| Variant ID: vg0317761986 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 17761986 |
| Reference Allele: CTCCGGA | Alternative Allele: C |
| Primary Allele: CTCCGGA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAG[CTCCGGA/C]
TCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCCGCCAGCAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGC
GCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTGCTGGCGGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGA[TCCGGAG/G]
CTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCT
| Populations | Population Size | Frequency of CTCCGGA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.60% | 0.60% | 6.18% | 42.59% | NA |
| All Indica | 2759 | 33.60% | 1.00% | 8.95% | 56.47% | NA |
| All Japonica | 1512 | 85.30% | 0.00% | 0.60% | 14.09% | NA |
| Aus | 269 | 11.90% | 0.00% | 11.15% | 76.95% | NA |
| Indica I | 595 | 8.40% | 1.00% | 10.92% | 79.66% | NA |
| Indica II | 465 | 29.00% | 0.00% | 6.02% | 64.95% | NA |
| Indica III | 913 | 52.90% | 2.00% | 9.53% | 35.60% | NA |
| Indica Intermediate | 786 | 32.80% | 0.50% | 8.52% | 58.14% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 63.50% | 0.00% | 1.59% | 34.92% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.00% | 0.41% | 14.94% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 3.33% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761986 | CTCCGGA -> C | LOC_Os03g31190.1 | inframe_deletion ; p.Ser26_Gly27del; MODERATE | inframe_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317761986 | CTCCGGA -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |