| Variant ID: vg1101693521 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1693521 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 236. )
GCTACAAACTTAGTTCAGTTCGAGATGAAATGCTAAAACTGACAGGACTCCTGGAAATTCCTTTCAACTTTCAGGCTGATGCTGATGGCAATGGAATTAT[C/T]
GACTATGAGGAGTTCGTCACCGCGACAGTGCACATGAACAAAATGGATCGAGAAGAGCACCTTTACACGGCATTCCAGTACTTTGACAAGGATAATAGTG
CACTATTATCCTTGTCAAAGTACTGGAATGCCGTGTAAAGGTGCTCTTCTCGATCCATTTTGTTCATGTGCACTGTCGCGGTGACGAACTCCTCATAGTC[G/A]
ATAATTCCATTGCCATCAGCATCAGCCTGAAAGTTGAAAGGAATTTCCAGGAGTCCTGTCAGTTTTAGCATTTCATCTCGAACTGAACTAAGTTTGTAGC
| 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 | 55.20% | 1.10% | 9.67% | 33.96% | NA |
| All Indica | 2759 | 31.10% | 1.70% | 13.63% | 53.57% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.07% | 1.59% | NA |
| Aus | 269 | 37.90% | 1.50% | 26.77% | 33.83% | NA |
| Indica I | 595 | 37.60% | 3.90% | 19.83% | 38.66% | NA |
| Indica II | 465 | 39.60% | 1.10% | 11.83% | 47.53% | NA |
| Indica III | 913 | 18.30% | 0.20% | 11.06% | 70.43% | NA |
| Indica Intermediate | 786 | 35.90% | 2.30% | 12.98% | 48.85% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.13% | 3.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 6.67% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693521 | C -> T | LOC_Os11g04170.1 | synonymous_variant ; p.Ile440Ile; LOW | synonymous_codon | Average:37.008; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
| vg1101693521 | C -> DEL | LOC_Os11g04170.1 | N | frameshift_variant | Average:37.008; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |