Search for Variation information by Variation ID:
Detailed information for vg1109584748:
| Variant ID: vg1109584748 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584748 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
AGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGATAAGAAGAAAACAATGAGATGT[C/T]
AGCACAAACATGTACATTGGCCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATTACCATACCCGCTTCCATCTCCA
Reverse complement sequence
TGGAGATGGAAGCGGGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCT[G/A]
ACATCTCATTGTTTTCTTCTTATCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 0.30% | 14.28% | 34.53% | NA |
| All Indica | 2759 | 58.40% | 0.10% | 16.42% | 25.12% | NA |
| All Japonica | 1512 | 41.30% | 0.50% | 3.64% | 54.63% | NA |
| Aus | 269 | 16.00% | 1.90% | 56.13% | 26.02% | NA |
| Indica I | 595 | 31.90% | 0.00% | 20.67% | 47.39% | NA |
| Indica II | 465 | 47.50% | 0.00% | 19.78% | 32.69% | NA |
| Indica III | 913 | 84.40% | 0.00% | 11.61% | 3.94% | NA |
| Indica Intermediate | 786 | 54.50% | 0.40% | 16.79% | 28.37% | NA |
| Temperate Japonica | 767 | 21.80% | 0.00% | 4.43% | 73.79% | NA |
| Tropical Japonica | 504 | 65.30% | 1.20% | 3.17% | 30.36% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.40% | 2.07% | 44.40% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 6.25% | 12.50% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 11.11% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584748 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Asp313Asn; MODERATE | nonsynonymous_codon ; D313N | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.937 |
TOLERATED | 0.22 |
| vg1109584748 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:4.595; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |