Search for Variation information by Variation ID:
Detailed information for vg0112723228:
| Variant ID: vg0112723228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723228 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACGGTGAAAGCGAAGATGCCCACTAATGGCGGCATAATAGGTCAGCCGTGTAAGCGGAAACACCAGTCGACGGCAACGAAGGTGAGCCAACGGTGACGA[T/C]
GTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCA
Reverse complement sequence
TGGGCGTCTACGACTTCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTAC[A/G]
TCGTCACCGTTGGCTCACCTTCGTTGCCGTCGACTGGTGTTTCCGCTTACACGGCTGACCTATTATGCCGCCATTAGTGGGCATCTTCGCTTTCACCGTC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 0.00% | 11.83% | 31.59% | NA |
| All Indica | 2759 | 31.00% | 0.00% | 19.43% | 49.55% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.07% | 1.59% | NA |
| Aus | 269 | 63.60% | 0.00% | 5.58% | 30.86% | NA |
| Indica I | 595 | 18.00% | 0.00% | 3.87% | 78.15% | NA |
| Indica II | 465 | 23.40% | 0.00% | 33.12% | 43.44% | NA |
| Indica III | 913 | 44.10% | 0.00% | 24.21% | 31.65% | NA |
| Indica Intermediate | 786 | 30.20% | 0.00% | 17.56% | 52.29% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 96.80% | 0.00% | 0.20% | 2.98% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 73.30% | 1.10% | 7.78% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723228 | T -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.97; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |
| vg0112723228 | T -> C | LOC_Os01g22620.1 | missense_variant ; p.Ile401Val; MODERATE | nonsynonymous_codon ; I401V | Average:16.97; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | benign  |
-0.168 |
TOLERATED | 1.00 |