Search for Variation information by Variation ID:
Detailed information for vg0221509608:
| Variant ID: vg0221509608 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509608 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAGGCACGGGGTTGGCTAATGAACTTGCCACCCGCGTCCGTCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCG[T/C]
GCCCAGGTGAAGAAGCGGACCTGCACGCAGTACAGCGAAGGGATGATGAGTCACTTCGCTCGTACATTCAGCGGTTCTGTCAAGTCCGCAACACCATACC
Reverse complement sequence
GGTATGGTGTTGCGGACTTGACAGAACCGCTGAATGTACGAGCGAAGTGACTCATCATCCCTTCGCTGTACTGCGTGCAGGTCCGCTTCTTCACCTGGGC[A/G]
CGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGACGGACGCGGGTGGCAAGTTCATTAGCCAACCCCGTGCCTGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.30% | 1.50% | 6.90% | 55.27% | NA |
| All Indica | 2759 | 4.00% | 0.40% | 5.07% | 90.50% | NA |
| All Japonica | 1512 | 96.70% | 0.60% | 1.46% | 1.26% | NA |
| Aus | 269 | 1.50% | 17.80% | 54.65% | 26.02% | NA |
| Indica I | 595 | 3.50% | 0.00% | 5.55% | 90.92% | NA |
| Indica II | 465 | 2.80% | 0.40% | 6.02% | 90.75% | NA |
| Indica III | 913 | 4.90% | 0.20% | 2.85% | 92.00% | NA |
| Indica Intermediate | 786 | 4.10% | 0.90% | 6.74% | 88.30% | NA |
| Temperate Japonica | 767 | 98.70% | 0.30% | 0.78% | 0.26% | NA |
| Tropical Japonica | 504 | 93.50% | 1.20% | 2.58% | 2.78% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 91.70% | 1.00% | 4.17% | 3.12% | NA |
| Intermediate | 90 | 57.80% | 2.20% | 14.44% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509608 | T -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:4.785; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0221509608 | T -> C | LOC_Os02g35800.1 | missense_variant ; p.Cys316Arg; MODERATE | nonsynonymous_codon ; C316R | Average:4.785; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.349 |
TOLERATED | 1.00 |