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Detailed information for vg1114174187:
| Variant ID: vg1114174187 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14174187 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCTGGGTCGATCGCGACATTCCAGGGATATGAGATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAAAACAGCGCTGTT[C/T]
GTGTCGATGTCATGGGACACGATGGAACAACTGTCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAAGGTTCCTCTGTT
Reverse complement sequence
AACAGAGGAACCTTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGACAGTTGTTCCATCGTGTCCCATGACATCGACAC[G/A]
AACAGCGCTGTTTTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATCTCATATCCCTGGAATGTCGCGATCGACCCAGAC
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 | 35.40% | 0.30% | 4.06% | 60.22% | NA |
| All Indica | 2759 | 3.60% | 0.10% | 6.34% | 90.03% | NA |
| All Japonica | 1512 | 96.80% | 0.10% | 0.20% | 2.98% | NA |
| Aus | 269 | 1.50% | 0.00% | 3.72% | 94.80% | NA |
| Indica I | 595 | 3.70% | 0.00% | 4.20% | 92.10% | NA |
| Indica II | 465 | 2.40% | 0.20% | 6.67% | 90.75% | NA |
| Indica III | 913 | 2.30% | 0.00% | 6.90% | 90.80% | NA |
| Indica Intermediate | 786 | 5.60% | 0.10% | 7.12% | 87.15% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.26% | 3.26% | NA |
| Tropical Japonica | 504 | 96.80% | 0.00% | 0.20% | 2.98% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 76.00% | 10.40% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 3.33% | 55.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114174187 | C -> T | LOC_Os11g24860.1 | missense_variant ; p.Arg940Cys; MODERATE | nonsynonymous_codon ; R940C | Average:5.813; most accessible tissue: Callus, score: 19.27 | benign  |
0.74 |
DELETERIOUS | 0.01 |
| vg1114174187 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:5.813; most accessible tissue: Callus, score: 19.27 | N | N | N | N |