| Variant ID: vg1120445037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445037 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACATAGTATATGTAATATACATGGA[T/C]
TATTATAAAATCAAACAAATTAAAACCAACACATATCTTGGCCAATTGTTCATCACAACATAATCATCACCATGATTTTACAGTTCCTACATGCTCAAGT
ACTTGAGCATGTAGGAACTGTAAAATCATGGTGATGATTATGTTGTGATGAACAATTGGCCAAGATATGTGTTGGTTTTAATTTGTTTGATTTTATAATA[A/G]
TCCATGTATATTACATATACTATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.90% | 18.60% | 0.42% | 23.13% | NA |
| All Indica | 2759 | 67.40% | 1.30% | 0.54% | 30.74% | NA |
| All Japonica | 1512 | 45.00% | 49.20% | 0.00% | 5.82% | NA |
| Aus | 269 | 50.20% | 1.10% | 1.12% | 47.58% | NA |
| Indica I | 595 | 49.70% | 1.00% | 1.34% | 47.90% | NA |
| Indica II | 465 | 77.00% | 0.40% | 0.22% | 22.37% | NA |
| Indica III | 913 | 67.80% | 1.20% | 0.33% | 30.67% | NA |
| Indica Intermediate | 786 | 74.70% | 2.20% | 0.38% | 22.77% | NA |
| Temperate Japonica | 767 | 36.50% | 59.20% | 0.00% | 4.30% | NA |
| Tropical Japonica | 504 | 45.20% | 44.80% | 0.00% | 9.92% | NA |
| Japonica Intermediate | 241 | 71.40% | 26.60% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 6.20% | 71.90% | 1.04% | 20.83% | NA |
| Intermediate | 90 | 60.00% | 28.90% | 1.11% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445037 | T -> DEL | N | N | silent_mutation | Average:40.801; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| vg1120445037 | T -> C | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 87.0bp to feature; MODIFIER | silent_mutation | Average:40.801; most accessible tissue: Callus, score: 74.376 | N | N | N | N |