| Variant ID: vg0135357594 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35357594 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTTCGCAATACTACTAGTACAACAATAGTCGGAGGTACTCATTACAACAACATTCAATTGAAATTACACGATACAAGTATTTAGTCCGAACACTCATCA[C/T]
ATCACAACAACATTTTATTTCCTAAATCGATAGCATTGTTACACCATGGAATCGCCTGCTGCGCGACGACGCCTTGGCCTTGCGCGCCTGCTTGTTGTTC
GAACAACAAGCAGGCGCGCAAGGCCAAGGCGTCGTCGCGCAGCAGGCGATTCCATGGTGTAACAATGCTATCGATTTAGGAAATAAAATGTTGTTGTGAT[G/A]
TGATGAGTGTTCGGACTAAATACTTGTATCGTGTAATTTCAATTGAATGTTGTTGTAATGAGTACCTCCGACTATTGTTGTACTAGTAGTATTGCGAACT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.40% | 3.00% | 22.98% | 26.64% | NA |
| All Indica | 2759 | 32.80% | 5.00% | 35.56% | 26.57% | NA |
| All Japonica | 1512 | 65.70% | 0.00% | 3.04% | 31.22% | NA |
| Aus | 269 | 71.40% | 0.00% | 14.13% | 14.50% | NA |
| Indica I | 595 | 27.60% | 2.50% | 49.58% | 20.34% | NA |
| Indica II | 465 | 29.00% | 3.70% | 35.48% | 31.83% | NA |
| Indica III | 913 | 35.90% | 8.00% | 27.71% | 28.37% | NA |
| Indica Intermediate | 786 | 35.50% | 4.30% | 34.10% | 26.08% | NA |
| Temperate Japonica | 767 | 57.40% | 0.00% | 0.91% | 41.72% | NA |
| Tropical Japonica | 504 | 70.20% | 0.00% | 6.35% | 23.41% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 2.90% | 14.11% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 62.20% | 2.20% | 21.11% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135357594 | C -> T | LOC_Os01g61100.1 | upstream_gene_variant ; 4837.0bp to feature; MODIFIER | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0135357594 | C -> T | LOC_Os01g61090.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0135357594 | C -> DEL | N | N | silent_mutation | Average:10.56; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |