| Variant ID: vg1105183835 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183835 |
| Reference Allele: CTT | Alternative Allele: C,TTT |
| Primary Allele: CTT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGGCTTCTAAGAACAATATGCCTGAGACGTTCTATTCAGCCAGAGATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGA[CTT/C,TTT]
TTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATA
TATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAA[AAG/G,AAA]
TCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAATCTCTGGCTGAATAGAACGTCTCAGGCATATTGTTCTTAGAAGCCA
| Populations | Population Size | Frequency of CTT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.50% | 1.10% | 1.02% | 30.41% | TTT: 0.04% |
| All Indica | 2759 | 49.40% | 1.80% | 1.52% | 47.34% | NA |
| All Japonica | 1512 | 98.60% | 0.00% | 0.13% | 1.12% | TTT: 0.13% |
| Aus | 269 | 69.10% | 0.00% | 0.74% | 30.11% | NA |
| Indica I | 595 | 30.10% | 0.20% | 1.51% | 68.24% | NA |
| Indica II | 465 | 21.10% | 0.00% | 3.01% | 75.91% | NA |
| Indica III | 913 | 68.80% | 4.20% | 1.42% | 25.63% | NA |
| Indica Intermediate | 786 | 58.10% | 1.30% | 0.76% | 39.82% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.26% | 1.96% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.00% | TTT: 0.40% |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 1.10% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183835 | CTT -> TTT | LOC_Os11g09710.1 | synonymous_variant ; p.Asp303Asp; LOW | synonymous_codon | Average:15.412; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183835 | CTT -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:15.412; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183835 | CTT -> C | LOC_Os11g09710.1 | frameshift_variant ; p.Phe305fs; HIGH | frameshift_variant | Average:15.412; most accessible tissue: Callus, score: 53.099 | N | N | N | N |