| Variant ID: vg1105974508 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974508 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGT[C/T]
TGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTC
GAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCA[G/A]
ACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCA
| 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 | 50.00% | 0.40% | 0.63% | 48.96% | NA |
| All Indica | 2759 | 33.20% | 0.50% | 0.80% | 65.57% | NA |
| All Japonica | 1512 | 83.10% | 0.30% | 0.40% | 16.20% | NA |
| Aus | 269 | 18.60% | 0.00% | 0.74% | 80.67% | NA |
| Indica I | 595 | 38.70% | 0.30% | 2.35% | 58.66% | NA |
| Indica II | 465 | 26.00% | 0.00% | 0.65% | 73.33% | NA |
| Indica III | 913 | 30.60% | 0.20% | 0.00% | 69.22% | NA |
| Indica Intermediate | 786 | 36.30% | 1.10% | 0.64% | 61.96% | NA |
| Temperate Japonica | 767 | 73.10% | 0.00% | 0.78% | 26.08% | NA |
| Tropical Japonica | 504 | 95.60% | 1.00% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 0.00% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974508 | C -> T | LOC_Os11g10840.1 | synonymous_variant ; p.Val63Val; LOW | synonymous_codon | Average:45.682; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974508 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:45.682; most accessible tissue: Callus, score: 75.127 | N | N | N | N |