| Variant ID: vg1225602644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25602644 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 390. )
ATTAGCAGACTTAGAAGTCTGCCCTGCAGGTGCCTTCATCCCCTTGCGCTGTGGACACTTTCTAGCCAGATGACCAACTTGGCCACACACAAAGCAAGTC[C/T]
TCTCATCCTGATTAGGATTGTTGTTGTTCTTCTTCTGCTTCTTGAAGTTGGTGGTCTGCTGAGCTTTGTATTTCCCCTTGCTCTTGTTCTGGGCCTTGTG
CACAAGGCCCAGAACAAGAGCAAGGGGAAATACAAAGCTCAGCAGACCACCAACTTCAAGAAGCAGAAGAAGAACAACAACAATCCTAATCAGGATGAGA[G/A]
GACTTGCTTTGTGTGTGGCCAAGTTGGTCATCTGGCTAGAAAGTGTCCACAGCGCAAGGGGATGAAGGCACCTGCAGGGCAGACTTCTAAGTCTGCTAAT
| 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 | 68.70% | 0.20% | 3.22% | 27.82% | NA |
| All Indica | 2759 | 57.50% | 0.40% | 4.71% | 37.44% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 6.30% | 0.00% | 5.20% | 88.48% | NA |
| Indica I | 595 | 90.10% | 0.20% | 1.18% | 8.57% | NA |
| Indica II | 465 | 33.30% | 0.00% | 4.52% | 62.15% | NA |
| Indica III | 913 | 54.10% | 0.40% | 7.12% | 38.34% | NA |
| Indica Intermediate | 786 | 51.00% | 0.60% | 4.71% | 43.64% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 3.12% | 26.04% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 5.56% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225602644 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:7.66; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1225602644 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Arg240Lys; MODERATE | nonsynonymous_codon ; R240K | Average:7.66; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | TOLERATED | 0.70 |