Search for Variation information by Variation ID:
Detailed information for vg0620602899:
| Variant ID: vg0620602899 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602899 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCCCTTCGAGTAGAAATTCTCAGTTTCAATCGGTGCAGCCTGTCCAGATTCACTAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTG[C/A]
TACTGCAACATTTCCATATAGGTTTGGATAAGGAGTCTGCATTCTATCTGGACATAACCGTCGGAGGATCGTTGATGCACAAAACGCCGTCGGAAGGAAG
Reverse complement sequence
CTTCCTTCCGACGGCGTTTTGTGCATCAACGATCCTCCGACGGTTATGTCCAGATAGAATGCAGACTCCTTATCCAAACCTATATGGAAATGTTGCAGTA[G/T]
CACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTAGTGAATCTGGACAGGCTGCACCGATTGAAACTGAGAATTTCTACTCGAAGGGCA
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 | 4.10% | 0.30% | 53.49% | 42.11% | NA |
| All Indica | 2759 | 4.50% | 0.10% | 48.13% | 47.23% | NA |
| All Japonica | 1512 | 4.00% | 0.70% | 56.02% | 39.35% | NA |
| Aus | 269 | 2.60% | 0.00% | 78.07% | 19.33% | NA |
| Indica I | 595 | 8.40% | 0.00% | 12.44% | 79.16% | NA |
| Indica II | 465 | 4.10% | 0.40% | 62.58% | 32.90% | NA |
| Indica III | 913 | 2.70% | 0.00% | 63.09% | 34.17% | NA |
| Indica Intermediate | 786 | 3.90% | 0.10% | 49.24% | 46.69% | NA |
| Temperate Japonica | 767 | 7.00% | 0.10% | 34.94% | 57.89% | NA |
| Tropical Japonica | 504 | 0.40% | 1.00% | 90.48% | 8.13% | NA |
| Japonica Intermediate | 241 | 1.70% | 1.70% | 51.04% | 45.64% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 87.50% | 10.42% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 65.56% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602899 | C -> A | LOC_Os06g35340.1 | missense_variant ; p.Leu115Ile; MODERATE | nonsynonymous_codon ; L115I | Average:15.051; most accessible tissue: Zhenshan97 root, score: 20.427 | benign  |
1.392 |
DELETERIOUS | 0.01 |
| vg0620602899 | C -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:15.051; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |