| Variant ID: vg0206044177 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6044177 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGATATGGATGAGTCAGAAGCAGGTGGGAGGACTTTACGCTGCAGCAAGTGTGATCTGCGCGGCCATACTTACAAGAAATGCCCGAAGAATGCAGAAGT[T/A]
CCAAGCGGCGCAGATGCTAGTCTATCTGGACAGGCAAGTGATGGTAGGCGACCACATGGTGAAGGAACAACAAGCAGGCGCGCAAGGCCAAGGCGTCGTC
GACGACGCCTTGGCCTTGCGCGCCTGCTTGTTGTTCCTTCACCATGTGGTCGCCTACCATCACTTGCCTGTCCAGATAGACTAGCATCTGCGCCGCTTGG[A/T]
ACTTCTGCATTCTTCGGGCATTTCTTGTAAGTATGGCCGCGCAGATCACACTTGCTGCAGCGTAAAGTCCTCCCACCTGCTTCTGACTCATCCATATCAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.90% | 0.70% | 4.08% | 63.31% | NA |
| All Indica | 2759 | 1.00% | 0.00% | 4.24% | 94.78% | NA |
| All Japonica | 1512 | 93.00% | 2.20% | 2.18% | 2.58% | NA |
| Aus | 269 | 0.40% | 0.00% | 8.55% | 91.08% | NA |
| Indica I | 595 | 0.50% | 0.00% | 0.50% | 98.99% | NA |
| Indica II | 465 | 1.10% | 0.00% | 6.88% | 92.04% | NA |
| Indica III | 913 | 0.80% | 0.00% | 5.81% | 93.43% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 3.69% | 94.78% | NA |
| Temperate Japonica | 767 | 90.50% | 4.40% | 2.74% | 2.35% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 1.59% | 2.38% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 1.66% | 3.73% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 14.58% | 47.92% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 6.67% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206044177 | T -> A | LOC_Os02g11730.1 | synonymous_variant ; p.Val857Val; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0206044177 | T -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |