| Variant ID: vg0131445777 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31445777 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTCGTCGGCAATCATGTTATCCCGTCTGGGCACATGCCGAAGCTCAATCCCGTCAAAATGGCGCTCCATACGCCGTACTTGGTGCACGTAGGCGTCCAT[C/T]
TGCGGGTCAGAGCACCGGTACTCCTTACAGACTTGGTTAACGACCAGCTGGGAGTCGCCTAACACCAGGAGGCGGTGGATCCCCAGTCCAGCTGCCACTC
GAGTGGCAGCTGGACTGGGGATCCACCGCCTCCTGGTGTTAGGCGACTCCCAGCTGGTCGTTAACCAAGTCTGTAAGGAGTACCGGTGCTCTGACCCGCA[G/A]
ATGGACGCCTACGTGCACCAAGTACGGCGTATGGAGCGCCATTTTGACGGGATTGAGCTTCGGCATGTGCCCAGACGGGATAACATGATTGCCGACGAAC
| 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 | 31.50% | 0.10% | 2.31% | 66.02% | NA |
| All Indica | 2759 | 3.10% | 0.00% | 3.04% | 93.87% | NA |
| All Japonica | 1512 | 82.30% | 0.50% | 1.26% | 15.94% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.86% | 96.28% | NA |
| Indica I | 595 | 3.90% | 0.00% | 0.84% | 95.29% | NA |
| Indica II | 465 | 1.30% | 0.00% | 1.94% | 96.77% | NA |
| Indica III | 913 | 1.50% | 0.00% | 5.15% | 93.32% | NA |
| Indica Intermediate | 786 | 5.30% | 0.00% | 2.93% | 91.73% | NA |
| Temperate Japonica | 767 | 86.20% | 0.70% | 1.43% | 11.73% | NA |
| Tropical Japonica | 504 | 90.90% | 0.00% | 0.79% | 8.33% | NA |
| Japonica Intermediate | 241 | 52.30% | 0.80% | 1.66% | 45.23% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 1.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131445777 | C -> T | LOC_Os01g54660.1 | splice_acceptor_variant&intron_variant ; HIGH | splice_acceptor_variant | Average:16.09; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| vg0131445777 | C -> DEL | LOC_Os01g54660.1 | N | splice_acceptor_variant | Average:16.09; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |