| Variant ID: vg0614962658 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14962658 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 363. )
CTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAACGTGTGCGTCTCAGGTCT[C/T]
CAGCGGTCTACAAGAGCGGCAAGGAGTGACCGGTCTGCATCCCACCGCTTCGCTGGGTCACGGTCGTCCGCCGCCGCCTCAACAAGCCTACAAAGTGGTA
TACCACTTTGTAGGCTTGTTGAGGCGGCGGCGGACGACCGTGACCCAGCGAAGCGGTGGGATGCAGACCGGTCACTCCTTGCCGCTCTTGTAGACCGCTG[G/A]
AGACCTGAGACGCACACGTTCCACCTTCCCTGTGGGGAGATGGCTCCGACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCGGGAGCACCAG
| 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 | 38.50% | 0.20% | 7.17% | 54.10% | NA |
| All Indica | 2759 | 11.20% | 0.00% | 8.92% | 79.92% | NA |
| All Japonica | 1512 | 78.90% | 0.70% | 4.70% | 15.67% | NA |
| Aus | 269 | 75.50% | 0.00% | 1.86% | 22.68% | NA |
| Indica I | 595 | 5.90% | 0.00% | 15.63% | 78.49% | NA |
| Indica II | 465 | 3.20% | 0.00% | 10.75% | 86.02% | NA |
| Indica III | 913 | 15.00% | 0.00% | 2.30% | 82.69% | NA |
| Indica Intermediate | 786 | 15.40% | 0.00% | 10.43% | 74.17% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.78% | 3.26% | NA |
| Tropical Japonica | 504 | 56.30% | 0.40% | 6.15% | 37.10% | NA |
| Japonica Intermediate | 241 | 71.80% | 3.70% | 14.11% | 10.37% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 9.38% | 16.67% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 8.89% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962658 | C -> T | LOC_Os06g25580.1 | N | stop_gained | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962658 | C -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |