| Variant ID: vg0322194006 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194006 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGCTGTGGACGATGTAGTCGGCGGCGTCCCGGACCCGCGCGCGCGCGCCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTC[A/G]
GGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCC
GGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCC[T/C]
GACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGGCGCGCGCGCGCGGGTCCGGGACGCCGCCGACTACATCGTCCACAGCT
| 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 | 39.90% | 0.10% | 1.61% | 58.38% | NA |
| All Indica | 2759 | 43.70% | 0.20% | 1.49% | 54.55% | NA |
| All Japonica | 1512 | 32.70% | 0.00% | 0.93% | 66.40% | NA |
| Aus | 269 | 46.80% | 0.00% | 7.43% | 45.72% | NA |
| Indica I | 595 | 22.20% | 0.00% | 1.01% | 76.81% | NA |
| Indica II | 465 | 28.60% | 0.90% | 2.37% | 68.17% | NA |
| Indica III | 913 | 70.60% | 0.20% | 1.20% | 27.93% | NA |
| Indica Intermediate | 786 | 37.80% | 0.00% | 1.65% | 60.56% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.91% | 83.57% | NA |
| Tropical Japonica | 504 | 58.30% | 0.00% | 1.19% | 40.48% | NA |
| Japonica Intermediate | 241 | 33.60% | 0.00% | 0.41% | 65.98% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 1.04% | 71.88% | NA |
| Intermediate | 90 | 35.60% | 0.00% | 0.00% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194006 | A -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0322194006 | A -> G | LOC_Os03g39930.1 | synonymous_variant ; p.Pro372Pro; LOW | synonymous_codon | Average:7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |