| Variant ID: vg0625222832 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25222832 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 96. )
TGGAAATAAAAAATTCAGTAGTTGTCCTATATTATGCAAGATAAATGACATAATTGTTGGAAGTAATACAAATTGGACGTACCGCCACGAAGTAGTCTCG[G/A]
TCACGGTGCGTGGGATACGCGTCCGTGACAGCGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGCACGAGTGCGAGGAAGGTACCAGC
GCTGGTACCTTCCTCGCACTCGTGCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCGCTGTCACGGACGCGTATCCCACGCACCGTGA[C/T]
CGAGACTACTTCGTGGCGGTACGTCCAATTTGTATTACTTCCAACAATTATGTCATTTATCTTGCATAATATAGGACAACTACTGAATTTTTTATTTCCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.00% | 0.50% | 3.64% | 79.86% | NA |
| All Indica | 2759 | 0.90% | 0.20% | 3.30% | 95.61% | NA |
| All Japonica | 1512 | 46.60% | 0.10% | 0.60% | 52.71% | NA |
| Aus | 269 | 2.60% | 0.00% | 20.07% | 77.32% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.34% | 98.49% | NA |
| Indica II | 465 | 1.10% | 0.00% | 3.44% | 95.48% | NA |
| Indica III | 913 | 0.50% | 0.30% | 4.60% | 94.52% | NA |
| Indica Intermediate | 786 | 1.80% | 0.30% | 3.18% | 94.78% | NA |
| Temperate Japonica | 767 | 72.60% | 0.00% | 0.65% | 26.73% | NA |
| Tropical Japonica | 504 | 8.90% | 0.00% | 0.60% | 90.48% | NA |
| Japonica Intermediate | 241 | 42.70% | 0.40% | 0.41% | 56.43% | NA |
| VI/Aromatic | 96 | 12.50% | 15.60% | 12.50% | 59.38% | NA |
| Intermediate | 90 | 10.00% | 1.10% | 6.67% | 82.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222832 | G -> A | LOC_Os06g42010.1 | synonymous_variant ; p.Asp772Asp; LOW | synonymous_codon | Average:4.781; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625222832 | G -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.781; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |