| Variant ID: vg0503844889 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844889 |
| Reference Allele: T | Alternative Allele: TTTGAG |
| Primary Allele: T | Secondary Allele: TTTGAG |
Inferred Ancestral Allele: Not determined.
GTAGAAAAGCAGATTTTTTTTCACAACCATTTACATTAAATCTAAAGAAAGATCCCCGCAAAATTAAATCTAAAAGAAAGATGTACAGAGGGGACATCTC[T/TTTGAG]
GGATTAGAATCCATTCCGTGGAATTAGGTATAAAATGTGAAAAGTTCTAGTTCGTGGTTTTGGATTCAAAGAGTTGAAATTAAAACTGCAATCCTCAACA
TGTTGAGGATTGCAGTTTTAATTTCAACTCTTTGAATCCAAAACCACGAACTAGAACTTTTCACATTTTATACCTAATTCCACGGAATGGATTCTAATCC[A/CTCAAA]
GAGATGTCCCCTCTGTACATCTTTCTTTTAGATTTAATTTTGCGGGGATCTTTCTTTAGATTTAATGTAAATGGTTGTGAAAAAAAATCTGCTTTTCTAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTTGAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.20% | 8.80% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 10.80% | 89.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 17.70% | 82.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844889 | T -> TTTGAG | LOC_Os05g07260.1 | downstream_gene_variant ; 1721.0bp to feature; MODIFIER | silent_mutation | Average:34.033; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0503844889 | T -> TTTGAG | LOC_Os05g07260.2 | downstream_gene_variant ; 1732.0bp to feature; MODIFIER | silent_mutation | Average:34.033; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0503844889 | T -> TTTGAG | LOC_Os05g07260.4 | downstream_gene_variant ; 1732.0bp to feature; MODIFIER | silent_mutation | Average:34.033; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0503844889 | T -> TTTGAG | LOC_Os05g07260.3 | downstream_gene_variant ; 1721.0bp to feature; MODIFIER | silent_mutation | Average:34.033; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0503844889 | T -> TTTGAG | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.033; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |