| Variant ID: vg0114587575 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587575 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 250. )
TGTACGAAGTTGAGTACTCACATATGTCAACGTCATTTACCTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCA[C/T]
ATCATGGTCCACATTTGGAGGGAAAATGAAAATTGAGACAGTACCGAGTAGATATCTCCATATATTTGTACCTCTGAAGAGAACAATCCCTGATACAAAT
ATTTGTATCAGGGATTGTTCTCTTCAGAGGTACAAATATATGGAGATATCTACTCGGTACTGTCTCAATTTTCATTTTCCCTCCAAATGTGGACCATGAT[G/A]
TGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAGGTAAATGACGTTGACATATGTGAGTACTCAACTTCGTACA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.60% | 2.20% | 1.57% | 16.63% | NA |
| All Indica | 2759 | 65.70% | 3.60% | 2.61% | 28.13% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 52.90% | 0.00% | 1.34% | 45.71% | NA |
| Indica II | 465 | 57.60% | 14.60% | 2.15% | 25.59% | NA |
| Indica III | 913 | 75.80% | 0.20% | 2.96% | 21.03% | NA |
| Indica Intermediate | 786 | 68.40% | 3.60% | 3.44% | 24.55% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 2.20% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587575 | C -> T | LOC_Os01g25740.1 | missense_variant ; p.Val1360Met; MODERATE | nonsynonymous_codon ; V1360M | Average:64.553; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | unknown | unknown | TOLERATED | 0.08 |
| vg0114587575 | C -> DEL | LOC_Os01g25740.1 | N | frameshift_variant | Average:64.553; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |