| Variant ID: vg0321793766 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 21793766 |
| Reference Allele: CT | Alternative Allele: C,CTT |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAGGCGCCGCACAGGAGACAGTGCCGCACAAGACTAGCGAGCTCATGTCGATCGCCACTTAATTTGTCATTATTAGTTAGTAGGTAGATTACCATGTGCT[CT/C,CTT]
TTTTTTTTGTCAGCTGTTAATCTAGATCTTGTACGCGCAATGGAATTACGGCGGGCTAGTTAGTCCATAATCGATGTGATGATTTTGTGCTACATGTAAT
ATTACATGTAGCACAAAATCATCACATCGATTATGGACTAACTAGCCCGCCGTAATTCCATTGCGCGTACAAGATCTAGATTAACAGCTGACAAAAAAAA[AG/G,AAG]
AGCACATGGTAATCTACCTACTAACTAATAATGACAAATTAAGTGGCGATCGACATGAGCTCGCTAGTCTTGTGCGGCACTGTCTCCTGTGCGGCGCCTC
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.40% | 2.50% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 92.30% | 7.30% | 0.46% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 0.90% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 67.20% | 32.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321793766 | CT -> C | LOC_Os03g39240.1 | 3_prime_UTR_variant ; 73.0bp to feature; MODIFIER | silent_mutation | Average:44.519; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0321793766 | CT -> C | LOC_Os03g39230.1 | upstream_gene_variant ; 2597.0bp to feature; MODIFIER | silent_mutation | Average:44.519; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0321793766 | CT -> CTT | LOC_Os03g39240.1 | 3_prime_UTR_variant ; 74.0bp to feature; MODIFIER | N | Average:44.519; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0321793766 | CT -> CTT | LOC_Os03g39230.1 | upstream_gene_variant ; 2598.0bp to feature; MODIFIER | N | Average:44.519; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |