| Variant ID: vg1120444968 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444968 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACATATATGGGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGCGATGGCA[C/T]
AGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACATAGTATATGTAATATACATGGATTATTATAAAATCAAACAAATTAAAACCAACA
TGTTGGTTTTAATTTGTTTGATTTTATAATAATCCATGTATATTACATATACTATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCT[G/A]
TGCCATCGCACTAGGCCCTCGAAGTCAAGGGGCCCAACCCCATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGC
| 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 | 77.90% | 0.40% | 1.14% | 20.55% | NA |
| All Indica | 2759 | 69.90% | 0.70% | 1.45% | 27.94% | NA |
| All Japonica | 1512 | 95.20% | 0.00% | 0.40% | 4.37% | NA |
| Aus | 269 | 55.00% | 0.00% | 2.97% | 42.01% | NA |
| Indica I | 595 | 52.80% | 0.00% | 1.34% | 45.88% | NA |
| Indica II | 465 | 79.60% | 0.00% | 1.29% | 19.14% | NA |
| Indica III | 913 | 69.00% | 2.10% | 1.53% | 27.38% | NA |
| Indica Intermediate | 786 | 78.20% | 0.00% | 1.53% | 20.23% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 0.26% | 3.00% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.79% | 8.13% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444968 | C -> T | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 156.0bp to feature; MODIFIER | silent_mutation | Average:38.509; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| vg1120444968 | C -> DEL | N | N | silent_mutation | Average:38.509; most accessible tissue: Callus, score: 74.376 | N | N | N | N |