| Variant ID: vg0329362069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29362069 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCTTGCCGGTCAGTTTCACGGGTCGCCTCGGAGGATGTCGTCGCCTCGGCCTGGCGGAGTCCGGCCTCCTCCCGAGCGGCTTCCTCGGTCTGGCGAGCC[T/A]
GGGCGGCCTCCCGAGCGGCCTCCTCGGCTTCCCGAAGGCGATCCGCGGCTTCTCGCCGGTCAGATTCCCGCCTCCGGGCCTCTGTGGTCGCCGGGTCCTC
GAGGACCCGGCGACCACAGAGGCCCGGAGGCGGGAATCTGACCGGCGAGAAGCCGCGGATCGCCTTCGGGAAGCCGAGGAGGCCGCTCGGGAGGCCGCCC[A/T]
GGCTCGCCAGACCGAGGAAGCCGCTCGGGAGGAGGCCGGACTCCGCCAGGCCGAGGCGACGACATCCTCCGAGGCGACCCGTGAAACTGACCGGCAAGAG
| 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 | 56.10% | 0.20% | 0.78% | 42.91% | NA |
| All Indica | 2759 | 37.60% | 0.30% | 0.58% | 61.58% | NA |
| All Japonica | 1512 | 99.40% | 0.00% | 0.13% | 0.46% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.00% | 98.51% | NA |
| Indica I | 595 | 53.30% | 0.20% | 0.50% | 46.05% | NA |
| Indica II | 465 | 38.30% | 0.00% | 0.22% | 61.51% | NA |
| Indica III | 913 | 27.50% | 0.50% | 0.77% | 71.19% | NA |
| Indica Intermediate | 786 | 37.00% | 0.10% | 0.64% | 62.21% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 52.10% | 1.00% | 18.75% | 28.12% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329362069 | T -> A | LOC_Os03g51320.1 | missense_variant ; p.Gln432Leu; MODERATE | nonsynonymous_codon ; Q432L | Average:32.311; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0329362069 | T -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:32.311; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | N | N | N | N |