| Variant ID: vg0614962529 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 14962529 |
| Reference Allele: CCACCCAAAAACACCG | Alternative Allele: C,CTGTGTGCGTCTCACCCAAAAACACCG |
| Primary Allele: CCACCCAAAAACACCG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTTGCTAGGCCCGACTGTAGAGTACGGAGGAAGGGTGGTGGTCGGTCCTAGGTGTGGAAGGCGCATCACCTGCTCGAAGCGCGCAGTGATATCCTCCTT[CCACCCAAAAACACCG/C,CTGTGTGCGTCTCACCCAAAAACACCG]
TCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAACGTGT
ACACGTTCCACCTTCCCTGTGGGGAGATGGCTCCGACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCGGGAGCACCAGTTGGTCCCGTCGA[CGGTGTTTTTGGGTGG/G,CGGTGTTTTTGGGTGAGACGCACACAG]
AAGGAGGATATCACTGCGCGCTTCGAGCAGGTGATGCGCCTTCCACACCTAGGACCGACCACCACCCTTCCTCCGTACTCTACAGTCGGGCCTAGCAAGG
| Populations | Population Size | Frequency of CCACCCAAAAACACCG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.70% | 0.10% | 3.55% | 60.66% | CTGTGTGCGTCTCACCCAAAAACACCG: 0.04% |
| All Indica | 2759 | 4.50% | 0.00% | 4.42% | 90.97% | CTGTGTGCGTCTCACCCAAAAACACCG: 0.07% |
| All Japonica | 1512 | 82.70% | 0.10% | 1.85% | 15.34% | NA |
| Aus | 269 | 73.60% | 0.00% | 2.60% | 23.79% | NA |
| Indica I | 595 | 4.90% | 0.00% | 1.34% | 93.78% | NA |
| Indica II | 465 | 2.20% | 0.00% | 1.51% | 96.34% | NA |
| Indica III | 913 | 2.30% | 0.00% | 8.00% | 89.70% | NA |
| Indica Intermediate | 786 | 8.10% | 0.10% | 4.33% | 87.15% | CTGTGTGCGTCTCACCCAAAAACACCG: 0.25% |
| Temperate Japonica | 767 | 96.50% | 0.10% | 0.52% | 2.87% | NA |
| Tropical Japonica | 504 | 59.10% | 0.20% | 3.97% | 36.71% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 1.66% | 10.37% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 6.25% | 17.71% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 5.56% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962529 | CCACCCAAAAACACCG -> CTGTGTGCGTCTCACCCAAAAACACCG | LOC_Os06g25580.1 | frameshift_variant&stop_gained ; p.Trp970fs; HIGH | frameshift_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962529 | CCACCCAAAAACACCG -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962529 | CCACCCAAAAACACCG -> C | LOC_Os06g25580.1 | N | inframe_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |