Search for Variation information by Variation ID:
Detailed information for vg0629027309:
| Variant ID: vg0629027309 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027309 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
CGTGTGCCATGTCATCAGTTGGGGAACCTGCAGTCGCGGCGGATCTCGCCGCCGGTGGCCGGCGACTTGACGCCGACCCTGCCGAGCTTGGTCATGGCGG[C/A]
GACGAAGTCGTTGAAGAAGGCGCCCTGGTTGGCGGCGTAGCGGTCGACGAGGCCGCGGGACCTCGGGTCGGAGTAGAGCGTCTGGTCGGAGCCGAGGAGG
Reverse complement sequence
CCTCCTCGGCTCCGACCAGACGCTCTACTCCGACCCGAGGTCCCGCGGCCTCGTCGACCGCTACGCCGCCAACCAGGGCGCCTTCTTCAACGACTTCGTC[G/T]
CCGCCATGACCAAGCTCGGCAGGGTCGGCGTCAAGTCGCCGGCCACCGGCGGCGAGATCCGCCGCGACTGCAGGTTCCCCAACTGATGACATGGCACACG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.70% | 35.40% | 11.07% | 1.90% | NA |
| All Indica | 2759 | 28.20% | 50.40% | 18.41% | 2.97% | NA |
| All Japonica | 1512 | 96.90% | 2.80% | 0.07% | 0.26% | NA |
| Aus | 269 | 55.00% | 41.60% | 2.23% | 1.12% | NA |
| Indica I | 595 | 24.00% | 65.50% | 8.40% | 2.02% | NA |
| Indica II | 465 | 12.70% | 59.10% | 24.52% | 3.66% | NA |
| Indica III | 913 | 33.30% | 39.10% | 23.99% | 3.61% | NA |
| Indica Intermediate | 786 | 34.70% | 46.80% | 15.90% | 2.54% | NA |
| Temperate Japonica | 767 | 97.30% | 2.20% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 3.30% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 7.30% | 91.70% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 43.30% | 7.78% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027309 | C -> A | LOC_Os06g48010.1 | missense_variant ; p.Ala287Ser; MODERATE | nonsynonymous_codon ; A287S | Average:70.633; most accessible tissue: Minghui63 panicle, score: 82.797 | benign  |
0.544 |
TOLERATED | 0.48 |
| vg0629027309 | C -> DEL | LOC_Os06g48010.1 | N | frameshift_variant | Average:70.633; most accessible tissue: Minghui63 panicle, score: 82.797 | N | N | N | N |