| Variant ID: vg0317762026 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762026 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGG[C/A]
GTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGGT
ACCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTAC[G/T]
CCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.70% | 0.10% | 4.02% | 44.20% | NA |
| All Indica | 2759 | 33.60% | 0.20% | 5.29% | 60.89% | NA |
| All Japonica | 1512 | 86.20% | 0.00% | 0.99% | 12.83% | NA |
| Aus | 269 | 24.50% | 0.00% | 9.67% | 65.80% | NA |
| Indica I | 595 | 17.60% | 0.00% | 2.86% | 79.50% | NA |
| Indica II | 465 | 26.50% | 0.00% | 3.44% | 70.11% | NA |
| Indica III | 913 | 49.30% | 0.40% | 7.67% | 42.61% | NA |
| Indica Intermediate | 786 | 31.80% | 0.10% | 5.47% | 62.60% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 65.90% | 0.00% | 2.98% | 31.15% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 0.00% | 14.94% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762026 | C -> A | LOC_Os03g31190.1 | synonymous_variant ; p.Thr14Thr; LOW | synonymous_codon | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317762026 | C -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |