| Variant ID: vg0139512419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512419 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCCTTCACCCGTAGGGCGAGCTCCATCTGCTGCTGATCCTGATAGTCCTGCCTCCGCCGCACTTGGTTTCTCCTTGTCTTTAGGACAATGCTTGTAGGT[G/A]
TGCCCATGTTCATTGTATTTGCTGCAACGCTTCACCCTGCCAGCCTCCGACTCGTCCATATTGTTGCGGATGCGACGAGTCCTCCTCCTTCCAGCCTTGC
GCAAGGCTGGAAGGAGGAGGACTCGTCGCATCCGCAACAATATGGACGAGTCGGAGGCTGGCAGGGTGAAGCGTTGCAGCAAATACAATGAACATGGGCA[C/T]
ACCTACAAGCATTGTCCTAAAGACAAGGAGAAACCAAGTGCGGCGGAGGCAGGACTATCAGGATCAGCAGCAGATGGAGCTCGCCCTACGGGTGAAGGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.10% | 0.90% | 6.20% | 63.88% | NA |
| All Indica | 2759 | 5.60% | 1.50% | 8.52% | 84.38% | NA |
| All Japonica | 1512 | 74.90% | 0.00% | 1.65% | 23.41% | NA |
| Aus | 269 | 6.30% | 0.00% | 10.41% | 83.27% | NA |
| Indica I | 595 | 5.00% | 1.80% | 7.39% | 85.71% | NA |
| Indica II | 465 | 3.20% | 0.40% | 4.95% | 91.40% | NA |
| Indica III | 913 | 4.70% | 2.70% | 10.30% | 82.26% | NA |
| Indica Intermediate | 786 | 8.50% | 0.40% | 9.41% | 81.68% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.13% | 2.48% | NA |
| Tropical Japonica | 504 | 52.80% | 0.00% | 3.77% | 43.45% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 2.07% | 48.13% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 2.08% | 70.83% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 3.33% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512419 | G -> A | LOC_Os01g67990.1 | synonymous_variant ; p.His825His; LOW | synonymous_codon | Average:6.789; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0139512419 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:6.789; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |