| Variant ID: vg1212666243 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666243 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCTCCCATGACTATGTTGATTTTCAGCAGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGT[T/A]
TTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACA
TGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAA[A/T]
ACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCTGCTGAAAATCAACATAGTCATGGGAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.50% | 0.40% | 12.17% | 36.99% | NA |
| All Indica | 2759 | 50.70% | 0.50% | 15.22% | 33.56% | NA |
| All Japonica | 1512 | 47.00% | 0.00% | 4.56% | 48.48% | NA |
| Aus | 269 | 65.40% | 1.50% | 20.07% | 13.01% | NA |
| Indica I | 595 | 50.40% | 0.20% | 6.05% | 43.36% | NA |
| Indica II | 465 | 37.40% | 0.00% | 20.22% | 42.37% | NA |
| Indica III | 913 | 60.00% | 0.80% | 18.18% | 21.03% | NA |
| Indica Intermediate | 786 | 48.10% | 0.60% | 15.78% | 35.50% | NA |
| Temperate Japonica | 767 | 79.00% | 0.00% | 0.91% | 20.08% | NA |
| Tropical Japonica | 504 | 6.90% | 0.00% | 9.52% | 83.53% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 5.81% | 65.56% | NA |
| VI/Aromatic | 96 | 53.10% | 0.00% | 19.79% | 27.08% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 14.44% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666243 | T -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666243 | T -> A | LOC_Os12g22430.1 | synonymous_variant ; p.Val236Val; LOW | synonymous_codon | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |