| Variant ID: vg1209004497 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004497 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGG[C/T]
GGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTG
CACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCC[G/A]
CCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTG
| 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 | 78.20% | 0.20% | 0.89% | 20.65% | NA |
| All Indica | 2759 | 65.90% | 0.00% | 0.91% | 33.20% | NA |
| All Japonica | 1512 | 97.20% | 0.70% | 1.12% | 0.93% | NA |
| Aus | 269 | 87.40% | 0.00% | 0.00% | 12.64% | NA |
| Indica I | 595 | 58.20% | 0.00% | 2.02% | 39.83% | NA |
| Indica II | 465 | 67.10% | 0.00% | 0.22% | 32.69% | NA |
| Indica III | 913 | 68.30% | 0.00% | 0.44% | 31.22% | NA |
| Indica Intermediate | 786 | 68.20% | 0.00% | 1.02% | 30.79% | NA |
| Temperate Japonica | 767 | 96.30% | 1.40% | 1.43% | 0.78% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.40% | 0.79% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 1.66% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004497 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:44.613; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| vg1209004497 | C -> T | LOC_Os12g15770.1 | synonymous_variant ; p.Pro47Pro; LOW | synonymous_codon | Average:44.613; most accessible tissue: Callus, score: 82.589 | N | N | N | N |