| Variant ID: vg0139403610 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39403610 |
| 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, others allele: 0.00, population size: 117. )
CGATCGTCGCCTGTGGAACGCGGCAGTGGAGTTCACCGAGCAGCTGGCGCAACCAAGTGCACTCCGCCACCGCGTTCGCCACACCTCTGTACTCGGCTTC[C/T]
GCACTTGACCTCGAGACGGTCGTCTGCCGCTTGGACGACCAGGAGATGAGGGAGTCGCCGAGGAAGATGCAAAAGCCGGACGTGGAACGCCGGGTGTCGG
CCGACACCCGGCGTTCCACGTCCGGCTTTTGCATCTTCCTCGGCGACTCCCTCATCTCCTGGTCGTCCAAGCGGCAGACGACCGTCTCGAGGTCAAGTGC[G/A]
GAAGCCGAGTACAGAGGTGTGGCGAACGCGGTGGCGGAGTGCACTTGGTTGCGCCAGCTGCTCGGTGAACTCCACTGCCGCGTTCCACAGGCGACGATCG
| 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 | 9.50% | 0.10% | 14.77% | 75.62% | NA |
| All Indica | 2759 | 0.50% | 0.00% | 1.41% | 98.08% | NA |
| All Japonica | 1512 | 28.10% | 0.30% | 41.93% | 29.63% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.80% | 0.00% | 1.01% | 98.15% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.65% | 98.92% | NA |
| Indica III | 913 | 0.20% | 0.00% | 0.33% | 99.45% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 3.44% | 95.93% | NA |
| Temperate Japonica | 767 | 19.40% | 0.00% | 57.11% | 23.47% | NA |
| Tropical Japonica | 504 | 40.90% | 0.00% | 19.05% | 40.08% | NA |
| Japonica Intermediate | 241 | 29.00% | 2.10% | 41.49% | 27.39% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 26.67% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139403610 | C -> T | LOC_Os01g67800.1 | synonymous_variant ; p.Ala1292Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0139403610 | C -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |