| Variant ID: vg0202540146 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 2540146 |
| Reference Allele: A | Alternative Allele: ATTT |
| Primary Allele: A | Secondary Allele: ATTT |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 313. )
CTCAAGATACGCGGCGTACCAAAAGACGTCAGATCATATGATGTCAAACAAGTACGCGGTAAGAGTAATTGGTAGATTGGTTTTTTAAATTAATCTACTA[A/ATTT]
TTTCGTAGATACATCCGGCATGTATCTACAAAGGTACGCAATATTTTATATGCAATTTATCATACCTATTCAGATCATACAGAATTGTCAGATCTATAAT
ATTATAGATCTGACAATTCTGTATGATCTGAATAGGTATGATAAATTGCATATAAAATATTGCGTACCTTTGTAGATACATGCCGGATGTATCTACGAAA[T/AAAT]
TAGTAGATTAATTTAAAAAACCAATCTACCAATTACTCTTACCGCGTACTTGTTTGACATCATATGATCTGACGTCTTTTGGTACGCCGCGTATCTTGAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ATTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540146 | A -> ATTT | LOC_Os02g05270.1 | upstream_gene_variant ; 3972.0bp to feature; MODIFIER | silent_mutation | Average:40.531; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540146 | A -> ATTT | LOC_Os02g05280.1 | downstream_gene_variant ; 1477.0bp to feature; MODIFIER | silent_mutation | Average:40.531; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540146 | A -> ATTT | LOC_Os02g05300.1 | downstream_gene_variant ; 1943.0bp to feature; MODIFIER | silent_mutation | Average:40.531; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540146 | A -> ATTT | LOC_Os02g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.531; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |