Variant ID: vg0512023367 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 12023367 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGGAGCTGCAACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCC[C/A]
TGTGGCATGGGCTGGGGTCCTAAAGTAAGACGCGGCTTCTGATTATTTCCCTGTTGTGTCTTGAATTGAGCAATCCGACGTTTCTTCTGCTCCATGCGAT
ATCGCATGGAGCAGAAGAAACGTCGGATTGCTCAATTCAAGACACAACAGGGAAATAATCAGAAGCCGCGTCTTACTTTAGGACCCCAGCCCATGCCACA[G/T]
GGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGTTGCAGCTCCAG
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 87.30% | 0.40% | 5.37% | 6.94% | NA |
All Indica | 2759 | 86.50% | 0.40% | 6.96% | 6.16% | NA |
All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.26% | NA |
Aus | 269 | 23.00% | 2.20% | 20.07% | 54.65% | NA |
Indica I | 595 | 92.10% | 0.00% | 2.02% | 5.88% | NA |
Indica II | 465 | 98.30% | 0.00% | 0.65% | 1.08% | NA |
Indica III | 913 | 77.20% | 0.70% | 15.22% | 6.90% | NA |
Indica Intermediate | 786 | 86.00% | 0.60% | 4.83% | 8.52% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
Intermediate | 90 | 88.90% | 0.00% | 4.44% | 6.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0512023367 | C -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:26.557; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
vg0512023367 | C -> A | LOC_Os05g20480.1 | missense_variant ; p.Gln32His; MODERATE | nonsynonymous_codon ; Q32H | Average:26.557; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | benign | 0.026 | TOLERATED | 0.10 |