| Variant ID: vg0100994949 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 994949 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACAGCAAAACGGGCATACAAATTAAGTAAAAACAATCATCATAAATGTACTTGCTACTAAGTTACTGGTAGCTTTCGAACAGACATATGCTTTCGTCGTC[G/A]
TCGTCCTCATGCTCCTCGGAGATTGCAGTTAGATCAGATGGCATATTGTAAGACTCCACTCCAGGGAATTGCTCATCATCACAGAAGAATGGCCTTGGAG
CTCCAAGGCCATTCTTCTGTGATGATGAGCAATTCCCTGGAGTGGAGTCTTACAATATGCCATCTGATCTAACTGCAATCTCCGAGGAGCATGAGGACGA[C/T]
GACGACGAAAGCATATGTCTGTTCGAAAGCTACCAGTAACTTAGTAGCAAGTACATTTATGATGATTGTTTTTACTTAATTTGTATGCCCGTTTTGCTGT
| 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 | 86.80% | 4.40% | 1.69% | 7.11% | NA |
| All Indica | 2759 | 81.10% | 6.90% | 1.99% | 10.00% | NA |
| All Japonica | 1512 | 94.00% | 0.90% | 1.46% | 3.57% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.60% | 1.50% | 3.03% | 7.90% | NA |
| Indica II | 465 | 99.10% | 0.20% | 0.22% | 0.43% | NA |
| Indica III | 913 | 65.30% | 17.50% | 1.64% | 15.55% | NA |
| Indica Intermediate | 786 | 84.00% | 2.50% | 2.67% | 10.81% | NA |
| Temperate Japonica | 767 | 94.00% | 0.00% | 1.56% | 4.43% | NA |
| Tropical Japonica | 504 | 96.00% | 2.20% | 1.39% | 0.40% | NA |
| Japonica Intermediate | 241 | 90.00% | 1.20% | 1.24% | 7.47% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 1.11% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100994949 | G -> A | LOC_Os01g02830.1 | synonymous_variant ; p.Asp694Asp; LOW | synonymous_codon | Average:18.481; most accessible tissue: Callus, score: 41.617 | N | N | N | N |
| vg0100994949 | G -> DEL | LOC_Os01g02830.1 | N | frameshift_variant | Average:18.481; most accessible tissue: Callus, score: 41.617 | N | N | N | N |