| Variant ID: vg0512023250 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023250 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGCATAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCCCTCTT[G/A]
GCAGGTTGTTGCTGTGCTGGAGCTGCAACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAA
TTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGTTGCAGCTCCAGCACAGCAACAACCTGC[C/T]
AAGAGGGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTATGCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCC
| 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 | 93.60% | 0.00% | 1.59% | 4.78% | NA |
| All Indica | 2759 | 93.60% | 0.00% | 2.28% | 4.10% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Aus | 269 | 56.50% | 0.00% | 4.46% | 39.03% | NA |
| Indica I | 595 | 95.00% | 0.00% | 4.37% | 0.67% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.65% | 0.43% | NA |
| Indica III | 913 | 91.90% | 0.10% | 2.19% | 5.81% | NA |
| Indica Intermediate | 786 | 91.30% | 0.00% | 1.78% | 6.87% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023250 | G -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:27.227; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0512023250 | G -> A | LOC_Os05g20480.1 | synonymous_variant ; p.Ala71Ala; LOW | synonymous_codon | Average:27.227; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |