| Variant ID: vg0209334614 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9334614 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )
GGTATACAGGCGGAAGACGTGACATAGTTCCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGC[A/C]
GGCAGGACTGAGCCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGATGT
ACATCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGGCTCAGTCCTGCC[T/G]
GCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGGAACTATGTCACGTCTTCCGCCTGTATACC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.20% | 0.20% | 6.54% | 50.08% | NA |
| All Indica | 2759 | 14.20% | 0.30% | 10.11% | 75.35% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.07% | 2.71% | NA |
| Aus | 269 | 13.80% | 0.00% | 8.92% | 77.32% | NA |
| Indica I | 595 | 25.50% | 0.00% | 2.52% | 71.93% | NA |
| Indica II | 465 | 17.20% | 1.30% | 19.57% | 61.94% | NA |
| Indica III | 913 | 4.40% | 0.00% | 8.65% | 86.97% | NA |
| Indica Intermediate | 786 | 15.30% | 0.40% | 11.96% | 72.39% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 0.00% | 3.97% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 2.08% | 9.38% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 3.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209334614 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209334614 | A -> C | LOC_Os02g16390.1 | upstream_gene_variant ; 1216.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209334614 | A -> C | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |