| Variant ID: vg1222420003 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22420003 |
| Reference Allele: A | Alternative Allele: ATG |
| Primary Allele: A | Secondary Allele: ATG |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 72. )
TTTGCTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAA[A/ATG]
TATGTTTCTGTATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCC
GGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATACAGAAACATA[T/CAT]
TTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAGCAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ATG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.90% | 12.10% | 0.70% | 43.27% | NA |
| All Indica | 2759 | 18.70% | 20.30% | 0.72% | 60.28% | NA |
| All Japonica | 1512 | 86.40% | 0.30% | 0.46% | 12.83% | NA |
| Aus | 269 | 35.30% | 0.70% | 1.49% | 62.45% | NA |
| Indica I | 595 | 26.70% | 14.50% | 0.67% | 58.15% | NA |
| Indica II | 465 | 7.70% | 13.50% | 1.08% | 77.63% | NA |
| Indica III | 913 | 15.90% | 28.90% | 0.55% | 54.65% | NA |
| Indica Intermediate | 786 | 22.50% | 18.60% | 0.76% | 58.14% | NA |
| Temperate Japonica | 767 | 91.10% | 0.00% | 0.39% | 8.47% | NA |
| Tropical Japonica | 504 | 77.60% | 1.00% | 0.40% | 21.03% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 0.83% | 9.54% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 71.10% | 8.90% | 2.22% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420003 | A -> ATG | LOC_Os12g36600.1 | downstream_gene_variant ; 4388.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420003 | A -> ATG | LOC_Os12g36610.1 | downstream_gene_variant ; 739.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420003 | A -> ATG | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420003 | A -> DEL | N | N | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |