| Variant ID: vg0143001631 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001631 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCGGAAGTTGGCGGATCCACCGAAGGTGACCGGTAGGTCGATGTGACCTAACGGCCACGTGTGCCCCGGCGTCACACCGATAATTGGCTGGGACGGCCG[G/A]
AGCACCATCCCCGGGGCCTTGATGGCGTCAAAGGCCGCAGGGGAAAGGATGTTGAGGGCCACTCCCCCATCAATGAGGACACGCTCCAACTTCACGTTGC
GCAACGTGAAGTTGGAGCGTGTCCTCATTGATGGGGGAGTGGCCCTCAACATCCTTTCCCCTGCGGCCTTTGACGCCATCAAGGCCCCGGGGATGGTGCT[C/T]
CGGCCGTCCCAGCCAATTATCGGTGTGACGCCGGGGCACACGTGGCCGTTAGGTCACATCGACCTACCGGTCACCTTCGGTGGATCCGCCAACTTCCGCA
| 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 | 7.60% | 0.30% | 2.94% | 89.17% | NA |
| All Indica | 2759 | 1.20% | 0.50% | 4.13% | 94.20% | NA |
| All Japonica | 1512 | 20.60% | 0.00% | 1.06% | 78.31% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.97% | 96.28% | NA |
| Indica I | 595 | 0.70% | 1.30% | 2.18% | 95.80% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.58% | 96.34% | NA |
| Indica III | 913 | 0.90% | 0.00% | 6.57% | 92.55% | NA |
| Indica Intermediate | 786 | 2.00% | 0.60% | 3.69% | 93.64% | NA |
| Temperate Japonica | 767 | 38.50% | 0.00% | 0.78% | 60.76% | NA |
| Tropical Japonica | 504 | 1.60% | 0.00% | 1.79% | 96.63% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 0.41% | 95.85% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 1.11% | 84.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001631 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Leu481Leu; LOW | synonymous_codon | Average:16.535; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0143001631 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:16.535; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |