| Variant ID: vg1212722891 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 12722891 |
| Reference Allele: CTT | Alternative Allele: C |
| Primary Allele: CTT | Secondary Allele: C |
Inferred Ancestral Allele : CTT (evidence from allele frequency in Oryza rufipogon: CTT: 0.99, C: 0.02, others allele: 0.00, population size: 268. )
CACTATGGTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGT[CTT/C]
GTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGGGCGGGTTGAGTAATGTTTTTCGTGATTAGTCTCAC
GTGAGACTAATCACGAAAAACATTACTCAACCCGCCCATAACCGTGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACAC[AAG/G]
ACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCACCATAGTG
| Populations | Population Size | Frequency of CTT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.50% | 24.40% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 61.10% | 38.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 61.70% | 38.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 64.70% | 35.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 55.50% | 44.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 65.10% | 34.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 13.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722891 | CTT -> C | LOC_Os12g22530.1 | downstream_gene_variant ; 4438.0bp to feature; MODIFIER | silent_mutation | Average:54.62; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |
| vg1212722891 | CTT -> C | LOC_Os12g22540.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.62; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |