| Variant ID: vg0118270500 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270500 |
| Reference Allele: GAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCA | Alternative Allele: G |
| Primary Allele: GAGTAGAATCATCTCTCAAA CACCAATGGAGGTTGCGGTG CGGGAGATTGCTACGTACTG GTTCGAGAACCAGCGAGCA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACTGGTTTGAGGACCAGCGAACGTGTAGAATTATCTCTCGGACACCAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGC[GAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCA/G]
AGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGC
GCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACT[TGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTC/C]
GCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTGGTGTCCGAGAGATAATTCTACACGTTCGCTGGTCCTCAAACCAGT
| Populations | Population Size | Frequency of GAGTAGAATCATCTCTCAAA CACCAATGGAGGTTGCGGTG CGGGAGATTGCTACGTACTG GTTCGAGAACCAGCGAGCA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.10% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.20% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270500 | GAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCA -> G | LOC_Os01g33180.1 | disruptive_inframe_deletion ; p.Gln24_Ser49del; MODERATE | N | Average:52.891; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |
| vg0118270500 | GAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCA -> G | LOC_Os01g33160.1 | downstream_gene_variant ; 3303.0bp to feature; MODIFIER | N | Average:52.891; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |
| vg0118270500 | GAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCA -> G | LOC_Os01g33190.1 | downstream_gene_variant ; 1982.0bp to feature; MODIFIER | N | Average:52.891; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |