| Variant ID: vg0141809389 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809389 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCGGTTCAACACCGGCCCCCGCGGTTGGAAGTAGCAGCCACCAACCACCGACGGCGGCGACACCGA[C/T]
TGTACGGTGAAGAACCACCGGAACAGCCGAAGGGATGGGCGCACCCCGATGAACATTTCGCACAGGTGCGCGAAGATGGCCAATGTCATTACCGCGTTGG
CCAACGCGGTAATGACATTGGCCATCTTCGCGCACCTGTGCGAAATGTTCATCGGGGTGCGCCCATCCCTTCGGCTGTTCCGGTGGTTCTTCACCGTACA[G/A]
TCGGTGTCGCCGCCGTCGGTGGTTGGTGGCTGCTACTTCCAACCGCGGGGGCCGGTGTTGAACCGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATG
| 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 | 17.90% | 0.60% | 2.22% | 79.20% | NA |
| All Indica | 2759 | 1.90% | 0.00% | 1.67% | 96.38% | NA |
| All Japonica | 1512 | 44.00% | 1.90% | 3.44% | 50.73% | NA |
| Aus | 269 | 34.90% | 0.00% | 0.37% | 64.68% | NA |
| Indica I | 595 | 3.20% | 0.00% | 3.87% | 92.94% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.00% | 99.14% | NA |
| Indica III | 913 | 0.40% | 0.10% | 0.77% | 98.69% | NA |
| Indica Intermediate | 786 | 3.30% | 0.00% | 2.04% | 94.66% | NA |
| Temperate Japonica | 767 | 77.20% | 0.10% | 1.04% | 21.64% | NA |
| Tropical Japonica | 504 | 4.60% | 5.40% | 6.94% | 83.13% | NA |
| Japonica Intermediate | 241 | 20.70% | 0.00% | 3.73% | 75.52% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 0.00% | 86.46% | NA |
| Intermediate | 90 | 25.60% | 1.10% | 6.67% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809389 | C -> T | LOC_Os01g72070.1 | synonymous_variant ; p.Gln61Gln; LOW | synonymous_codon | Average:4.668; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0141809389 | C -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:4.668; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |