Search for Variation information by Variation ID:
Detailed information for vg0704650509:
| Variant ID: vg0704650509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650509 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
CCTAGTGGTGATGCTGCTTGGTCCCAACGTCAAACACTTGGTGGGCGTCATGTCGACACCGTTCCCGTTGAAAGGATGCACGTGCTGGACATCAAGCAGG[T/C]
AACACCCATCATAGATGTTGCGTCCATTGGTGACAGAAAGAGTCATCTCTGCATCACAGCATGACCGGAACCACACGAAAGCCTCAACACCCTAAGAGCT
Reverse complement sequence
AGCTCTTAGGGTGTTGAGGCTTTCGTGTGGTTCCGGTCATGCTGTGATGCAGAGATGACTCTTTCTGTCACCAATGGACGCAACATCTATGATGGGTGTT[A/G]
CCTGCTTGATGTCCAGCACGTGCATCCTTTCAACGGGAACGGTGTCGACATGACGCCCACCAAGTGTTTGACGTTGGGACCAAGCAGCATCACCACTAGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.30% | 40.40% | 0.08% | 0.25% | NA |
| All Indica | 2759 | 97.60% | 2.00% | 0.04% | 0.36% | NA |
| All Japonica | 1512 | 0.50% | 99.30% | 0.07% | 0.07% | NA |
| Aus | 269 | 25.70% | 74.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.30% | 0.00% | 0.34% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.00% | 0.22% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 95.90% | 3.60% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 0.70% | 99.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 60.00% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650509 | T -> DEL | LOC_Os07g08940.1 | N | frameshift_variant | Average:63.35; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0704650509 | T -> C | LOC_Os07g08940.1 | missense_variant ; p.Tyr16Cys; MODERATE | nonsynonymous_codon ; Y16C | Average:63.35; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | benign  |
-0.226 |
TOLERATED | 1.00 |