| Variant ID: vg0118270532 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270532 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATCTCTCGGACACCAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGG[T/C]
TGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACG
CGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCA[A/G]
CCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTGGTGTCCGAGAGAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270532 | T -> C | LOC_Os01g33180.1 | missense_variant ; p.Val29Ala; MODERATE | N | Average:55.403; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |
| vg0118270532 | T -> C | LOC_Os01g33160.1 | downstream_gene_variant ; 3334.0bp to feature; MODIFIER | N | Average:55.403; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |
| vg0118270532 | T -> C | LOC_Os01g33190.1 | downstream_gene_variant ; 1951.0bp to feature; MODIFIER | N | Average:55.403; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |