| Variant ID: vg1105974521 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5974521 |
| Reference Allele: T | Alternative Allele: TAGCTAGCACGG |
| Primary Allele: T | Secondary Allele: TAGCTAGCACGG |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 99. )
GGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCAC[T/TAGCTAGCACGG]
AGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTCAGGAAGTAATATC
GATATTACTTCCTGAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCT[A/CCGTGCTAGCTA]
GTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TAGCTAGCACGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.60% | 47.50% | 2.05% | 0.76% | NA |
| All Indica | 2759 | 32.70% | 63.70% | 2.61% | 1.01% | NA |
| All Japonica | 1512 | 82.90% | 15.90% | 0.73% | 0.46% | NA |
| Aus | 269 | 17.50% | 78.40% | 4.09% | 0.00% | NA |
| Indica I | 595 | 37.10% | 59.80% | 1.85% | 1.18% | NA |
| Indica II | 465 | 24.70% | 67.70% | 5.59% | 1.94% | NA |
| Indica III | 913 | 30.90% | 67.80% | 1.20% | 0.11% | NA |
| Indica Intermediate | 786 | 36.00% | 59.50% | 3.05% | 1.40% | NA |
| Temperate Japonica | 767 | 72.40% | 25.70% | 1.04% | 0.91% | NA |
| Tropical Japonica | 504 | 96.20% | 3.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.40% | 10.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 9.40% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 31.10% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974521 | T -> TAGCTAGCACGG | LOC_Os11g10840.1 | frameshift_variant&stop_gained ; p.Val58fs; HIGH | frameshift_variant | Average:46.673; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974521 | T -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:46.673; most accessible tissue: Callus, score: 75.127 | N | N | N | N |