| Variant ID: vg0118270621 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270621 |
| Reference Allele: GAGATTGCTACGTACTGGTTCAAGAACC | Alternative Allele: G |
| Primary Allele: GAGATTGCTACGTACTGGTT CAAGAACC | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
ACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGG[GAGATTGCTACGTACTGGTTCAAGAACC/G]
AGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGTGGTGTAGGAGATTGCTACGTACTGGTTCGA
TCGAACCAGTACGTAGCAATCTCCTACACCACAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCT[GGTTCTTGAACCAGTACGTAGCAATCTC/C]
CCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGT
| Populations | Population Size | Frequency of GAGATTGCTACGTACTGGTT CAAGAACC(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.80% | 0.00% | 2.75% | 33.45% | NA |
| All Indica | 2759 | 46.20% | 0.00% | 4.49% | 49.29% | NA |
| All Japonica | 1512 | 98.00% | 0.00% | 0.00% | 1.98% | NA |
| Aus | 269 | 36.10% | 0.00% | 2.23% | 61.71% | NA |
| Indica I | 595 | 13.10% | 0.00% | 5.38% | 81.51% | NA |
| Indica II | 465 | 66.90% | 0.00% | 5.38% | 27.74% | NA |
| Indica III | 913 | 54.50% | 0.00% | 2.41% | 43.04% | NA |
| Indica Intermediate | 786 | 49.40% | 0.00% | 5.73% | 44.91% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 0.00% | 4.96% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 0.00% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270621 | GAGATTGCTACGTACTGGTTCAAGAACC -> G | LOC_Os01g33180.1 | inframe_deletion ; p.Lys66_Phe74del; MODERATE | N | Average:51.804; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0118270621 | GAGATTGCTACGTACTGGTTCAAGAACC -> G | LOC_Os01g33160.1 | downstream_gene_variant ; 3424.0bp to feature; MODIFIER | N | Average:51.804; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0118270621 | GAGATTGCTACGTACTGGTTCAAGAACC -> G | LOC_Os01g33190.1 | downstream_gene_variant ; 1861.0bp to feature; MODIFIER | N | Average:51.804; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |