| Variant ID: vg0625554229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25554229 |
| 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: 124. )
GTTCCGGCCAATTGGCTGTTGCCGGTTCGATACCCCTCTCAATCAAGCTAGCCTCCATCTGCTCCCACTTCGGCATCGCGACGCTATAGCCTCCTGACCC[C/T]
AAGTGGTGATGGTACTTCTTCTTGGCGGCATTTTCTTTGTTTCTTTCCATCATCGCCTGCCCTTGTTCACCTGTCTTATATGCAACGAACTCGTCCCAGT
ACTGGGACGAGTTCGTTGCATATAAGACAGGTGAACAAGGGCAGGCGATGATGGAAAGAAACAAAGAAAATGCCGCCAAGAAGAAGTACCATCACCACTT[G/A]
GGGTCAGGAGGCTATAGCGTCGCGATGCCGAAGTGGGAGCAGATGGAGGCTAGCTTGATTGAGAGGGGTATCGAACCGGCAACAGCCAATTGGCCGGAAC
| 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 | 0.70% | 0.30% | 14.24% | 84.74% | NA |
| All Indica | 2759 | 1.00% | 0.10% | 7.18% | 91.77% | NA |
| All Japonica | 1512 | 0.30% | 0.00% | 27.12% | 72.55% | NA |
| Aus | 269 | 0.40% | 0.00% | 19.33% | 80.30% | NA |
| Indica I | 595 | 0.30% | 0.00% | 2.52% | 97.14% | NA |
| Indica II | 465 | 0.60% | 0.00% | 6.45% | 92.90% | NA |
| Indica III | 913 | 1.40% | 0.10% | 8.87% | 89.59% | NA |
| Indica Intermediate | 786 | 1.10% | 0.10% | 9.16% | 89.57% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 43.55% | 55.93% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 2.18% | 97.82% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 26.97% | 72.61% | NA |
| VI/Aromatic | 96 | 0.00% | 13.50% | 4.17% | 82.29% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 10.00% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625554229 | C -> T | LOC_Os06g42500.1 | synonymous_variant ; p.Leu244Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625554229 | C -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |