Search for Variation information by Variation ID:
Detailed information for vg0101920409:
| Variant ID: vg0101920409 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920409 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
TTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGG[A/G]
CACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCATCTC
Reverse complement sequence
GAGATGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTG[T/C]
CCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAA
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 | 89.40% | 0.10% | 1.74% | 8.82% | NA |
| All Indica | 2759 | 92.30% | 0.10% | 2.65% | 4.97% | NA |
| All Japonica | 1512 | 81.50% | 0.00% | 0.46% | 18.06% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.50% | 0.00% | 3.70% | 12.77% | NA |
| Indica II | 465 | 91.60% | 0.00% | 4.95% | 3.44% | NA |
| Indica III | 913 | 97.30% | 0.20% | 1.10% | 1.42% | NA |
| Indica Intermediate | 786 | 93.50% | 0.10% | 2.29% | 4.07% | NA |
| Temperate Japonica | 767 | 88.90% | 0.00% | 0.26% | 10.82% | NA |
| Tropical Japonica | 504 | 78.40% | 0.00% | 0.79% | 20.83% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 0.41% | 35.27% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 1.11% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920409 | A -> G | LOC_Os01g04310.1 | missense_variant ; p.Val8Ala; MODERATE | nonsynonymous_codon ; V8A | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
0.134 |
TOLERATED | 0.16 |
| vg0101920409 | A -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |