Variant ID: vg0112723651 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 12723651 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCGGCGGCGACGGAGGCAGGCCGGCGGTGTAGATGACGATGCCCATCAACGGTGGTGTGACCAACCGACCGTGTAGGCGGGGACACCAGTCGGCGGCGAC[A/G]
GAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCAACGGCGGTGGTGTGACCAACCAACCATATAGGCGAAGACACCAGTCGGCGGCGACGGAGGCAGGCCG
CGGCCTGCCTCCGTCGCCGCCGACTGGTGTCTTCGCCTATATGGTTGGTTGGTCACACCACCGCCGTTGGGCGTCTACGACTTCACCGCCGGCCTGCCTC[T/C]
GTCGCCGCCGACTGGTGTCCCCGCCTACACGGTCGGTTGGTCACACCACCGTTGATGGGCATCGTCATCTACACCGCCGGCCTGCCTCCGTCGCCGCCGA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 70.60% | 0.00% | 10.64% | 18.75% | NA |
All Indica | 2759 | 54.80% | 0.00% | 16.20% | 29.00% | NA |
All Japonica | 1512 | 98.30% | 0.10% | 0.86% | 0.73% | NA |
Aus | 269 | 61.70% | 0.00% | 13.38% | 24.91% | NA |
Indica I | 595 | 24.40% | 0.00% | 14.12% | 61.51% | NA |
Indica II | 465 | 66.20% | 0.00% | 16.56% | 17.20% | NA |
Indica III | 913 | 70.10% | 0.00% | 17.74% | 12.16% | NA |
Indica Intermediate | 786 | 53.30% | 0.00% | 15.78% | 30.92% | NA |
Temperate Japonica | 767 | 98.70% | 0.10% | 0.78% | 0.39% | NA |
Tropical Japonica | 504 | 97.60% | 0.00% | 1.19% | 1.19% | NA |
Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 83.30% | 0.00% | 7.78% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0112723651 | A -> G | LOC_Os01g22620.1 | missense_variant ; p.Cys260Arg; MODERATE | nonsynonymous_codon ; C260R | Average:19.746; most accessible tissue: Minghui63 panicle, score: 50.413 | probably damaging | -2.993 | TOLERATED | 0.44 |
vg0112723651 | A -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:19.746; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |