| Variant ID: vg1120445038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445038 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACATAGTATATGTAATATACATGGAT[T/C]
ATTATAAAATCAAACAAATTAAAACCAACACATATCTTGGCCAATTGTTCATCACAACATAATCATCACCATGATTTTACAGTTCCTACATGCTCAAGTC
GACTTGAGCATGTAGGAACTGTAAAATCATGGTGATGATTATGTTGTGATGAACAATTGGCCAAGATATGTGTTGGTTTTAATTTGTTTGATTTTATAAT[A/G]
ATCCATGTATATTACATATACTATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGG
| 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 | 73.40% | 4.10% | 1.06% | 21.48% | NA |
| All Indica | 2759 | 68.20% | 1.60% | 1.05% | 29.14% | NA |
| All Japonica | 1512 | 93.50% | 1.10% | 1.26% | 4.17% | NA |
| Aus | 269 | 6.70% | 47.60% | 0.74% | 44.98% | NA |
| Indica I | 595 | 51.90% | 0.00% | 1.01% | 47.06% | NA |
| Indica II | 465 | 78.10% | 0.20% | 0.43% | 21.29% | NA |
| Indica III | 913 | 67.90% | 2.80% | 1.86% | 27.38% | NA |
| Indica Intermediate | 786 | 74.90% | 2.30% | 0.51% | 22.26% | NA |
| Temperate Japonica | 767 | 94.00% | 2.20% | 2.48% | 1.30% | NA |
| Tropical Japonica | 504 | 90.30% | 0.00% | 0.00% | 9.72% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 88.90% | 3.30% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445038 | T -> DEL | N | N | silent_mutation | Average:40.801; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| vg1120445038 | T -> C | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 86.0bp to feature; MODIFIER | silent_mutation | Average:40.801; most accessible tissue: Callus, score: 74.376 | N | N | N | N |