| Variant ID: vg0329362884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29362884 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCATTACCTTGAAGTCTTCGGGGACCCAGTCCCATTTGACCCCCCGGTGGGTCCTCATACAGTCCTCGGACCCGGTGTACTCCCAGGCATCCCGGGCGC[G/A]
CCGCTGGAGTGGCGCGATCCGGCGACGAAGATAGTCGCTGTACACCATGGCCCCTGTGAGCCCCAGGGATCACAGGCCCGCCAGGCGGTCGAGGACGGCG
CGCCGTCCTCGACCGCCTGGCGGGCCTGTGATCCCTGGGGCTCACAGGGGCCATGGTGTACAGCGACTATCTTCGTCGCCGGATCGCGCCACTCCAGCGG[C/T]
GCGCCCGGGATGCCTGGGAGTACACCGGGTCCGAGGACTGTATGAGGACCCACCGGGGGGTCAAATGGGACTGGGTCCCCGAAGACTTCAAGGTAATGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.40% | 3.20% | 2.14% | 42.28% | NA |
| All Indica | 2759 | 30.60% | 5.40% | 3.41% | 60.64% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.07% | 0.40% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.74% | 98.51% | NA |
| Indica I | 595 | 48.60% | 2.50% | 2.35% | 46.55% | NA |
| Indica II | 465 | 34.00% | 0.40% | 6.67% | 58.92% | NA |
| Indica III | 913 | 19.50% | 8.20% | 2.08% | 70.21% | NA |
| Indica Intermediate | 786 | 27.90% | 7.10% | 3.82% | 61.20% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 0.00% | 29.17% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329362884 | G -> A | LOC_Os03g51320.1 | missense_variant ; p.Arg192Cys; MODERATE | nonsynonymous_codon ; R192C | Average:28.374; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0329362884 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:28.374; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |