| Variant ID: vg0143001802 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001802 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAATGAGGACACGCTCCAACTTCACGTTGCAAACGGTGGGAGAAACCACCATCGCAATCTGCCCTCCCCGGGCAACGCACGGTGGGTGGTCGGTCTGGTC[G/A]
AAGGTGAGGGCAACCTCCGACCACCGCGCCCGACACGTCGCCTCATGAGTAGGGGCCGCGGCCAGAAGCTCTCGCTTCATGGCCTTGAAGCTCCGGCGAG
CTCGCCGGAGCTTCAAGGCCATGAAGCGAGAGCTTCTGGCCGCGGCCCCTACTCATGAGGCGACGTGTCGGGCGCGGTGGTCGGAGGTTGCCCTCACCTT[C/T]
GACCAGACCGACCACCCACCGTGCGTTGCCCGGGGAGGGCAGATTGCGATGGTGGTTTCTCCCACCGTTTGCAACGTGAAGTTGGAGCGTGTCCTCATTG
| 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 | 7.70% | 0.10% | 3.72% | 88.49% | NA |
| All Indica | 2759 | 1.00% | 0.10% | 2.97% | 95.87% | NA |
| All Japonica | 1512 | 21.00% | 0.10% | 3.31% | 75.60% | NA |
| Aus | 269 | 0.70% | 0.00% | 10.78% | 88.48% | NA |
| Indica I | 595 | 1.00% | 0.20% | 1.85% | 96.97% | NA |
| Indica II | 465 | 1.30% | 0.00% | 2.58% | 96.13% | NA |
| Indica III | 913 | 1.10% | 0.30% | 3.72% | 94.85% | NA |
| Indica Intermediate | 786 | 0.80% | 0.00% | 3.18% | 96.06% | NA |
| Temperate Japonica | 767 | 39.00% | 0.00% | 1.56% | 59.45% | NA |
| Tropical Japonica | 504 | 1.80% | 0.20% | 4.17% | 93.85% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.00% | 7.05% | 88.80% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 10.42% | 87.50% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 5.56% | 80.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001802 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Phe424Phe; LOW | synonymous_codon | Average:12.084; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0143001802 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:12.084; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |