| Variant ID: vg0719562788 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562788 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 377. )
AGTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATA[C/T]
GGAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACT
AGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTCC[G/A]
TATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAACT
| 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 | 22.60% | 0.10% | 26.60% | 50.70% | NA |
| All Indica | 2759 | 1.30% | 0.10% | 21.89% | 76.69% | NA |
| All Japonica | 1512 | 67.30% | 0.00% | 25.53% | 7.14% | NA |
| Aus | 269 | 0.00% | 0.00% | 70.26% | 29.74% | NA |
| Indica I | 595 | 0.30% | 0.20% | 6.39% | 93.11% | NA |
| Indica II | 465 | 2.60% | 0.00% | 14.62% | 82.80% | NA |
| Indica III | 913 | 0.50% | 0.00% | 38.23% | 61.23% | NA |
| Indica Intermediate | 786 | 2.00% | 0.40% | 18.96% | 78.63% | NA |
| Temperate Japonica | 767 | 93.70% | 0.00% | 4.43% | 1.83% | NA |
| Tropical Japonica | 504 | 31.20% | 0.00% | 57.74% | 11.11% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.00% | 25.31% | 15.77% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 52.08% | 47.92% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 31.11% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562788 | C -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0719562788 | C -> T | LOC_Os07g32740.1 | synonymous_variant ; p.Tyr535Tyr; LOW | synonymous_codon | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |