| Variant ID: vg1007670429 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670429 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATATTAATGACTACACATATCAAGTCTTTGCAATAAAACAAAATACTTCATTCATTACAATAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTC[G/A]
GTATGATCTGAACGAGCATATGCCACAGGCTCTTGGGGATCATCGTCAAGGTCAATGTGAGGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGA
TCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACCTCACATTGACCTTGACGATGATCCCCAAGAGCCTGTGGCATATGCTCGTTCAGATCATAC[C/T]
GAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTATTGTAATGAATGAAGTATTTTGTTTTATTGCAAAGACTTGATATGTGTAGTCATTAATAT
| 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 | 80.80% | 0.60% | 1.33% | 17.29% | NA |
| All Indica | 2759 | 83.10% | 0.50% | 1.49% | 14.86% | NA |
| All Japonica | 1512 | 73.80% | 0.70% | 1.19% | 24.34% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.00% | 4.46% | NA |
| Indica I | 595 | 75.50% | 0.30% | 1.85% | 22.35% | NA |
| Indica II | 465 | 79.40% | 0.40% | 2.80% | 17.42% | NA |
| Indica III | 913 | 92.00% | 0.80% | 0.55% | 6.68% | NA |
| Indica Intermediate | 786 | 80.90% | 0.40% | 1.53% | 17.18% | NA |
| Temperate Japonica | 767 | 92.60% | 0.30% | 0.78% | 6.39% | NA |
| Tropical Japonica | 504 | 42.70% | 0.20% | 2.18% | 54.96% | NA |
| Japonica Intermediate | 241 | 79.30% | 2.90% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 2.08% | 14.58% | NA |
| Intermediate | 90 | 81.10% | 2.20% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670429 | G -> A | LOC_Os10g14130.1 | synonymous_variant ; p.Thr494Thr; LOW | synonymous_codon | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670429 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |