| Variant ID: vg0143001495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001495 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGCCACCGGGGCCCGGCATCTTCATCTGTAGGTAGGCGTAGTGGACCGCCGCCATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCA[G/A]
ACTGAGGTCCGCCACATCGAAGTTCACCCGCTCCATGCGGAAGTTGGCGGATCCACCGAAGGTGACCGGTAGGTCGATGTGACCTAACGGCCACGTGTGC
GCACACGTGGCCGTTAGGTCACATCGACCTACCGGTCACCTTCGGTGGATCCGCCAACTTCCGCATGGAGCGGGTGAACTTCGATGTGGCGGACCTCAGT[C/T]
TGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATGGCGGCGGTCCACTACGCCTACCTACAGATGAAGATGCCGGGCCCCGGTGGCCC
| 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 | 12.10% | 0.10% | 6.77% | 81.06% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 7.79% | 89.24% | NA |
| All Japonica | 1512 | 20.80% | 0.30% | 3.31% | 75.66% | NA |
| Aus | 269 | 56.90% | 0.00% | 7.43% | 35.69% | NA |
| Indica I | 595 | 2.70% | 0.00% | 3.53% | 93.78% | NA |
| Indica II | 465 | 0.90% | 0.00% | 2.37% | 96.77% | NA |
| Indica III | 913 | 3.00% | 0.00% | 12.81% | 84.23% | NA |
| Indica Intermediate | 786 | 4.50% | 0.00% | 8.40% | 87.15% | NA |
| Temperate Japonica | 767 | 38.90% | 0.00% | 0.39% | 60.76% | NA |
| Tropical Japonica | 504 | 1.00% | 0.40% | 7.74% | 90.87% | NA |
| Japonica Intermediate | 241 | 4.60% | 0.80% | 3.32% | 91.29% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 26.04% | 68.75% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 11.11% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001495 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Leu527Leu; LOW | synonymous_codon | Average:18.618; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg0143001495 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:18.618; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |