| Variant ID: vg0123776540 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776540 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTGCACTAGTTCTCAACGAGGGTTGCATTGCATTGCGTAGCGTGGACTATCACTAACACACAATGGCTAGAATGGCTAGAACTCCAGTTCATCCACGATC[G/C]
TCCTCGATTGTAGCTGCATTCACTTACCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGCTGCATCTCCCAAAGCTCCGGCATCCACCAATG
CATTGGTGGATGCCGGAGCTTTGGGAGATGCAGCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGGTAAGTGAATGCAGCTACAATCGAGGA[C/G]
GATCGTGGATGAACTGGAGTTCTAGCCATTCTAGCCATTGTGTGTTAGTGATAGTCCACGCTACGCAATGCAATGCAACCCTCGTTGAGAACTAGTGCAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.60% | 0.10% | 0.17% | 56.18% | NA |
| All Indica | 2759 | 9.90% | 0.00% | 0.18% | 89.89% | NA |
| All Japonica | 1512 | 92.10% | 0.00% | 0.00% | 7.94% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 2.90% | 0.00% | 0.34% | 96.81% | NA |
| Indica II | 465 | 6.00% | 0.00% | 0.00% | 93.98% | NA |
| Indica III | 913 | 11.20% | 0.00% | 0.11% | 88.72% | NA |
| Indica Intermediate | 786 | 16.00% | 0.10% | 0.25% | 83.59% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 0.00% | 21.03% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 57.80% | 2.20% | 3.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776540 | G -> DEL | LOC_Os01g41930.1 | N | frameshift_variant | Average:67.92; most accessible tissue: Minghui63 root, score: 86.064 | N | N | N | N |
| vg0123776540 | G -> C | LOC_Os01g41930.1 | synonymous_variant ; p.Ser13Ser; LOW | synonymous_codon | Average:67.92; most accessible tissue: Minghui63 root, score: 86.064 | N | N | N | N |