| Variant ID: vg1105974435 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5974435 |
| Reference Allele: TCG | Alternative Allele: T |
| Primary Allele: TCG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGC[TCG/T]
CGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGACAG
CTGTCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCG[CGA/A]
GCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCC
| Populations | Population Size | Frequency of TCG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.60% | 6.50% | 6.56% | 45.30% | NA |
| All Indica | 2759 | 32.60% | 1.20% | 6.09% | 60.09% | NA |
| All Japonica | 1512 | 61.90% | 14.50% | 8.07% | 15.54% | NA |
| Aus | 269 | 17.10% | 0.40% | 4.09% | 78.44% | NA |
| Indica I | 595 | 32.90% | 1.80% | 12.10% | 53.11% | NA |
| Indica II | 465 | 27.10% | 0.40% | 6.45% | 66.02% | NA |
| Indica III | 913 | 32.50% | 1.00% | 1.10% | 65.39% | NA |
| Indica Intermediate | 786 | 35.60% | 1.50% | 7.12% | 55.73% | NA |
| Temperate Japonica | 767 | 57.10% | 5.90% | 12.26% | 24.77% | NA |
| Tropical Japonica | 504 | 64.30% | 29.80% | 2.38% | 3.57% | NA |
| Japonica Intermediate | 241 | 72.20% | 10.00% | 6.64% | 11.20% | NA |
| VI/Aromatic | 96 | 37.50% | 46.90% | 5.21% | 10.42% | NA |
| Intermediate | 90 | 56.70% | 8.90% | 4.44% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974435 | TCG -> T | LOC_Os11g10840.1 | frameshift_variant ; p.Gly42fs; HIGH | frameshift_variant | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974435 | TCG -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |