| Variant ID: vg0609018595 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018595 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAGAGAGGTGCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCC[G/C,A]
TTAGGGGCGAAATCCCCAAACTTTGTGCTCTGCCGGTCTGACCGAAGGTATGTGGCCGGTCAGACCATGCTACTCTGCAACGGCTAGAAAACTAGCCGTT
AACGGCTAGTTTTCTAGCCGTTGCAGAGTAGCATGGTCTGACCGGCCACATACCTTCGGTCAGACCGGCAGAGCACAAAGTTTGGGGATTTCGCCCCTAA[C/G,T]
GGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGCACCTCTCTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.50% | 0.70% | 11.43% | 25.33% | A: 0.02% |
| All Indica | 2759 | 65.80% | 1.20% | 3.48% | 29.47% | A: 0.04% |
| All Japonica | 1512 | 67.30% | 0.00% | 24.14% | 8.60% | NA |
| Aus | 269 | 6.30% | 0.00% | 15.24% | 78.44% | NA |
| Indica I | 595 | 58.80% | 0.50% | 2.52% | 38.15% | NA |
| Indica II | 465 | 88.20% | 0.00% | 5.38% | 6.45% | NA |
| Indica III | 913 | 53.90% | 3.00% | 2.52% | 40.53% | A: 0.11% |
| Indica Intermediate | 786 | 71.80% | 0.40% | 4.20% | 23.66% | NA |
| Temperate Japonica | 767 | 82.40% | 0.00% | 13.30% | 4.30% | NA |
| Tropical Japonica | 504 | 54.40% | 0.00% | 34.52% | 11.11% | NA |
| Japonica Intermediate | 241 | 46.10% | 0.00% | 36.93% | 17.01% | NA |
| VI/Aromatic | 96 | 41.70% | 0.00% | 27.08% | 31.25% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 13.33% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018595 | G -> C | LOC_Os06g15880.1 | missense_variant ; p.Val96Leu; MODERATE | nonsynonymous_codon ; V96L | Average:38.469; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 | unknown | unknown | TOLERATED | 0.88 |
| vg0609018595 | G -> A | LOC_Os06g15880.1 | missense_variant ; p.Val96Ile; MODERATE | nonsynonymous_codon ; V96I | Average:38.469; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 | unknown | unknown | TOLERATED | 0.24 |
| vg0609018595 | G -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:38.469; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 | N | N | N | N |