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Detailed information for vg0118270517:
| Variant ID: vg0118270517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270517 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.20, others allele: 0.00, population size: 218. )
Flanking Sequence (100 bp) in Reference Genome:
CGAACGTGTAGAATTATCTCTCGGACACCAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTC[A/G]
AACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTG
Reverse complement sequence
CACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTT[T/C]
GAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTGGTGTCCGAGAGATAATTCTACACGTTCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.30% | 0.60% | 5.10% | 20.02% | NA |
| All Indica | 2759 | 64.30% | 0.70% | 6.67% | 28.34% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.07% | 1.65% | NA |
| Aus | 269 | 31.20% | 2.60% | 19.33% | 46.84% | NA |
| Indica I | 595 | 55.60% | 0.80% | 6.55% | 36.97% | NA |
| Indica II | 465 | 83.20% | 0.40% | 10.54% | 5.81% | NA |
| Indica III | 913 | 58.10% | 1.10% | 5.04% | 35.82% | NA |
| Indica Intermediate | 786 | 66.90% | 0.30% | 6.36% | 26.46% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.60% | 0.00% | 0.00% | 4.37% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 3.33% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270517 | A -> G | LOC_Os01g33180.1 | missense_variant ; p.Gln24Arg; MODERATE | nonsynonymous_codon ; Q24R | Average:53.561; most accessible tissue: Minghui63 young leaf, score: 73.49 | benign  |
-0.383 |
TOLERATED | 1.00 |
| vg0118270517 | A -> DEL | LOC_Os01g33180.1 | N | frameshift_variant | Average:53.561; most accessible tissue: Minghui63 young leaf, score: 73.49 | N | N | N | N |