| Variant ID: vg0329362963 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29362963 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACTCCCAGGCATCCCGGGCGCGCCGCTGGAGTGGCGCGATCCGGCGACGAAGATAGTCGCTGTACACCATGGCCCCTGTGAGCCCCAGGGATCACAGGCC[C/T]
GCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGGAGGCCTGCGCCGGGGGCTGGCTCGGAAGACGGAGGCGCG
CGCGCCTCCGTCTTCCGAGCCAGCCCCCGGCGCAGGCCTCCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGC[G/A]
GGCCTGTGATCCCTGGGGCTCACAGGGGCCATGGTGTACAGCGACTATCTTCGTCGCCGGATCGCGCCACTCCAGCGGCGCGCCCGGGATGCCTGGGAGT
| 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 | 56.70% | 0.10% | 2.56% | 40.61% | NA |
| All Indica | 2759 | 38.00% | 0.00% | 4.10% | 57.92% | NA |
| All Japonica | 1512 | 99.00% | 0.30% | 0.26% | 0.40% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 53.10% | 0.00% | 8.07% | 38.82% | NA |
| Indica II | 465 | 38.90% | 0.00% | 3.44% | 57.63% | NA |
| Indica III | 913 | 28.30% | 0.00% | 3.18% | 68.57% | NA |
| Indica Intermediate | 786 | 37.30% | 0.00% | 2.54% | 60.18% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 97.80% | 1.00% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 0.00% | 28.12% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 1.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329362963 | C -> T | LOC_Os03g51310.1 | downstream_gene_variant ; 3830.0bp to feature; MODIFIER | silent_mutation | Average:30.009; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| vg0329362963 | C -> T | LOC_Os03g51320.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.009; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| vg0329362963 | C -> DEL | N | N | silent_mutation | Average:30.009; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |