| Variant ID: vg0815411661 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 15411661 |
| Reference Allele: CTAGAGATCAACTGGT | Alternative Allele: C |
| Primary Allele: CTAGAGATCAACTGGT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTCCGGAACTGAGCTGCCTTCCTCTTACGGTTTATTTTGTTACAGTGCTCCTCCTGACGGATAGCCTTATCCACCAGCTTCTCAAAGTCCTCATAATCT[CTAGAGATCAACTGGT/C]
TAGTCAATTCATCATCAAGACCAGACAGAAACTTCTCCTGCTTCTCGGCATCGGTACGCACGTCCTCAGGGGCGTAGCGCGCGAGGAGGTTGAACTCATG
CATGAGTTCAACCTCCTCGCGCGCTACGCCCCTGAGGACGTGCGTACCGATGCCGAGAAGCAGGAGAAGTTTCTGTCTGGTCTTGATGATGAATTGACTA[ACCAGTTGATCTCTAG/G]
AGATTATGAGGACTTTGAGAAGCTGGTGGATAAGGCTATCCGTCAGGAGGAGCACTGTAACAAAATAAACCGTAAGAGGAAGGCAGCTCAGTTCCGGACT
| Populations | Population Size | Frequency of CTAGAGATCAACTGGT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.40% | 0.10% | 10.79% | 69.66% | NA |
| All Indica | 2759 | 0.70% | 0.20% | 13.81% | 85.36% | NA |
| All Japonica | 1512 | 58.00% | 0.00% | 2.84% | 39.15% | NA |
| Aus | 269 | 0.40% | 0.00% | 28.62% | 71.00% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.67% | 99.33% | NA |
| Indica II | 465 | 1.10% | 0.00% | 9.25% | 89.68% | NA |
| Indica III | 913 | 0.30% | 0.50% | 22.89% | 76.23% | NA |
| Indica Intermediate | 786 | 1.30% | 0.00% | 15.90% | 82.82% | NA |
| Temperate Japonica | 767 | 83.60% | 0.00% | 1.04% | 15.38% | NA |
| Tropical Japonica | 504 | 26.80% | 0.00% | 4.17% | 69.05% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.00% | 5.81% | 52.28% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 10.00% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815411661 | CTAGAGATCAACTGGT -> C | LOC_Os08g25330.1 | disruptive_inframe_deletion ; p.Asn237_Ser241del; MODERATE | inframe_variant | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815411661 | CTAGAGATCAACTGGT -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |