16.13% | 39.14% | AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG: 0.04% |
| All Japonica | 1512 | 98.10% | 0.10% | 0.13% | 1.72% | NA |
| Aus | 269 | 27.10% | 8.90% | 2.23% | 61.71% | NA |
| Indica I | 595 | 4.20% | 10.80% | 28.40% | 56.64% | NA |
| Indica II | 465 | 6.90% | 50.30% | 25.81% | 16.99% | NA |
| Indica III | 913 | 2.70% | 52.10% | 3.50% | 41.62% | NA |
| Indica Intermediate | 786 | 7.40% | 40.60% | 15.78% | 36.13% | AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG: 0.13% |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.20% | 4.37% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 56.70% | 17.80% | 6.67% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270578 | A -> G | LOC_Os01g33180.1 | synonymous_variant ; p.Ala44Ala; LOW | synonymous_codon | Average:52.913; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |
| vg0118270578 | A -> DEL | LOC_Os01g33180.1 | N | frameshift_variant | Average:52.913; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |
| vg0118270578 | A -> AGTAGAATCATCCCTCGAACACCAATGGAG GTTGTGGTGCGGGAGATTGCTACGTACTAG TTCGAGAACCAGCGAGCG | LOC_Os01g33180.1 | frameshift_variant ; p.Ser45fs; HIGH | frameshift_variant | Average:52.913; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |