Search for Variation information by Variation ID:
Detailed information for vg0719562880:
| Variant ID: vg0719562880 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562880 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
GGTGTATACGGAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAA[G/A]
CCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATAAAGGTACCGTCTGGATACTCCATG
Reverse complement sequence
CATGGAGTATCCAGACGGTACCTTTATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGG[C/T]
TTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTCCGTATACACC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.80% | 0.30% | 19.19% | 41.77% | NA |
| All Indica | 2759 | 30.30% | 0.20% | 15.48% | 54.04% | NA |
| All Japonica | 1512 | 60.80% | 0.00% | 20.90% | 18.32% | NA |
| Aus | 269 | 14.90% | 2.60% | 51.30% | 31.23% | NA |
| Indica I | 595 | 8.40% | 0.00% | 10.42% | 81.18% | NA |
| Indica II | 465 | 25.40% | 0.00% | 12.69% | 61.94% | NA |
| Indica III | 913 | 49.30% | 0.20% | 18.40% | 32.09% | NA |
| Indica Intermediate | 786 | 27.70% | 0.40% | 17.56% | 54.33% | NA |
| Temperate Japonica | 767 | 93.40% | 0.00% | 2.61% | 4.04% | NA |
| Tropical Japonica | 504 | 13.90% | 0.00% | 53.77% | 32.34% | NA |
| Japonica Intermediate | 241 | 55.20% | 0.00% | 10.37% | 34.44% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 11.46% | 83.33% | NA |
| Intermediate | 90 | 35.60% | 1.10% | 16.67% | 46.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562880 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719562880 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Ser566Asn; MODERATE | nonsynonymous_codon ; S566N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.665 |
DELETERIOUS | 0.01 |