| Variant ID: vg0234180328 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34180328 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCTGCAGCAGGTAAGAAAAAATTACAGTGGAGCAGAATTTGGGGCGGTTCATCTTCTAGCCATGGTGGTGGTACCAGTTCATCAGCAGCAAGTGGGGAC[G/A]
CTAGATCGCATGGTCCTGCCGAAGAGTTGTCCAACTATTTGGATAGCGATGCCATCAGGCATGAAACGTCAGACTTCAACGTACTCGGGTGGTGGAATGA
TCATTCCACCACCCGAGTACGTTGAAGTCTGACGTTTCATGCCTGATGGCATCGCTATCCAAATAGTTGGACAACTCTTCGGCAGGACCATGCGATCTAG[C/T]
GTCCCCACTTGCTGCTGATGAACTGGTACCACCACCATGGCTAGAAGATGAACCGCCCCAAATTCTGCTCCACTGTAATTTTTTCTTACCTGCTGCAGGG
| 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 | 71.40% | 0.10% | 12.02% | 16.46% | NA |
| All Indica | 2759 | 69.30% | 0.00% | 11.05% | 19.57% | NA |
| All Japonica | 1512 | 79.50% | 0.00% | 12.83% | 7.67% | NA |
| Aus | 269 | 55.80% | 1.50% | 17.10% | 25.65% | NA |
| Indica I | 595 | 57.00% | 0.00% | 27.73% | 15.29% | NA |
| Indica II | 465 | 61.10% | 0.00% | 7.31% | 31.61% | NA |
| Indica III | 913 | 83.70% | 0.00% | 3.83% | 12.49% | NA |
| Indica Intermediate | 786 | 66.90% | 0.10% | 9.03% | 23.92% | NA |
| Temperate Japonica | 767 | 75.10% | 0.00% | 18.25% | 6.65% | NA |
| Tropical Japonica | 504 | 85.90% | 0.00% | 5.95% | 8.13% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 9.96% | 9.96% | NA |
| VI/Aromatic | 96 | 46.90% | 1.00% | 8.33% | 43.75% | NA |
| Intermediate | 90 | 70.00% | 1.10% | 16.67% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234180328 | G -> A | LOC_Os02g55830.1 | missense_variant ; p.Ala437Thr; MODERATE | nonsynonymous_codon ; A437T | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | TOLERATED | 0.10 |
| vg0234180328 | G -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |