| Variant ID: vg1120598158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20598158 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGACCCTTCAGATGAAAGAAAAACTATTGTCATATCCGGAAAGCAACAGATCGTCGGCATCGACAACATCGAAGACCCCAATGATTACAACCAGTTCGA[T/C]
GATGTACCATTGTTTACTGATCTTCCTATGCGAATTAAGAAGGTTGAGAGAACAATCGATGAAGCAAATATGTCGTACGTTCGAGCAGATGGTGTTGCCA
TGGCAACACCATCTGCTCGAACGTACGACATATTTGCTTCATCGATTGTTCTCTCAACCTTCTTAATTCGCATAGGAAGATCAGTAAACAATGGTACATC[A/G]
TCGAACTGGTTGTAATCATTGGGGTCTTCGATGTTGTCGATGCCGACGATCTGTTGCTTTCCGGATATGACAATAGTTTTTCTTTCATCTGAAGGGTCCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 0.10% | 5.61% | 59.50% | NA |
| All Indica | 2759 | 21.10% | 0.00% | 7.18% | 71.69% | NA |
| All Japonica | 1512 | 59.80% | 0.10% | 3.04% | 37.04% | NA |
| Aus | 269 | 10.40% | 0.40% | 4.83% | 84.39% | NA |
| Indica I | 595 | 52.40% | 0.00% | 2.18% | 45.38% | NA |
| Indica II | 465 | 7.30% | 0.00% | 6.67% | 86.02% | NA |
| Indica III | 913 | 12.20% | 0.00% | 10.62% | 77.22% | NA |
| Indica Intermediate | 786 | 16.00% | 0.00% | 7.25% | 76.72% | NA |
| Temperate Japonica | 767 | 73.80% | 0.30% | 2.22% | 23.73% | NA |
| Tropical Japonica | 504 | 49.40% | 0.00% | 2.98% | 47.62% | NA |
| Japonica Intermediate | 241 | 36.90% | 0.00% | 5.81% | 57.26% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 2.08% | 8.33% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 6.67% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120598158 | T -> DEL | LOC_Os11g35130.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1120598158 | T -> C | LOC_Os11g35130.1 | synonymous_variant ; p.Asp924Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |