| Variant ID: vg0317761623 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761623 |
| Reference Allele: CTG | Alternative Allele: C,CTTG |
| Primary Allele: CTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCTCTAAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAA[CTG/C,CTTG]
TTGGAAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCAT
ATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTTCCAA[CAG/G,CAAG]
TTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTTAGAGAC
| Populations | Population Size | Frequency of CTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.80% | 3.00% | 4.51% | 57.81% | CTTG: 0.85% |
| All Indica | 2759 | 6.40% | 4.20% | 5.44% | 83.04% | CTTG: 0.98% |
| All Japonica | 1512 | 85.20% | 0.90% | 2.38% | 10.98% | CTTG: 0.53% |
| Aus | 269 | 3.00% | 3.70% | 8.18% | 83.64% | CTTG: 1.49% |
| Indica I | 595 | 5.40% | 2.20% | 4.20% | 87.90% | CTTG: 0.34% |
| Indica II | 465 | 7.50% | 4.70% | 2.80% | 83.66% | CTTG: 1.29% |
| Indica III | 913 | 5.60% | 5.70% | 7.56% | 80.07% | CTTG: 1.10% |
| Indica Intermediate | 786 | 7.40% | 3.60% | 5.47% | 82.44% | CTTG: 1.15% |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.70% | 1.80% | 3.37% | 30.16% | CTTG: 0.99% |
| Japonica Intermediate | 241 | 83.80% | 2.10% | 7.88% | 4.98% | CTTG: 1.24% |
| VI/Aromatic | 96 | 84.40% | 3.10% | 3.12% | 8.33% | CTTG: 1.04% |
| Intermediate | 90 | 50.00% | 1.10% | 2.22% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761623 | CTG -> C | LOC_Os03g31190.1 | frameshift_variant ; p.Thr148fs; HIGH | frameshift_variant | Average:34.958; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761623 | CTG -> CTTG | LOC_Os03g31190.1 | frameshift_variant ; p.Val149fs; HIGH | frameshift_variant | Average:34.958; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761623 | CTG -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.958; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |