| Variant ID: vg0108457671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457671 |
| Reference Allele: C | Alternative Allele: G,A |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTC[C/G,A]
ACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGAATAAAAGCAATACCGGCTTCGGCCAACAGGATGTAGGGTTATTACCTGAC
GTCAGGTAATAACCCTACATCCTGTTGGCCGAAGCCGGTATTGCTTTTATTCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGT[G/C,T]
GACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.60% | 7.30% | 0.08% | 0.00% | A: 0.02% |
| All Indica | 2759 | 96.20% | 3.80% | 0.04% | 0.00% | A: 0.04% |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 13.00% | 86.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.10% | 4.80% | 0.00% | 0.00% | A: 0.11% |
| Indica Intermediate | 786 | 93.80% | 6.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457671 | C -> G | LOC_Os01g15070.1 | synonymous_variant ; p.Ser82Ser; LOW | synonymous_codon | Average:57.238; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| vg0108457671 | C -> A | LOC_Os01g15070.1 | synonymous_variant ; p.Ser82Ser; LOW | synonymous_codon | Average:57.238; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |