| Variant ID: vg0614962545 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 14962545 |
| Reference Allele: TCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAAC | Alternative Allele: T |
| Primary Allele: TCGACGGGACCAACTGGTGC TCCCGCCAGCGGTAGCCCGA GCAGGTACGACACGTCCTGC AGTGTCGGAGCCATCTCCCC ACAGGGAAGGTGGAAC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTAGAGTACGGAGGAAGGGTGGTGGTCGGTCCTAGGTGTGGAAGGCGCATCACCTGCTCGAAGCGCGCAGTGATATCCTCCTTCCACCCAAAAACACCG[TCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAAC/T]
GTGTGCGTCTCAGGTCTCCAGCGGTCTACAAGAGCGGCAAGGAGTGACCGGTCTGCATCCCACCGCTTCGCTGGGTCACGGTCGTCCGCCGCCGCCTCAA
TTGAGGCGGCGGCGGACGACCGTGACCCAGCGAAGCGGTGGGATGCAGACCGGTCACTCCTTGCCGCTCTTGTAGACCGCTGGAGACCTGAGACGCACAC[GTTCCACCTTCCCTGTGGGGAGATGGCTCCGACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCGGGAGCACCAGTTGGTCCCGTCGA/A]
CGGTGTTTTTGGGTGGAAGGAGGATATCACTGCGCGCTTCGAGCAGGTGATGCGCCTTCCACACCTAGGACCGACCACCACCCTTCCTCCGTACTCTACA
| Populations | Population Size | Frequency of TCGACGGGACCAACTGGTGC TCCCGCCAGCGGTAGCCCGA GCAGGTACGACACGTCCTGC AGTGTCGGAGCCATCTCCCC ACAGGGAAGGTGGAAC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.60% | 0.10% | 3.53% | 60.77% | NA |
| All Indica | 2759 | 4.40% | 0.00% | 4.42% | 91.16% | NA |
| All Japonica | 1512 | 82.60% | 0.20% | 1.85% | 15.34% | NA |
| Aus | 269 | 73.60% | 0.00% | 2.60% | 23.79% | NA |
| Indica I | 595 | 4.70% | 0.00% | 1.34% | 93.95% | NA |
| Indica II | 465 | 2.20% | 0.00% | 1.51% | 96.34% | NA |
| Indica III | 913 | 2.20% | 0.00% | 8.11% | 89.70% | NA |
| Indica Intermediate | 786 | 8.00% | 0.10% | 4.20% | 87.66% | NA |
| Temperate Japonica | 767 | 96.50% | 0.30% | 0.52% | 2.74% | NA |
| Tropical Japonica | 504 | 58.90% | 0.20% | 3.97% | 36.90% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 1.66% | 10.37% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 5.21% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962545 | TCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAAC -> T | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962545 | TCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAAC -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.869; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |