| Variant ID: vg0318608644 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 18608644 |
| Reference Allele: CGAG | Alternative Allele: GGAG,C |
| Primary Allele: CGAG | Secondary Allele: GGAG |
Inferred Ancestral Allele: Not determined.
GCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGA[CGAG/GGAG,C]
GAGGAGGAGGCGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGCGGCGGCGAGAGAAGGGGGTTCTGGG
CCCAGAACCCCCTTCTCTCGCCGCCGCGCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGGCGCCTCCTCCTC[CTCG/CTCC,G]
TCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGC
| Populations | Population Size | Frequency of CGAG(primary allele) | Frequency of GGAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.30% | 0.40% | 0.38% | C: 0.04% |
| All Indica | 2759 | 99.90% | 0.00% | 0.00% | 0.00% | C: 0.07% |
| All Japonica | 1512 | 97.40% | 0.50% | 0.99% | 1.12% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 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 | 99.80% | 0.10% | 0.00% | 0.00% | C: 0.11% |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.00% | C: 0.13% |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.30% | 1.40% | 2.98% | 3.37% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 6.20% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608644 | CGAG -> C | LOC_Os03g32526.1 | disruptive_inframe_deletion ; p.Ser19del; MODERATE | inframe_variant | Average:31.487; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| vg0318608644 | CGAG -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:31.487; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| vg0318608644 | CGAG -> GGAG | LOC_Os03g32526.1 | synonymous_variant ; p.Ser19Ser; LOW | synonymous_codon | Average:31.487; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |