Search for Variation information by Variation ID:
Detailed information for vg1109585503:
| Variant ID: vg1109585503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585503 |
| 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: 413. )
Flanking Sequence (100 bp) in Reference Genome:
GAATTTAGTATTCAGTGCATCCCACAACTTCTTAGCGTCGGTCATATGCATATACACCTCGACCAGACGATCGCCAAGAACGCTAAGAATGCATCCCACA[A/G]
AGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCA
Reverse complement sequence
TGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAGCAGAAGCAATTCGAGGAAGCCACTACTCTCT[T/C]
TGTGGGATGCATTCTTAGCGTTCTTGGCGATCGTCTGGTCGAGGTGTATATGCATATGACCGACGCTAAGAAGTTGTGGGATGCACTGAATACTAAATTC
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 | 72.30% | 0.30% | 6.56% | 20.80% | NA |
| All Indica | 2759 | 96.90% | 0.00% | 1.63% | 1.49% | NA |
| All Japonica | 1512 | 26.90% | 0.10% | 12.17% | 60.85% | NA |
| Aus | 269 | 79.60% | 0.40% | 18.59% | 1.49% | NA |
| Indica I | 595 | 95.00% | 0.00% | 1.34% | 3.70% | NA |
| Indica II | 465 | 96.10% | 0.00% | 3.01% | 0.86% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 95.50% | 0.00% | 2.67% | 1.78% | NA |
| Temperate Japonica | 767 | 22.80% | 0.00% | 2.09% | 75.10% | NA |
| Tropical Japonica | 504 | 22.80% | 0.20% | 31.15% | 45.83% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 4.56% | 46.89% | NA |
| VI/Aromatic | 96 | 54.20% | 11.50% | 26.04% | 8.33% | NA |
| Intermediate | 90 | 78.90% | 3.30% | 6.67% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585503 | A -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:7.386; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1109585503 | A -> G | LOC_Os11g17200.1 | missense_variant ; p.Phe61Ser; MODERATE | nonsynonymous_codon ; F61S | Average:7.386; most accessible tissue: Minghui63 root, score: 13.235 | possibly damaging  |
1.806 |
DELETERIOUS | 0.01 |