| Variant ID: vg1120444882 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444882 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCTGATAATATAATGATGTTTCTAACAAATGTAATGCATAAAAAAAACATTCTTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTA[A/G]
GTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACATATATGGGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCT
AGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGGGGCCCAACCCCATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAAC[T/C]
TAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAAGAATGTTTTTTTTATGCATTACATTTGTTAGAAACATCATTATATTATCAGAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.20% | 1.20% | 3.30% | 15.28% | NA |
| All Indica | 2759 | 71.00% | 2.00% | 4.57% | 22.44% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.79% | 1.85% | NA |
| Aus | 269 | 72.90% | 0.00% | 5.58% | 21.56% | NA |
| Indica I | 595 | 52.90% | 0.00% | 4.03% | 43.03% | NA |
| Indica II | 465 | 80.00% | 0.60% | 4.73% | 14.62% | NA |
| Indica III | 913 | 70.80% | 5.10% | 6.24% | 17.85% | NA |
| Indica Intermediate | 786 | 79.50% | 0.80% | 2.93% | 16.79% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.52% | 0.52% | NA |
| Tropical Japonica | 504 | 94.00% | 0.00% | 1.19% | 4.76% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 3.12% | 10.42% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444882 | A -> DEL | N | N | silent_mutation | Average:34.996; most accessible tissue: Minghui63 flower, score: 62.076 | N | N | N | N |
| vg1120444882 | A -> G | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 242.0bp to feature; MODIFIER | silent_mutation | Average:34.996; most accessible tissue: Minghui63 flower, score: 62.076 | N | N | N | N |