Search for Variation information by Variation ID:
Detailed information for vg0721993610:
| Variant ID: vg0721993610 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993610 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 359. )
Flanking Sequence (100 bp) in Reference Genome:
ACCAGAGTTTACAAAGCCTAAGTTTAAGGTTCCCTCATCCATTCTCTCTTTAATAAAGAAGCGATCTATTTCCACATGCTTCGTTCGATCATGCTGGACT[G/A]
GATTGTTAGCAATATTTATGGCTGATTTGTTGTCACACCACAACTTCATGGAAGTGCTTGTCGACAGCTTCAATTCAGCCAAAAGATTTTTCAACCATAA
Reverse complement sequence
TTATGGTTGAAAAATCTTTTGGCTGAATTGAAGCTGTCGACAAGCACTTCCATGAAGTTGTGGTGTGACAACAAATCAGCCATAAATATTGCTAACAATC[C/T]
AGTCCAGCATGATCGAACGAAGCATGTGGAAATAGATCGCTTCTTTATTAAAGAGAGAATGGATGAGGGAACCTTAAACTTAGGCTTTGTAAACTCTGGT
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 | 34.90% | 0.10% | 34.32% | 30.70% | NA |
| All Indica | 2759 | 12.30% | 0.20% | 45.09% | 42.44% | NA |
| All Japonica | 1512 | 81.30% | 0.00% | 10.38% | 8.27% | NA |
| Aus | 269 | 1.10% | 0.00% | 59.11% | 39.78% | NA |
| Indica I | 595 | 4.90% | 0.00% | 24.20% | 70.92% | NA |
| Indica II | 465 | 18.10% | 0.00% | 34.41% | 47.53% | NA |
| Indica III | 913 | 13.10% | 0.00% | 66.37% | 20.48% | NA |
| Indica Intermediate | 786 | 13.50% | 0.60% | 42.49% | 43.38% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 1.96% | 3.78% | NA |
| Tropical Japonica | 504 | 68.10% | 0.00% | 21.43% | 10.52% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 14.11% | 17.84% | NA |
| VI/Aromatic | 96 | 31.20% | 0.00% | 41.67% | 27.08% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 24.44% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993610 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:9.702; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0721993610 | G -> A | LOC_Os07g36710.1 | missense_variant ; p.Pro738Leu; MODERATE | nonsynonymous_codon ; P738L | Average:9.702; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
1.193 |
DELETERIOUS | 0.04 |