| Variant ID: vg0512020079 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12020079 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCTTAAACATTTTTTCAATTGTGACACATGGAACACATTATGGACTCCTGCCAAAGATTGAGGTAATTCTAACTGATAAGCAACCTCTCCTCTTCTACT[G/A]
ACAATCTTATAAGGTCCCACAAAACGCGGTGCCAATTTTCCCTTGGTGTGAAAACGATGAACTCCTCGAAGAGGCGTGACACGAAGATACACATAGTCTC
GAGACTATGTGTATCTTCGTGTCACGCCTCTTCGAGGAGTTCATCGTTTTCACACCAAGGGAAAATTGGCACCGCGTTTTGTGGGACCTTATAAGATTGT[C/T]
AGTAGAAGAGGAGAGGTTGCTTATCAGTTAGAATTACCTCAATCTTTGGCAGGAGTCCATAATGTGTTCCATGTGTCACAATTGAAAAAATGTTTAAGGG
| 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 | 88.00% | 0.10% | 3.83% | 8.10% | NA |
| All Indica | 2759 | 87.50% | 0.10% | 4.49% | 7.90% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Aus | 269 | 23.40% | 0.00% | 18.96% | 57.62% | NA |
| Indica I | 595 | 91.80% | 0.20% | 3.03% | 5.04% | NA |
| Indica II | 465 | 97.80% | 0.20% | 0.65% | 1.29% | NA |
| Indica III | 913 | 80.20% | 0.00% | 8.87% | 10.95% | NA |
| Indica Intermediate | 786 | 86.50% | 0.30% | 2.80% | 10.43% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512020079 | G -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:6.18; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0512020079 | G -> A | LOC_Os05g20480.1 | synonymous_variant ; p.Val1128Val; LOW | synonymous_codon | Average:6.18; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |