Search for Variation information by Variation ID:
Detailed information for vg0625224688:
| Variant ID: vg0625224688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25224688 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 395. )
Flanking Sequence (100 bp) in Reference Genome:
ATACTTCTCCACCCCTTGTAAGTAGCACTTGTGCTCGGTCACAATGCTAACTTTCCAATAATCATTCCATTTACCCTTATATGCATGGACACGCCACGGA[C/A]
AATCTTCCTTCATGCACCTCACTTCATACACATAATTTGTTGACTTGACCACCCTAAACTCTCTCTGCAATGAAACTGCCCAATGCTTCACCGCCTCCTT
Reverse complement sequence
AAGGAGGCGGTGAAGCATTGGGCAGTTTCATTGCAGAGAGAGTTTAGGGTGGTCAAGTCAACAAATTATGTGTATGAAGTGAGGTGCATGAAGGAAGATT[G/T]
TCCGTGGCGTGTCCATGCATATAAGGGTAAATGGAATGATTATTGGAAAGTTAGCATTGTGACCGAGCACAAGTGCTACTTACAAGGGGTGGAGAAGTAT
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 | 15.70% | 0.20% | 11.74% | 72.39% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 8.74% | 90.47% | NA |
| All Japonica | 1512 | 45.60% | 0.60% | 12.70% | 41.07% | NA |
| Aus | 269 | 2.20% | 0.00% | 26.02% | 71.75% | NA |
| Indica I | 595 | 0.30% | 0.00% | 7.39% | 92.27% | NA |
| Indica II | 465 | 1.10% | 0.00% | 8.82% | 90.11% | NA |
| Indica III | 913 | 0.20% | 0.00% | 8.21% | 91.57% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 10.31% | 88.04% | NA |
| Temperate Japonica | 767 | 71.60% | 1.20% | 3.39% | 23.86% | NA |
| Tropical Japonica | 504 | 8.90% | 0.00% | 25.99% | 65.08% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 14.52% | 45.64% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 32.29% | 54.17% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 23.33% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625224688 | C -> A | LOC_Os06g42010.1 | missense_variant ; p.Cys264Phe; MODERATE | nonsynonymous_codon ; C264F | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.391 |
DELETERIOUS | 0.01 |
| vg0625224688 | C -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |