| Variant ID: vg0317762038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17762038 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCC[G/A]
CCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGGTGCAGATCTCAGG
CCTGAGATCTGCACCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGG[C/T]
GGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.20% | 0.30% | 6.22% | 46.23% | NA |
| All Indica | 2759 | 26.10% | 0.50% | 8.95% | 64.37% | NA |
| All Japonica | 1512 | 86.20% | 0.10% | 1.06% | 12.63% | NA |
| Aus | 269 | 24.20% | 0.00% | 9.29% | 66.54% | NA |
| Indica I | 595 | 16.30% | 0.20% | 3.19% | 80.34% | NA |
| Indica II | 465 | 17.60% | 0.60% | 8.82% | 72.90% | NA |
| Indica III | 913 | 37.30% | 0.70% | 13.58% | 48.41% | NA |
| Indica Intermediate | 786 | 25.60% | 0.60% | 8.02% | 65.78% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 66.10% | 0.20% | 3.17% | 30.56% | 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 | 60.00% | 0.00% | 4.44% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317762038 | G -> A | LOC_Os03g31190.1 | synonymous_variant ; p.Gly10Gly; LOW | synonymous_codon | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317762038 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |