| Variant ID: vg1120444915 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444915 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATGCATAAAAAAAACATTCTTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATA[G/T]
CATACATATATGGGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACAT
ATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGGGGCCCAACCCCATATATGTATG[C/A]
TATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAAGAATGTTTTTTTTATGCATT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.30% | 3.40% | 4.25% | 15.04% | NA |
| All Indica | 2759 | 69.40% | 3.20% | 4.78% | 22.62% | NA |
| All Japonica | 1512 | 94.60% | 1.40% | 2.84% | 1.19% | NA |
| Aus | 269 | 53.90% | 19.00% | 6.69% | 20.45% | NA |
| Indica I | 595 | 52.40% | 0.70% | 3.87% | 43.03% | NA |
| Indica II | 465 | 78.90% | 1.90% | 4.09% | 15.05% | NA |
| Indica III | 913 | 68.70% | 6.00% | 7.01% | 18.29% | NA |
| Indica Intermediate | 786 | 77.50% | 2.50% | 3.31% | 16.67% | NA |
| Temperate Japonica | 767 | 96.50% | 0.40% | 2.61% | 0.52% | NA |
| Tropical Japonica | 504 | 89.50% | 3.60% | 4.17% | 2.78% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 1.00% | 6.25% | 7.29% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444915 | G -> T | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 209.0bp to feature; MODIFIER | silent_mutation | Average:36.251; most accessible tissue: Minghui63 flower, score: 62.973 | N | N | N | N |
| vg1120444915 | G -> DEL | N | N | silent_mutation | Average:36.251; most accessible tissue: Minghui63 flower, score: 62.973 | N | N | N | N |