| Variant ID: vg0605310169 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5310169 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )
ATCATTGACTTTCTTCGCCGACAAATTCACCAGGATACAGTGGTACAAATATAGCTTGTAGGTTCATCTGAGTTGAATCAACATGCTTAGAAATTTGTTG[A/AT]
TTTTTTTTTGTTTTACCTGCAGTTTCTCTATGTGAACAGTGCATTTTCACCAAATCCAGATGAGTTGATAATCGACCTATACAATGTAAGCTTTGATGTC
GACATCAAAGCTTACATTGTATAGGTCGATTATCAACTCATCTGGATTTGGTGAAAATGCACTGTTCACATAGAGAAACTGCAGGTAAAACAAAAAAAAA[T/AT]
CAACAAATTTCTAAGCATGTTGATTCAACTCAGATGAACCTACAAGCTATATTTGTACCACTGTATCCTGGTGAATTTGTCGGCGAAGAAAGTCAATGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.60% | 13.10% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 79.90% | 20.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 98.00% | 1.10% | 0.93% | 0.00% | NA |
| Aus | 269 | 88.10% | 11.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 66.20% | 33.40% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 75.40% | 24.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.80% | 16.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.40% | 1.20% | 1.43% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 12.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605310169 | A -> AT | LOC_Os06g10320.1 | downstream_gene_variant ; 3439.0bp to feature; MODIFIER | silent_mutation | Average:45.826; most accessible tissue: Callus, score: 65.669 | N | N | N | N |
| vg0605310169 | A -> AT | LOC_Os06g10330.1 | downstream_gene_variant ; 2423.0bp to feature; MODIFIER | silent_mutation | Average:45.826; most accessible tissue: Callus, score: 65.669 | N | N | N | N |
| vg0605310169 | A -> AT | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.826; most accessible tissue: Callus, score: 65.669 | N | N | N | N |