| Variant ID: vg1209004381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004381 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCAATCCCAATAAAAACACCAGTCGGCGGCGATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGG[C/T]
GAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGT
ACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTC[G/A]
CCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCATCGCCGCCGACTGGTGTTTTTATTGGGATTGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.80% | 0.10% | 0.83% | 20.25% | NA |
| All Indica | 2759 | 66.10% | 0.00% | 1.34% | 32.58% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Aus | 269 | 85.10% | 2.20% | 0.74% | 11.90% | NA |
| Indica I | 595 | 58.80% | 0.00% | 2.18% | 38.99% | NA |
| Indica II | 465 | 66.50% | 0.00% | 0.86% | 32.69% | NA |
| Indica III | 913 | 69.10% | 0.00% | 1.10% | 29.79% | NA |
| Indica Intermediate | 786 | 67.80% | 0.00% | 1.27% | 30.92% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004381 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:39.482; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |
| vg1209004381 | C -> T | LOC_Os12g15770.1 | missense_variant ; p.Arg86His; MODERATE | nonsynonymous_codon ; R86H | Average:39.482; most accessible tissue: Minghui63 young leaf, score: 66.656 | unknown | unknown | DELETERIOUS | 0.02 |