| Variant ID: vg0620132098 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20132098 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCGGCGTGCAAGCACCTGTACCACGTGGAGTGCATCGACATGTGGCTGGCCTCGCACGCCACGTGCCCAATCTGCCGGACGGAGGTCGAGCCACCGCCGG[A/G]
GGACGACGACGGCCGACCTGCGCCGGCGGCAGATGAGTCGTCGCCGACGGAGGCGCTGCCACCGGTGTAGCTAGTTCTGTGCTAGCTAACTAGATCTCCA
TGGAGATCTAGTTAGCTAGCACAGAACTAGCTACACCGGTGGCAGCGCCTCCGTCGGCGACGACTCATCTGCCGCCGGCGCAGGTCGGCCGTCGTCGTCC[T/C]
CCGGCGGTGGCTCGACCTCCGTCCGGCAGATTGGGCACGTGGCGTGCGAGGCCAGCCACATGTCGATGCACTCCACGTGGTACAGGTGCTTGCACGCCGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.70% | 4.30% | 12.76% | 13.22% | NA |
| All Indica | 2759 | 75.30% | 0.10% | 12.40% | 12.21% | NA |
| All Japonica | 1512 | 54.20% | 10.80% | 16.73% | 18.19% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 65.70% | 0.00% | 24.71% | 9.58% | NA |
| Indica II | 465 | 63.90% | 0.20% | 14.19% | 21.72% | NA |
| Indica III | 913 | 87.30% | 0.10% | 3.18% | 9.42% | NA |
| Indica Intermediate | 786 | 75.30% | 0.10% | 12.72% | 11.83% | NA |
| Temperate Japonica | 767 | 50.10% | 3.90% | 25.68% | 20.34% | NA |
| Tropical Japonica | 504 | 67.70% | 12.90% | 7.14% | 12.30% | NA |
| Japonica Intermediate | 241 | 39.40% | 28.60% | 8.30% | 23.65% | NA |
| VI/Aromatic | 96 | 65.60% | 31.20% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 72.20% | 7.80% | 7.78% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620132098 | A -> G | LOC_Os06g34620.1 | missense_variant ; p.Glu152Gly; MODERATE | nonsynonymous_codon ; E152G | Average:66.117; most accessible tissue: Zhenshan97 panicle, score: 81.135 | unknown | unknown | TOLERATED | 0.31 |
| vg0620132098 | A -> DEL | LOC_Os06g34620.1 | N | frameshift_variant | Average:66.117; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |