| Variant ID: vg0143001130 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001130 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 72. )
GCCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGC[G/A]
TTTGCCCGTAGGAAGGAGACGAGCGCGTCTTCCTATTTGCCGTCCAAAAGACCACCGATCCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACCTCCT
AGGAGGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGGATCGGTGGTCTTTTGGACGGCAAATAGGAAGACGCGCTCGTCTCCTTCCTACGGGCAAA[C/T]
GCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGC
| 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 | 11.50% | 5.10% | 21.98% | 61.43% | NA |
| All Indica | 2759 | 2.80% | 8.60% | 30.30% | 58.28% | NA |
| All Japonica | 1512 | 21.20% | 0.10% | 4.30% | 74.40% | NA |
| Aus | 269 | 46.80% | 0.40% | 34.20% | 18.59% | NA |
| Indica I | 595 | 2.20% | 3.70% | 34.45% | 59.66% | NA |
| Indica II | 465 | 2.80% | 6.50% | 15.91% | 74.84% | NA |
| Indica III | 913 | 2.50% | 14.50% | 35.60% | 47.43% | NA |
| Indica Intermediate | 786 | 3.70% | 6.70% | 29.52% | 60.05% | NA |
| Temperate Japonica | 767 | 38.30% | 0.00% | 2.61% | 59.06% | NA |
| Tropical Japonica | 504 | 2.00% | 0.20% | 4.56% | 93.25% | NA |
| Japonica Intermediate | 241 | 7.10% | 0.00% | 9.13% | 83.82% | NA |
| VI/Aromatic | 96 | 4.20% | 2.10% | 21.88% | 71.88% | NA |
| Intermediate | 90 | 14.40% | 1.10% | 27.78% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001130 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Asn624Asn; LOW | synonymous_codon | Average:12.962; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |
| vg0143001130 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:12.962; most accessible tissue: Minghui63 young leaf, score: 28.65 | N | N | N | N |