| Variant ID: vg0521976780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21976780 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTCCTGAGTATGCTGATCCTCAAATTCTTACTCCGATGCTGGGACAAAGATTTAAGACTGAGAGGGATGCCTATAATTTTTATAATGTTTATGCTGTTAG[T/C]
AAAGGATTTGGGATACGACTGGACAAAGATCGCATGAATACTAAAAAGCAGAGAACAATGCGGCAAATATGTTGTTCTCACCAGGTACATACATTATGTA
TACATAATGTATGTACCTGGTGAGAACAACATATTTGCCGCATTGTTCTCTGCTTTTTAGTATTCATGCGATCTTTGTCCAGTCGTATCCCAAATCCTTT[A/G]
CTAACAGCATAAACATTATAAAAATTATAGGCATCCCTCTCAGTCTTAAATCTTTGTCCCAGCATCGGAGTAAGAATTTGAGGATCAGCATACTCAGGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.50% | 2.30% | 37.96% | 14.28% | NA |
| All Indica | 2759 | 14.10% | 3.80% | 61.36% | 20.70% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.73% | 0.53% | NA |
| Aus | 269 | 46.10% | 0.00% | 24.16% | 29.74% | NA |
| Indica I | 595 | 16.10% | 3.40% | 54.29% | 26.22% | NA |
| Indica II | 465 | 9.20% | 2.20% | 59.78% | 28.82% | NA |
| Indica III | 913 | 14.20% | 5.80% | 68.24% | 11.72% | NA |
| Indica Intermediate | 786 | 15.30% | 2.90% | 59.67% | 22.14% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.39% | 0.65% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.60% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 2.07% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 55.60% | 1.10% | 26.67% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976780 | T -> DEL | LOC_Os05g37540.1 | N | frameshift_variant | Average:5.54; most accessible tissue: Callus, score: 16.271 | N | N | N | N |
| vg0521976780 | T -> C | LOC_Os05g37540.1 | synonymous_variant ; p.Ser146Ser; LOW | synonymous_codon | Average:5.54; most accessible tissue: Callus, score: 16.271 | N | N | N | N |