| Variant ID: vg0302880671 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 2880671 |
| Reference Allele: CT | Alternative Allele: C,CTT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele: Not determined.
ACTACCGCTAATTACTAGGCTTAATTTTGCAAGTAATGTCGTGTCGAGTTTTTTTTAACAGCGACCAAAAGCTCGATGATATTTTCTCTTTTCATTTTCC[CT/C,CTT]
TTTTTTTTTGTCATTCTTGTTAAGAATTCGTTGCCAACTCAATCTGGCTGGCAAATAAAAGTGTATTAAATTTCCCCTTTTTATATAGAGAGACAGGTAC
GTACCTGTCTCTCTATATAAAAAGGGGAAATTTAATACACTTTTATTTGCCAGCCAGATTGAGTTGGCAACGAATTCTTAACAAGAATGACAAAAAAAAA[AG/G,AAG]
GGAAAATGAAAAGAGAAAATATCATCGAGCTTTTGGTCGCTGTTAAAAAAAACTCGACACGACATTACTTGCAAAATTAAGCCTAGTAATTAGCGGTAGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.40% | 36.20% | 2.86% | 0.23% | CTT: 0.34% |
| All Indica | 2759 | 95.20% | 4.20% | 0.54% | 0.00% | CTT: 0.04% |
| All Japonica | 1512 | 1.10% | 90.10% | 7.34% | 0.66% | CTT: 0.73% |
| Aus | 269 | 48.70% | 50.20% | 0.74% | 0.00% | CTT: 0.37% |
| Indica I | 595 | 96.60% | 2.50% | 0.84% | 0.00% | NA |
| Indica II | 465 | 92.50% | 6.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 91.00% | 8.10% | 0.76% | 0.00% | CTT: 0.13% |
| Temperate Japonica | 767 | 0.40% | 86.60% | 10.82% | 1.17% | CTT: 1.04% |
| Tropical Japonica | 504 | 2.20% | 94.00% | 3.17% | 0.00% | CTT: 0.60% |
| Japonica Intermediate | 241 | 1.20% | 93.40% | 4.98% | 0.41% | NA |
| VI/Aromatic | 96 | 39.60% | 55.20% | 1.04% | 1.04% | CTT: 3.12% |
| Intermediate | 90 | 46.70% | 46.70% | 6.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880671 | CT -> C | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 265.0bp to feature; MODIFIER | silent_mutation | Average:47.66; most accessible tissue: Callus, score: 70.114 | N | N | N | N |
| vg0302880671 | CT -> C | LOC_Os03g05780.1 | downstream_gene_variant ; 2333.0bp to feature; MODIFIER | silent_mutation | Average:47.66; most accessible tissue: Callus, score: 70.114 | N | N | N | N |
| vg0302880671 | CT -> CTT | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 266.0bp to feature; MODIFIER | silent_mutation | Average:47.66; most accessible tissue: Callus, score: 70.114 | N | N | N | N |
| vg0302880671 | CT -> CTT | LOC_Os03g05780.1 | downstream_gene_variant ; 2332.0bp to feature; MODIFIER | silent_mutation | Average:47.66; most accessible tissue: Callus, score: 70.114 | N | N | N | N |
| vg0302880671 | CT -> DEL | N | N | silent_mutation | Average:47.66; most accessible tissue: Callus, score: 70.114 | N | N | N | N |