| Variant ID: vg1212666287 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666287 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
ATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGC[C/A]
ACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTA
TACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGT[G/T]
GCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.30% | 1.40% | 2.98% | 17.31% | NA |
| All Indica | 2759 | 80.60% | 1.80% | 2.07% | 15.44% | NA |
| All Japonica | 1512 | 70.70% | 0.90% | 4.96% | 23.41% | NA |
| Aus | 269 | 93.70% | 0.70% | 1.49% | 4.09% | NA |
| Indica I | 595 | 70.10% | 0.00% | 2.35% | 27.56% | NA |
| Indica II | 465 | 79.40% | 2.80% | 1.94% | 15.91% | NA |
| Indica III | 913 | 87.60% | 2.70% | 1.86% | 7.78% | NA |
| Indica Intermediate | 786 | 81.30% | 1.70% | 2.16% | 14.89% | NA |
| Temperate Japonica | 767 | 84.00% | 0.00% | 0.91% | 15.12% | NA |
| Tropical Japonica | 504 | 57.10% | 2.60% | 10.52% | 29.76% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.40% | 6.22% | 36.51% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 3.33% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666287 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666287 | C -> A | LOC_Os12g22430.1 | missense_variant ; p.Pro251Gln; MODERATE | nonsynonymous_codon ; P251Q | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.01 |