| Variant ID: vg0602220450 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 2220450 |
| Reference Allele: TAAG | Alternative Allele: T |
| Primary Allele: TAAG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGCGTGGGCGCGTGTCGAAGAGGGGCGACGCTCGGTGGAGGCCATGGTGGAGGTGGGCCGTAAGGCTCACCGCCGGCATGTCTCGGAGCTTGAAACTCG[TAAG/T]
AAGGTGCTGGCGGAGATCGCCAAGGAAGTGGAGGAGGAGCGGGGGGCTGCCCTCATTGCCACCACCGTGATGAACGAGGCGCAGGACACCCTCCGCCTTC
GAAGGCGGAGGGTGTCCTGCGCCTCGTTCATCACGGTGGTGGCAATGAGGGCAGCCCCCCGCTCCTCCTCCACTTCCTTGGCGATCTCCGCCAGCACCTT[CTTA/A]
CGAGTTTCAAGCTCCGAGACATGCCGGCGGTGAGCCTTACGGCCCACCTCCACCATGGCCTCCACCGAGCGTCGCCCCTCTTCGACACGCGCCCACGCGG
| Populations | Population Size | Frequency of TAAG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.80% | 3.30% | 1.23% | 52.69% | NA |
| All Indica | 2759 | 19.30% | 2.20% | 1.05% | 77.49% | NA |
| All Japonica | 1512 | 92.80% | 5.80% | 0.40% | 1.06% | NA |
| Aus | 269 | 5.20% | 0.00% | 7.81% | 86.99% | NA |
| Indica I | 595 | 5.20% | 0.00% | 1.85% | 92.94% | NA |
| Indica II | 465 | 42.20% | 4.90% | 0.65% | 52.26% | NA |
| Indica III | 913 | 14.50% | 0.30% | 0.66% | 84.56% | NA |
| Indica Intermediate | 786 | 22.00% | 4.30% | 1.15% | 72.52% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 81.50% | 15.90% | 1.19% | 1.39% | NA |
| Japonica Intermediate | 241 | 95.00% | 2.90% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 0.00% | 73.96% | NA |
| Intermediate | 90 | 55.60% | 7.80% | 2.22% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602220450 | TAAG -> T | LOC_Os06g05030.1 | inframe_deletion ; p.Lys663del; MODERATE | inframe_variant | Average:15.819; most accessible tissue: Minghui63 root, score: 45.031 | N | N | N | N |
| vg0602220450 | TAAG -> DEL | LOC_Os06g05030.1 | N | frameshift_variant | Average:15.819; most accessible tissue: Minghui63 root, score: 45.031 | N | N | N | N |