| Variant ID: vg0903742334 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3742334 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 145. )
GGTTGGCTATTGTCGACTATATATGTCTGACCTAGTTGTCCGCCTCCGGGAAGGTTACTGGGTCGAACGGAGTTTACCTCAGTAGAGAGTTGACCACGCA[C/T]
GGTGAAGTGTTTGGCAGGAGTTCGAACCGGCTCGACTGGTTCACGTGGTGGAACAGGAGCTCGCGGTTCATCTCCAAAACGAATCTCGCCCTCTTCGTGT
ACACGAAGAGGGCGAGATTCGTTTTGGAGATGAACCGCGAGCTCCTGTTCCACCACGTGAACCAGTCGAGCCGGTTCGAACTCCTGCCAAACACTTCACC[G/A]
TGCGTGGTCAACTCTCTACTGAGGTAAACTCCGTTCGACCCAGTAACCTTCCCGGAGGCGGACAACTAGGTCAGACATATATAGTCGACAATAGCCAACC
| 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 | 82.80% | 0.80% | 9.71% | 6.67% | NA |
| All Indica | 2759 | 71.30% | 1.40% | 16.17% | 11.09% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 96.70% | 0.00% | 1.49% | 1.86% | NA |
| Indica I | 595 | 68.20% | 0.50% | 26.05% | 5.21% | NA |
| Indica II | 465 | 73.10% | 0.00% | 15.05% | 11.83% | NA |
| Indica III | 913 | 70.20% | 1.60% | 11.83% | 16.32% | NA |
| Indica Intermediate | 786 | 73.90% | 2.70% | 14.38% | 9.03% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 7.78% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903742334 | C -> DEL | LOC_Os09g07470.1 | N | frameshift_variant | Average:66.902; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | N | N | N | N |
| vg0903742334 | C -> T | LOC_Os09g07470.1 | missense_variant ; p.Val102Met; MODERATE | nonsynonymous_codon ; V102M | Average:66.902; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | unknown | unknown | DELETERIOUS | 0.02 |