| Variant ID: vg1101255641 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255641 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 104. )
TTCGTGATCGGAACATTACTCCGGTCAAAGTGAAGAAATGGTCAGACATTAGTAACACAGAGCAGGAACACATATTTGCCTCGATTACGGTACGCATCTA[T/C]
CTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAAGTTTGAAAATGAAGATCCA
TGGATCTTCATTTTCAAACTTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAG[A/G]
TAGATGCGTACCGTAATCGAGGCAAATATGTGTTCCTGCTCTGTGTTACTAATGTCTGACCATTTCTTCACTTTGACCGGAGTAATGTTCCGATCACGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.50% | 5.80% | 16.48% | 41.13% | NA |
| All Indica | 2759 | 6.00% | 4.10% | 26.75% | 63.18% | NA |
| All Japonica | 1512 | 97.30% | 0.10% | 0.20% | 2.45% | NA |
| Aus | 269 | 7.10% | 58.00% | 6.32% | 28.62% | NA |
| Indica I | 595 | 4.50% | 4.40% | 8.57% | 82.52% | NA |
| Indica II | 465 | 5.80% | 0.60% | 12.90% | 80.65% | NA |
| Indica III | 913 | 3.40% | 4.30% | 48.08% | 44.25% | NA |
| Indica Intermediate | 786 | 10.20% | 5.70% | 23.92% | 60.18% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 97.20% | 0.20% | 0.20% | 2.38% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 28.10% | 4.20% | 17.71% | 50.00% | NA |
| Intermediate | 90 | 50.00% | 2.20% | 4.44% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255641 | T -> DEL | N | N | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255641 | T -> C | LOC_Os11g03330.1 | downstream_gene_variant ; 1661.0bp to feature; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255641 | T -> C | LOC_Os11g03340.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |