| Variant ID: vg1212722887 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722887 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 313. )
GGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCT[G/C]
TGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGGGCGGGTTGAGTAATGTTTTTCGTGATTAG
CTAATCACGAAAAACATTACTCAACCCGCCCATAACCGTGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACACAAGACA[C/G]
AGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCACCATAGTGCACC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.00% | 0.10% | 1.57% | 21.31% | NA |
| All Indica | 2759 | 63.80% | 0.00% | 2.21% | 33.96% | NA |
| All Japonica | 1512 | 96.00% | 0.20% | 0.73% | 3.11% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 63.20% | 0.00% | 4.20% | 32.61% | NA |
| Indica II | 465 | 66.90% | 0.00% | 1.51% | 31.61% | NA |
| Indica III | 913 | 59.70% | 0.10% | 0.88% | 39.32% | NA |
| Indica Intermediate | 786 | 67.20% | 0.00% | 2.67% | 30.15% | NA |
| Temperate Japonica | 767 | 94.10% | 0.00% | 0.65% | 5.22% | NA |
| Tropical Japonica | 504 | 97.60% | 0.20% | 0.99% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 2.22% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722887 | G -> C | LOC_Os12g22530.1 | downstream_gene_variant ; 4433.0bp to feature; MODIFIER | silent_mutation | Average:54.62; most accessible tissue: Minghui63 young leaf, score: 76.82 | N | N | N | N |
| vg1212722887 | G -> C | LOC_Os12g22540.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.62; most accessible tissue: Minghui63 young leaf, score: 76.82 | N | N | N | N |
| vg1212722887 | G -> DEL | N | N | silent_mutation | Average:54.62; most accessible tissue: Minghui63 young leaf, score: 76.82 | N | N | N | N |