Variant ID: vg0112723317 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 12723317 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACGGTGACGATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGAAGT[C/T]
GTAGACGCCCAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGGAGTCGTAGACGCCCA
TGGGCGTCTACGACTCCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCGCCTACACGGCTGGCCTATTATGCCGCCGCTGTTGGGCGTCTAC[G/A]
ACTTCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTT
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 | 99.40% | 0.10% | 0.53% | 0.00% | NA |
All Indica | 2759 | 99.00% | 0.10% | 0.91% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.00% | 0.20% | 0.77% | 0.00% | NA |
Indica Intermediate | 786 | 97.60% | 0.10% | 2.29% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0112723317 | C -> T | LOC_Os01g22620.1 | missense_variant ; p.Arg371Gln; MODERATE | nonsynonymous_codon ; R371Q | Average:16.479; most accessible tissue: Zhenshan97 root, score: 27.411 | possibly damaging | 1.6 | DELETERIOUS | 0.00 |