| Variant ID: vg1120444886 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444886 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATAATATAATGATGTTTCTAACAAATGTAATGCATAAAAAAAACATTCTTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTAAGTT[C/A]
CTATGGCCTATGGGCTCCTATATCCATAGCATACATATATGGGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCTCAGG
CCTGAGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGGGGCCCAACCCCATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAG[G/T]
AACTTAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAAGAATGTTTTTTTTATGCATTACATTTGTTAGAAACATCATTATATTATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.20% | 3.80% | 5.95% | 13.01% | NA |
| All Indica | 2759 | 71.60% | 1.60% | 7.54% | 19.25% | NA |
| All Japonica | 1512 | 95.20% | 1.10% | 2.25% | 1.39% | NA |
| Aus | 269 | 26.80% | 43.90% | 11.15% | 18.22% | NA |
| Indica I | 595 | 52.80% | 0.00% | 5.38% | 41.85% | NA |
| Indica II | 465 | 80.00% | 0.20% | 8.82% | 10.97% | NA |
| Indica III | 913 | 74.40% | 2.70% | 8.65% | 14.24% | NA |
| Indica Intermediate | 786 | 77.70% | 2.30% | 7.12% | 12.85% | NA |
| Temperate Japonica | 767 | 94.90% | 2.20% | 2.09% | 0.78% | NA |
| Tropical Japonica | 504 | 94.00% | 0.00% | 2.98% | 2.98% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 5.21% | 10.42% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444886 | C -> A | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 238.0bp to feature; MODIFIER | silent_mutation | Average:35.141; most accessible tissue: Minghui63 flower, score: 62.529 | N | N | N | N |
| vg1120444886 | C -> DEL | N | N | silent_mutation | Average:35.141; most accessible tissue: Minghui63 flower, score: 62.529 | N | N | N | N |