Search for Variation information by Variation ID:
Detailed information for vg0609240321:
| Variant ID: vg0609240321 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9240321 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, others allele: 0.00, population size: 53. )
Flanking Sequence (100 bp) in Reference Genome:
CGGCCCTCCCACAGTGGCCTCGGGGCCGTCCTGGGGGTCGGGGACTCCTGGCATCGTCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTC[T/A]
GGCCTCCGTTCGGCTCGGGGGCCCCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGCCAAAGGGCTTTAAGTGCAGCCTTCC
Reverse complement sequence
GGAAGGCTGCACTTAAAGCCCTTTGGCCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGGGGCCCCCGAGCCGAACGGAGGCC[A/T]
GAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGACGATGCCAGGAGTCCCCGACCCCCAGGACGGCCCCGAGGCCACTGTGGGAGGGCCG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.10% | 0.10% | 4.38% | 82.46% | NA |
| All Indica | 2759 | 1.50% | 0.20% | 2.10% | 96.19% | NA |
| All Japonica | 1512 | 36.70% | 0.00% | 1.98% | 61.31% | NA |
| Aus | 269 | 1.10% | 0.00% | 40.89% | 57.99% | NA |
| Indica I | 595 | 1.50% | 0.50% | 1.18% | 96.81% | NA |
| Indica II | 465 | 1.30% | 0.20% | 1.51% | 96.99% | NA |
| Indica III | 913 | 1.40% | 0.10% | 2.52% | 95.95% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 2.67% | 95.55% | NA |
| Temperate Japonica | 767 | 68.20% | 0.00% | 1.43% | 30.38% | NA |
| Tropical Japonica | 504 | 1.80% | 0.00% | 1.19% | 97.02% | NA |
| Japonica Intermediate | 241 | 9.50% | 0.00% | 5.39% | 85.06% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 5.21% | 92.71% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 4.44% | 78.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609240321 | T -> A | LOC_Os06g16230.1 | missense_variant ; p.Gln1240Leu; MODERATE | nonsynonymous_codon ; Q1240L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.646 |
TOLERATED | 1.00 |
| vg0609240321 | T -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |