Search for Variation information by Variation ID:
Detailed information for vg1101752536:
| Variant ID: vg1101752536 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1752536 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, T: 0.16, others allele: 0.00, population size: 115. )
Flanking Sequence (100 bp) in Reference Genome:
AGGCCCAGGAGGACATCGCGCGACACGGCGTGTACTCGAGCGTACTTGCTCGGCGGCTGCATCGGGGCATCCCCGTCGGCGGCGCGGCGACGTCGTCCTA[T/G]
CACGGGCGTTGGCATGGACGAAGGACGAGGCCTGATGACTCGGCCAGCCCAGTACACCTCTCCATGGTACACCACTCGATAGAACTCTTGTAGCATGTCG
Reverse complement sequence
CGACATGCTACAAGAGTTCTATCGAGTGGTGTACCATGGAGAGGTGTACTGGGCTGGCCGAGTCATCAGGCCTCGTCCTTCGTCCATGCCAACGCCCGTG[A/C]
TAGGACGACGTCGCCGCGCCGCCGACGGGGATGCCCCGATGCAGCCGCCGAGCAAGTACGCTCGAGTACACGCCGTGTCGCGCGATGTCCTCCTGGGCCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 33.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 4.00% | 96.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.80% | 95.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 64.60% | 35.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 47.80% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101752536 | T -> G | LOC_Os11g04280.1 | missense_variant ; p.Ile119Leu; MODERATE | nonsynonymous_codon ; I119L | Average:15.842; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
-0.878 |
TOLERATED | 1.00 |