| Variant ID: vg0721995140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21995140 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACACCTTGAGCTTCAAAACCATACCTTTGTGGAGGTTTACCTGCATTGCTTCTTACCCCCATTCTTATAACAATAGGAAGATTAGTTTCTTCTCCCCCT[G/A]
TTTCAAACTCCTCTCCTTCCGTATCCGATGAAATCTGTATAGTATCACACTGATCAGATGGTTTATCACCTACTTCAGCAACAATTGAAGATTGTTGCTG
CAGCAACAATCTTCAATTGTTGCTGAAGTAGGTGATAAACCATCTGATCAGTGTGATACTATACAGATTTCATCGGATACGGAAGGAGAGGAGTTTGAAA[C/T]
AGGGGGAGAAGAAACTAATCTTCCTATTGTTATAAGAATGGGGGTAAGAAGCAATGCAGGTAAACCTCCACAAAGGTATGGTTTTGAAGCTCAAGGTGTG
| 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 | 76.20% | 0.20% | 14.39% | 9.14% | NA |
| All Indica | 2759 | 76.90% | 0.00% | 13.23% | 9.86% | NA |
| All Japonica | 1512 | 82.20% | 0.00% | 7.54% | 10.25% | NA |
| Aus | 269 | 46.10% | 0.00% | 53.16% | 0.74% | NA |
| Indica I | 595 | 32.80% | 0.00% | 38.49% | 28.74% | NA |
| Indica II | 465 | 89.20% | 0.00% | 5.59% | 5.16% | NA |
| Indica III | 913 | 98.10% | 0.00% | 1.42% | 0.44% | NA |
| Indica Intermediate | 786 | 78.40% | 0.00% | 12.34% | 9.29% | NA |
| Temperate Japonica | 767 | 95.20% | 0.00% | 1.04% | 3.78% | NA |
| Tropical Japonica | 504 | 68.70% | 0.00% | 15.48% | 15.87% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 11.62% | 19.09% | NA |
| VI/Aromatic | 96 | 45.80% | 11.50% | 42.71% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 18.89% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721995140 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:5.426; most accessible tissue: Callus, score: 15.021 | N | N | N | N |
| vg0721995140 | G -> A | LOC_Os07g36710.1 | missense_variant ; p.Thr228Ile; MODERATE | nonsynonymous_codon ; T228I | Average:5.426; most accessible tissue: Callus, score: 15.021 | unknown | unknown | TOLERATED | 0.32 |