Search for Variation information by Variation ID:
Detailed information for vg0625222862:
| Variant ID: vg0625222862 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 25222862 |
| Reference Allele: A | Alternative Allele: G,ACGCCTTGGCCTTGC,ACGCCTTGGCCTT |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTATGCAAGATAAATGACATAATTGTTGGAAGTAATACAAATTGGACGTACCGCCACGAAGTAGTCTCGGTCACGGTGCGTGGGATACGCGTCCGTGAC[A/G,ACGCCTTGGCCTTGC,ACGCCTTGGCCTT]
GCGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGCACGAGTGCGAGGAAGGTACCAGCGAAGGTCACACTTGCTGCAGCGTAAAGTCC
Reverse complement sequence
GGACTTTACGCTGCAGCAAGTGTGACCTTCGCTGGTACCTTCCTCGCACTCGTGCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCGC[T/C,GCAAGGCCAAGGCGT,AAGGCCAAGGCGT]
GTCACGGACGCGTATCCCACGCACCGTGACCGAGACTACTTCGTGGCGGTACGTCCAATTTGTATTACTTCCAACAATTATGTCATTTATCTTGCATAAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.60% | 0.20% | 5.82% | 78.21% | ACGCCTTGGCCTT: 0.11%; ACGCCTTGGCCTTGC: 0.08% |
| All Indica | 2759 | 0.90% | 0.00% | 3.77% | 95.22% | ACGCCTTGGCCTT: 0.11%; ACGCCTTGGCCTTGC: 0.04% |
| All Japonica | 1512 | 45.80% | 0.10% | 6.48% | 47.55% | ACGCCTTGGCCTTGC: 0.07% |
| Aus | 269 | 2.20% | 0.00% | 14.13% | 83.64% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.67% | 98.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.80% | 96.13% | NA |
| Indica III | 913 | 0.50% | 0.00% | 5.26% | 93.98% | ACGCCTTGGCCTT: 0.22% |
| Indica Intermediate | 786 | 1.30% | 0.00% | 4.96% | 93.51% | ACGCCTTGGCCTTGC: 0.13%; ACGCCTTGGCCTT: 0.13% |
| Temperate Japonica | 767 | 72.50% | 0.00% | 0.91% | 26.60% | NA |
| Tropical Japonica | 504 | 8.10% | 0.20% | 14.48% | 77.18% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 7.47% | 52.28% | ACGCCTTGGCCTTGC: 0.41% |
| VI/Aromatic | 96 | 6.20% | 7.30% | 26.04% | 56.25% | ACGCCTTGGCCTTGC: 2.08%; ACGCCTTGGCCTT: 2.08% |
| Intermediate | 90 | 10.00% | 0.00% | 11.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222862 | A -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625222862 | A -> G | LOC_Os06g42010.1 | N | nonsynonymous_codon ; A762V | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.382 |
DELETERIOUS | 0.00 |
| vg0625222862 | A -> ACGCCTTGGCCTT | LOC_Os06g42010.1 | disruptive_inframe_insertion ; p.Ala762_Val763insArgProArgArg; MODERATE | inframe_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625222862 | A -> ACGCCTTGGCCTTGC | LOC_Os06g42010.1 | frameshift_variant ; p.Val763fs; HIGH | frameshift_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |