Search for Variation information by Variation ID:
Detailed information for vg1105974413:
| Variant ID: vg1105974413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974413 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATC[G/A]
GCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCT
Reverse complement sequence
AGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGC[C/T]
GATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGG
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 | 54.10% | 0.10% | 2.45% | 43.38% | NA |
| All Indica | 2759 | 39.10% | 0.10% | 3.23% | 57.48% | NA |
| All Japonica | 1512 | 83.80% | 0.00% | 0.99% | 15.21% | NA |
| Aus | 269 | 22.70% | 0.00% | 3.35% | 73.98% | NA |
| Indica I | 595 | 44.00% | 0.00% | 5.04% | 50.92% | NA |
| Indica II | 465 | 33.30% | 0.00% | 3.23% | 63.44% | NA |
| Indica III | 913 | 35.00% | 0.40% | 2.30% | 62.21% | NA |
| Indica Intermediate | 786 | 43.60% | 0.00% | 2.93% | 53.44% | NA |
| Temperate Japonica | 767 | 73.80% | 0.00% | 1.83% | 24.38% | NA |
| Tropical Japonica | 504 | 96.60% | 0.00% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.41% | 10.79% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974413 | G -> A | LOC_Os11g10840.1 | missense_variant ; p.Gly32Ser; MODERATE | nonsynonymous_codon ; G32S | Average:29.814; most accessible tissue: Minghui63 root, score: 40.262 | possibly damaging  |
1.834 |
DELETERIOUS | 0.00 |
| vg1105974413 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:29.814; most accessible tissue: Minghui63 root, score: 40.262 | N | N | N | N |