| Variant ID: vg0318604245 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 18604245 |
| Reference Allele: G | Alternative Allele: GTGATATGACA |
| Primary Allele: G | Secondary Allele: GTGATATGACA |
Inferred Ancestral Allele: Not determined.
TGGAATCCATCAACTGTATTTACGTCTATCACTTCCTTAGACTGATCACCGAAGGTCGACCGAAAATGGTCCTTCAAGAGCTTCACCTGATGCCTGTATG[G/GTGATATGACA]
TGATATGACAGCTACCTGGGAACTAGATTTGAGTTCTGGATAGCGCATAGCCATTTGATGATATAAGAGGGTTATGAATTCCACTTCATCCTCATTCACC
GGTGAATGAGGATGAAGTGGAATTCATAACCCTCTTATATCATCAAATGGCTATGCGCTATCCAGAACTCAAATCTAGTTCCCAGGTAGCTGTCATATCA[C/TGTCATATCAC]
CATACAGGCATCAGGTGAAGCTCTTGAAGGACCATTTTCGGTCGACCTTCGGTGATCAGTCTAAGGAAGTGATAGACGTAAATACAGTTGATGGATTCCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTGATATGACA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.90% | 0.60% | 0.87% | 2.69% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 89.90% | 0.50% | 1.39% | 8.27% | NA |
| Aus | 269 | 97.80% | 1.50% | 0.74% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 73.60% | 1.00% | 3.57% | 21.83% | NA |
| Japonica Intermediate | 241 | 91.70% | 0.80% | 1.24% | 6.22% | NA |
| VI/Aromatic | 96 | 71.90% | 13.50% | 14.58% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318604245 | G -> GTGATATGACA | LOC_Os03g32526.1 | N | frameshift_variant | Average:4.82; most accessible tissue: Callus, score: 8.348 | N | N | N | N |
| vg0318604245 | G -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:4.82; most accessible tissue: Callus, score: 8.348 | N | N | N | N |