Variant ID: vg0142999785 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 42999785 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCGGAGGATAACAGGGGCGGCCTTCCCACAGTGGCTTCGGGGCCGTCCTGGGGGTCGGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTC[C/T]
GGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGC
GCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACC[G/A]
GAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCCGACCCCCAGGACGGCCCCGAAGCCACTGTGGGAAGGCCGCCCCTGTTATCCTCCGA
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 | 7.50% | 0.10% | 3.91% | 88.47% | NA |
All Indica | 2759 | 1.10% | 0.20% | 4.35% | 94.35% | NA |
All Japonica | 1512 | 20.00% | 0.00% | 0.66% | 79.30% | NA |
Aus | 269 | 3.30% | 0.00% | 19.33% | 77.32% | NA |
Indica I | 595 | 1.00% | 0.00% | 2.18% | 96.81% | NA |
Indica II | 465 | 0.20% | 0.00% | 1.72% | 98.06% | NA |
Indica III | 913 | 1.40% | 0.30% | 6.79% | 91.46% | NA |
Indica Intermediate | 786 | 1.40% | 0.30% | 4.71% | 93.64% | NA |
Temperate Japonica | 767 | 37.70% | 0.00% | 1.17% | 61.15% | NA |
Tropical Japonica | 504 | 1.00% | 0.00% | 0.20% | 98.81% | NA |
Japonica Intermediate | 241 | 3.70% | 0.00% | 0.00% | 96.27% | NA |
VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
Intermediate | 90 | 13.30% | 0.00% | 2.22% | 84.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0142999785 | C -> T | LOC_Os01g74230.1 | missense_variant ; p.Gly1073Arg; MODERATE | nonsynonymous_codon ; G1073R | Average:5.12; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign | 1.14 | TOLERATED | 0.08 |
vg0142999785 | C -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:5.12; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |