| Variant ID: vg0814383064 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14383064 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCGGGGATGCTGCCGACCACATCGTCAACGGCTTCGAGGGCTCGGCCCCTCGGCTCGCGTTCGCCCCCGACTCCGACGAGGAGGGGAACGCCAGCAGTG[G/C]
AAGCGACGGTGGCAACGAGGCCGGCGACCTGGGCGCGTCAGAATGAGCCCCCAGGCCCCCGCCAATCTCCAATTTTTTCTTTTTGTATAGATCAACTTAA
TTAAGTTGATCTATACAAAAAGAAAAAATTGGAGATTGGCGGGGGCCTGGGGGCTCATTCTGACGCGCCCAGGTCGCCGGCCTCGTTGCCACCGTCGCTT[C/G]
CACTGCTGGCGTTCCCCTCCTCGTCGGAGTCGGGGGCGAACGCGAGCCGAGGGGCCGAGCCCTCGAAGCCGTTGACGATGTGGTCGGCAGCATCCCCGAC
| 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 | 19.10% | 0.70% | 3.58% | 76.58% | NA |
| All Indica | 2759 | 0.80% | 0.10% | 0.83% | 98.30% | NA |
| All Japonica | 1512 | 56.80% | 1.90% | 8.86% | 32.47% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.50% | 0.20% | 0.00% | 99.33% | NA |
| Indica II | 465 | 0.60% | 0.00% | 3.23% | 96.13% | NA |
| Indica III | 913 | 0.70% | 0.20% | 0.11% | 99.01% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 0.89% | 97.96% | NA |
| Temperate Japonica | 767 | 84.70% | 0.50% | 7.56% | 7.17% | NA |
| Tropical Japonica | 504 | 24.20% | 4.00% | 13.29% | 58.53% | NA |
| Japonica Intermediate | 241 | 36.10% | 1.70% | 3.73% | 58.51% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 7.29% | 91.67% | NA |
| Intermediate | 90 | 24.40% | 3.30% | 5.56% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814383064 | G -> C | LOC_Os08g23760.1 | missense_variant ; p.Gly1030Ala; MODERATE | nonsynonymous_codon ; G1030A | Average:5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | unknown | unknown | TOLERATED | 1.00 |
| vg0814383064 | G -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |