| Variant ID: vg1212666286 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666286 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
AATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAG[C/T]
CACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGT
ACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTG[G/A]
CTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.30% | 0.40% | 2.14% | 17.16% | NA |
| All Indica | 2759 | 83.40% | 0.10% | 1.59% | 14.90% | NA |
| All Japonica | 1512 | 72.30% | 0.50% | 3.24% | 23.94% | NA |
| Aus | 269 | 94.80% | 0.00% | 1.12% | 4.09% | NA |
| Indica I | 595 | 70.60% | 0.00% | 2.69% | 26.72% | NA |
| Indica II | 465 | 83.00% | 0.20% | 1.72% | 15.05% | NA |
| Indica III | 913 | 91.60% | 0.20% | 0.44% | 7.78% | NA |
| Indica Intermediate | 786 | 83.80% | 0.00% | 2.04% | 14.12% | NA |
| Temperate Japonica | 767 | 84.00% | 0.00% | 0.65% | 15.38% | NA |
| Tropical Japonica | 504 | 61.90% | 1.40% | 6.15% | 30.56% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.40% | 5.39% | 37.34% | NA |
| VI/Aromatic | 96 | 80.20% | 7.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666286 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666286 | C -> T | LOC_Os12g22430.1 | missense_variant ; p.Pro251Ser; MODERATE | nonsynonymous_codon ; P251S | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.80 |