| Variant ID: vg0710346937 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10346937 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGCCGCCGCCACGCCACGCCGCCGCCGTCACGCCACGCCACGCCGCCACCGCCATGGCCCCGCAACGCCACGCCGCCGCCGCCGTCGCCACGCTGCCGC[G/A]
CCAACCGCCGCCCCGATGCCGCCACACCGCCGTTAACGAACGAGAACGAGAACGATCGAACGAACGAGAGCGAGAACGAACACGTCAACGTACGTTGCCG
CGGCAACGTACGTTGACGTGTTCGTTCTCGCTCTCGTTCGTTCGATCGTTCTCGTTCTCGTTCGTTAACGGCGGTGTGGCGGCATCGGGGCGGCGGTTGG[C/T]
GCGGCAGCGTGGCGACGGCGGCGGCGGCGTGGCGTTGCGGGGCCATGGCGGTGGCGGCGTGGCGTGGCGTGACGGCGGCGGCGTGGCGTGGCGGCGGCGG
| 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 | 7.30% | 0.30% | 17.82% | 74.59% | NA |
| All Indica | 2759 | 2.00% | 0.50% | 7.79% | 89.78% | NA |
| All Japonica | 1512 | 16.30% | 0.10% | 32.74% | 50.93% | NA |
| Aus | 269 | 11.90% | 0.00% | 30.48% | 57.62% | NA |
| Indica I | 595 | 2.00% | 0.20% | 7.73% | 90.08% | NA |
| Indica II | 465 | 0.90% | 0.40% | 6.02% | 92.69% | NA |
| Indica III | 913 | 2.00% | 0.70% | 4.05% | 93.32% | NA |
| Indica Intermediate | 786 | 2.50% | 0.50% | 13.23% | 83.72% | NA |
| Temperate Japonica | 767 | 9.60% | 0.00% | 33.12% | 57.24% | NA |
| Tropical Japonica | 504 | 27.00% | 0.00% | 27.38% | 45.63% | NA |
| Japonica Intermediate | 241 | 14.90% | 0.40% | 42.74% | 41.91% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 37.50% | 54.17% | NA |
| Intermediate | 90 | 5.60% | 0.00% | 15.56% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710346937 | G -> DEL | N | N | silent_mutation | Average:5.443; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0710346937 | G -> A | LOC_Os07g17510.1 | 5_prime_UTR_variant ; 1493.0bp to feature; MODIFIER | silent_mutation | Average:5.443; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0710346937 | G -> A | LOC_Os07g17500.1 | downstream_gene_variant ; 1507.0bp to feature; MODIFIER | silent_mutation | Average:5.443; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |