Search for Variation information by Variation ID:
Detailed information for vg0409515201:
| Variant ID: vg0409515201 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515201 |
| Reference Allele: A | Alternative Allele: C,ATGTCACACCC |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAAC[A/C,ATGTCACACCC]
TTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTT
Reverse complement sequence
AAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAA[T/G,GGGTGTGACAT]
GTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.70% | 7.20% | 5.82% | 8.95% | ATGTCACACCC: 0.38% |
| All Indica | 2759 | 80.30% | 11.20% | 7.94% | 0.04% | ATGTCACACCC: 0.54% |
| All Japonica | 1512 | 72.00% | 0.30% | 1.46% | 26.19% | ATGTCACACCC: 0.07% |
| Aus | 269 | 90.70% | 4.50% | 4.46% | 0.00% | ATGTCACACCC: 0.37% |
| Indica I | 595 | 86.60% | 5.50% | 7.56% | 0.00% | ATGTCACACCC: 0.34% |
| Indica II | 465 | 83.70% | 8.40% | 7.10% | 0.22% | ATGTCACACCC: 0.65% |
| Indica III | 913 | 71.90% | 18.60% | 8.76% | 0.00% | ATGTCACACCC: 0.77% |
| Indica Intermediate | 786 | 83.30% | 8.50% | 7.76% | 0.00% | ATGTCACACCC: 0.38% |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 28.40% | 0.60% | 3.37% | 67.46% | ATGTCACACCC: 0.20% |
| Japonica Intermediate | 241 | 79.30% | 0.40% | 1.66% | 18.67% | NA |
| VI/Aromatic | 96 | 50.00% | 7.30% | 15.62% | 26.04% | ATGTCACACCC: 1.04% |
| Intermediate | 90 | 84.40% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515201 | A -> C | LOC_Os04g17380.1 | missense_variant ; p.Asn135Lys; MODERATE | nonsynonymous_codon | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | benign  |
-0.327 |
TOLERATED | 1.00 |
| vg0409515201 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515201 | A -> ATGTCACACCC | LOC_Os04g17380.1 | frameshift_variant ; p.Asn135fs; HIGH | frameshift_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |