| Variant ID: vg0800072380 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 72380 |
| Reference Allele: AAG | Alternative Allele: A,AAGAG,AAGAGAG |
| Primary Allele: AAG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCGCTGCCACCTCCACGGCCTGCTCCACCACCTGAGCCTCTGTAAGCACAGATCATAGGAAGAAGATGACGATGAGAATCGCAGATTCGTAGGCAGACA[AAG/A,AAGAG,AAGAGAG]
AGAGAGAGAAATGAGCAGCAACCTAGGCTGATGCGGATCTTGTCGTCGAGGCTGCAGTTGTGCATGTCGATGAGGACCACGGAGACGCTCTTGCCGCAAG
CTTGCGGCAAGAGCGTCTCCGTGGTCCTCATCGACATGCACAACTGCAGCCTCGACGACAAGATCCGCATCAGCCTAGGTTGCTGCTCATTTCTCTCTCT[CTT/T,CTCTT,CTCTCTT]
TGTCTGCCTACGAATCTGCGATTCTCATCGTCATCTTCTTCCTATGATCTGTGCTTACAGAGGCTCAGGTGGTGGAGCAGGCCGTGGAGGTGGCAGCGAG
| Populations | Population Size | Frequency of AAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.40% | 23.60% | 11.28% | 5.18% | AAGAG: 3.26%; AAGAGAG: 0.30% |
| All Indica | 2759 | 34.40% | 39.60% | 17.33% | 8.41% | AAGAG: 0.25%; AAGAGAG: 0.04% |
| All Japonica | 1512 | 98.60% | 0.60% | 0.66% | 0.07% | AAGAG: 0.07% |
| Aus | 269 | 27.90% | 0.40% | 12.64% | 2.97% | AAGAG: 51.30%; AAGAGAG: 4.83% |
| Indica I | 595 | 24.00% | 53.90% | 17.98% | 3.87% | AAGAG: 0.17% |
| Indica II | 465 | 43.00% | 22.20% | 24.95% | 9.89% | NA |
| Indica III | 913 | 33.80% | 41.30% | 12.27% | 12.49% | AAGAG: 0.11% |
| Indica Intermediate | 786 | 37.70% | 37.20% | 18.19% | 6.23% | AAGAG: 0.64%; AAGAGAG: 0.13% |
| Temperate Japonica | 767 | 99.00% | 0.10% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 1.20% | 0.40% | 0.00% | AAGAG: 0.20% |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 2.10% | 0.00% | 0.00% | AAGAG: 2.08% |
| Intermediate | 90 | 66.70% | 10.00% | 12.22% | 4.44% | AAGAG: 6.67% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800072380 | AAG -> AAGAGAG | LOC_Os08g01090.1 | upstream_gene_variant ; 4744.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> AAGAGAG | LOC_Os08g01090.2 | upstream_gene_variant ; 4544.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> AAGAGAG | LOC_Os08g01100.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> A | LOC_Os08g01090.1 | upstream_gene_variant ; 4742.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> A | LOC_Os08g01090.2 | upstream_gene_variant ; 4542.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> A | LOC_Os08g01100.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> AAGAG | LOC_Os08g01090.1 | upstream_gene_variant ; 4744.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> AAGAG | LOC_Os08g01090.2 | upstream_gene_variant ; 4544.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> AAGAG | LOC_Os08g01100.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800072380 | AAG -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |