| Variant ID: vg0331481996 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 31481996 |
| Reference Allele: CT | Alternative Allele: CTTT,C,CTT,CTTTT |
| Primary Allele: CT | Secondary Allele: CTTT |
Inferred Ancestral Allele: Not determined.
TCTTCATTTGTTATTTTTTGTGCACTAGTCCATTATTTATGCTACTCCTAAACATTTTGCTGCTAATTTCAGGGTTCATAAATTTTGATGTGCTGCAACA[CT/CTTT,C,CTT,CTTTT]
TTTTTTTTTTGGAACGATCACCGGAGGGGAGAGGTTCCCCACCTGAATTTCCATTAAATAAACAAGCAAGTCTGATACAAAGGGAGATGGATCAGCAGAG
CTCTGCTGATCCATCTCCCTTTGTATCAGACTTGCTTGTTTATTTAATGGAAATTCAGGTGGGGAACCTCTCCCCTCCGGTGATCGTTCCAAAAAAAAAA[AG/AAAG,G,AAG,AAAAG]
TGTTGCAGCACATCAAAATTTATGAACCCTGAAATTAGCAGCAAAATGTTTAGGAGTAGCATAAATAATGGACTAGTGCACAAAAAATAACAAATGAAGA
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of CTTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.90% | 38.60% | 5.14% | 0.47% | CTT: 7.43%; CTTTT: 0.38%; C: 0.04% |
| All Indica | 2759 | 22.10% | 56.40% | 8.23% | 0.72% | CTT: 12.03%; CTTTT: 0.51% |
| All Japonica | 1512 | 99.10% | 0.50% | 0.20% | 0.07% | CTT: 0.07% |
| Aus | 269 | 5.90% | 88.50% | 2.23% | 0.00% | CTT: 2.97%; CTTTT: 0.37% |
| Indica I | 595 | 11.60% | 76.10% | 11.26% | 0.17% | CTT: 0.84% |
| Indica II | 465 | 24.70% | 59.40% | 8.39% | 0.43% | CTT: 7.10% |
| Indica III | 913 | 33.20% | 36.50% | 5.04% | 1.20% | CTT: 23.11%; CTTTT: 0.99% |
| Indica Intermediate | 786 | 15.80% | 62.70% | 9.54% | 0.76% | CTT: 10.56%; CTTTT: 0.64% |
| Temperate Japonica | 767 | 99.10% | 0.50% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.00% | CTT: 0.41% |
| VI/Aromatic | 96 | 89.60% | 6.20% | 1.04% | 0.00% | C: 2.08%; CTT: 1.04% |
| Intermediate | 90 | 57.80% | 21.10% | 6.67% | 1.11% | CTT: 10.00%; CTTTT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0331481996 | CT -> C | LOC_Os03g55340.1 | 3_prime_UTR_variant ; 214.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> C | LOC_Os03g55330.1 | upstream_gene_variant ; 1935.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTTT | LOC_Os03g55340.1 | 3_prime_UTR_variant ; 215.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTTT | LOC_Os03g55330.1 | upstream_gene_variant ; 1936.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> DEL | N | N | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTTTT | LOC_Os03g55340.1 | 3_prime_UTR_variant ; 215.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTTTT | LOC_Os03g55330.1 | upstream_gene_variant ; 1936.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTT | LOC_Os03g55340.1 | 3_prime_UTR_variant ; 215.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |
| vg0331481996 | CT -> CTT | LOC_Os03g55330.1 | upstream_gene_variant ; 1936.0bp to feature; MODIFIER | silent_mutation | Average:51.061; most accessible tissue: Callus, score: 82.658 | N | N | N | N |