| Variant ID: vg0801634986 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 1634986 |
| Reference Allele: AACGGCGGCGACG | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: AACGGCGGCGACG |
Inferred Ancestral Allele: Not determined.
GGGCACCCGCGCGTTCATGCGGCGGCGCGACCTCGAGTCGTCGGCGTTCGTCCGCGACGACCGCCTCATCGTCGAGTGCGTCATCGACGTCGTCGTCGCC[AACGGCGGCGACG/A]
ACGACACGGCGGCCGCGGCGTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGC
GCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGACGCCGCGGCCGCCGTGTCGT[CGTCGCCGCCGTT/T]
GGCGACGACGACGTCGATGACGCACTCGACGATGAGGCGGTCGTCGCGGACGAACGCCGACGACTCGAGGTCGCGCCGCCGCATGAACGCGCGGGTGCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AACGGCGGCGACG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.30% | 42.80% | 0.15% | 0.78% | NA |
| All Indica | 2759 | 91.50% | 7.10% | 0.11% | 1.34% | NA |
| All Japonica | 1512 | 2.40% | 97.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 19.00% | 81.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.60% | 1.70% | 0.17% | 2.52% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.10% | 13.00% | 0.11% | 0.77% | NA |
| Indica Intermediate | 786 | 90.70% | 7.30% | 0.13% | 1.91% | NA |
| Temperate Japonica | 767 | 3.00% | 96.70% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 46.70% | 51.10% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634986 | AACGGCGGCGACG -> A | LOC_Os08g03490.1 | disruptive_inframe_deletion ; p.Gly163_Asp166del; MODERATE | inframe_variant | Average:75.91; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |
| vg0801634986 | AACGGCGGCGACG -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:75.91; most accessible tissue: Zhenshan97 root, score: 81.974 | N | N | N | N |