Variant ID: vg0206047442 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 6047442 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCACGGTGCACACCACCACGACGTACTAGGCTCCTCTCAGCTTGGAGGAGCTCCAGAGGCGCACACTCAGGAGCAGCCAGAGGTCACACCTGTACAGGC[A/T]
GGACGGGTTGGCCGTGCCGTACCCCCGGACCGACTCACGTACTCCCAGGGGCACATTAGGGCGCAGGGTAGGAGGGACAGGGGTAAGAGGCCTCGTCAGT
ACTGACGAGGCCTCTTACCCCTGTCCCTCCTACCCTGCGCCCTAATGTGCCCCTGGGAGTACGTGAGTCGGTCCGGGGGTACGGCACGGCCAACCCGTCC[T/A]
GCCTGTACAGGTGTGACCTCTGGCTGCTCCTGAGTGTGCGCCTCTGGAGCTCCTCCAAGCTGAGAGGAGCCTAGTACGTCGTGGTGGTGTGCACCGTGCA
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 37.70% | 13.90% | 17.77% | 30.60% | NA |
All Indica | 2759 | 3.20% | 23.30% | 23.89% | 49.58% | NA |
All Japonica | 1512 | 97.60% | 0.20% | 1.06% | 1.19% | NA |
Aus | 269 | 50.20% | 1.50% | 39.03% | 9.29% | NA |
Indica I | 595 | 3.20% | 14.50% | 33.61% | 48.74% | NA |
Indica II | 465 | 1.50% | 37.80% | 20.86% | 39.78% | NA |
Indica III | 913 | 2.20% | 24.00% | 17.31% | 56.52% | NA |
Indica Intermediate | 786 | 5.50% | 20.60% | 25.95% | 47.96% | NA |
Temperate Japonica | 767 | 98.00% | 0.10% | 1.30% | 0.52% | NA |
Tropical Japonica | 504 | 97.80% | 0.20% | 0.40% | 1.59% | NA |
Japonica Intermediate | 241 | 95.40% | 0.40% | 1.66% | 2.49% | NA |
VI/Aromatic | 96 | 42.70% | 0.00% | 42.71% | 14.58% | NA |
Intermediate | 90 | 48.90% | 6.70% | 21.11% | 23.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0206047442 | A -> T | LOC_Os02g11730.1 | synonymous_variant ; p.Ala1541Ala; LOW | synonymous_codon | Average:6.913; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
vg0206047442 | A -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:6.913; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |