| Variant ID: vg0409515202 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515202 |
| Reference Allele: T | Alternative Allele: TGTCACACCC,TGTCACACCCTTATTTTCG,TGTCACACCCTTATTTTTG |
| Primary Allele: T | Secondary Allele: TGTCACACCCTTATTTTCG |
Inferred Ancestral Allele: Not determined.
AACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACA[T/TGTCACACCC,TGTCACACCCTTATTTTCG,TGTCACACCCTTATTTTTG]
TATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTC
GAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATA[A/GGGTGTGACA,CGAAAATAAGGGTGTGACA,CAAAAATAAGGGTGTGACA]
TGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGTCACACCCTTATTTTCG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.20% | 0.30% | 0.36% | 8.87% | TGTCACACCC: 0.23%; TGTCACACCCTTATTTTTG: 0.02% |
| All Indica | 2759 | 99.10% | 0.40% | 0.14% | 0.00% | TGTCACACCC: 0.33%; TGTCACACCCTTATTTTTG: 0.04% |
| All Japonica | 1512 | 73.30% | 0.00% | 0.66% | 25.99% | NA |
| Aus | 269 | 98.10% | 0.40% | 0.74% | 0.00% | TGTCACACCC: 0.74% |
| Indica I | 595 | 99.50% | 0.30% | 0.00% | 0.00% | TGTCACACCC: 0.17% |
| Indica II | 465 | 98.90% | 0.00% | 0.43% | 0.00% | TGTCACACCC: 0.65% |
| Indica III | 913 | 98.60% | 0.80% | 0.22% | 0.00% | TGTCACACCC: 0.44% |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.00% | 0.00% | TGTCACACCCTTATTTTTG: 0.13%; TGTCACACCC: 0.13% |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 1.59% | 66.87% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515202 | T -> TGTCACACCC | LOC_Os04g17380.1 | stop_gained&inframe_insertion ; p.Asn135delinsArgValTerHis; HIGH | inframe_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515202 | T -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515202 | T -> TGTCACACCCTTATTTTTG | LOC_Os04g17380.1 | stop_gained&inframe_insertion ; p.Asn135delinsThrLysIleArgValT erHis; HIGH | inframe_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515202 | T -> TGTCACACCCTTATTTTCG | LOC_Os04g17380.1 | stop_gained&inframe_insertion ; p.Asn135delinsThrLysIleArgValT erHis; HIGH | inframe_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |