| Variant ID: vg0625553363 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25553363 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )
TGATGTACCGCCTGCGCCATAGAATAATGGCATGGCATGTGTCTCGTAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAGCTCGAGGTCCTCGTACGC[G/A]
CCTTCGACCAACTCAACTTCGACCTTCGAGTATCCTGCTGGAATCGGCCTGCAGTGGTAAGTACCTGAAGGGTCCGTTGGGATGGCCATGCCCGACGCCA
TGGCGTCGGGCATGGCCATCCCAACGGACCCTTCAGGTACTTACCACTGCAGGCCGATTCCAGCAGGATACTCGAAGGTCGAAGTTGAGTTGGTCGAAGG[C/T]
GCGTACGAGGACCTCGAGCTGGATTACCCTGGAGGAGACGGTGAGACGCATCTACGAGACACATGCCATGCCATTATTCTATGGCGCAGGCGGTACATCA
| 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 | 12.80% | 0.10% | 3.70% | 83.39% | NA |
| All Indica | 2759 | 0.70% | 0.30% | 4.57% | 94.53% | NA |
| All Japonica | 1512 | 37.40% | 0.00% | 0.00% | 62.63% | NA |
| Aus | 269 | 0.00% | 0.00% | 17.10% | 82.90% | NA |
| Indica I | 595 | 0.30% | 0.30% | 1.34% | 97.98% | NA |
| Indica II | 465 | 0.60% | 0.20% | 1.94% | 97.20% | NA |
| Indica III | 913 | 0.70% | 0.40% | 7.12% | 91.79% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 5.60% | 93.51% | NA |
| Temperate Japonica | 767 | 62.70% | 0.00% | 0.00% | 37.29% | NA |
| Tropical Japonica | 504 | 2.00% | 0.00% | 0.00% | 98.02% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.00% | 0.00% | 69.29% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 7.80% | 0.00% | 1.11% | 91.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625553363 | G -> A | LOC_Os06g42500.1 | synonymous_variant ; p.Gly469Gly; LOW | synonymous_codon | Average:4.5; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625553363 | G -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:4.5; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |