| Variant ID: vg1012223964 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223964 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGT[G/A]
AGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGG
CCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCT[C/T]
ACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCC
| 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 | 49.90% | 0.20% | 0.63% | 49.34% | NA |
| All Indica | 2759 | 33.50% | 0.10% | 0.76% | 65.64% | NA |
| All Japonica | 1512 | 88.60% | 0.10% | 0.26% | 10.98% | NA |
| Aus | 269 | 10.40% | 0.70% | 1.86% | 86.99% | NA |
| Indica I | 595 | 14.80% | 0.20% | 0.67% | 84.37% | NA |
| Indica II | 465 | 42.20% | 0.00% | 1.08% | 56.77% | NA |
| Indica III | 913 | 37.00% | 0.20% | 0.44% | 62.32% | NA |
| Indica Intermediate | 786 | 38.40% | 0.00% | 1.02% | 60.56% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.26% | 3.91% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.20% | 17.86% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.41% | 19.09% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 61.10% | 1.10% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223964 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Glu20Lys; MODERATE | nonsynonymous_codon ; E20K | Average:12.598; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.49 |
| vg1012223964 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.598; most accessible tissue: Callus, score: 51.074 | N | N | N | N |