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Detailed information for vg1114171761:
| Variant ID: vg1114171761 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14171761 |
| 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: 57. )
Flanking Sequence (100 bp) in Reference Genome:
GGATTTGAAGGAAATCAAACGGGCGAGGAGGAAATAGCTGTTGATGGTAACGACGTTGCGGATGATCTTGGTCAGATGTTGCAGGATGCCAGGGAAGACT[G/A]
CGAAAGTGAAAAGGAGGCCCATAAATTGGACAAGATGTTGGAGGACCATAGAACTTCGTTGTACCCAGGTTGCGAGCAGGGGCACAAAAAGTTGGATACC
Reverse complement sequence
GGTATCCAACTTTTTGTGCCCCTGCTCGCAACCTGGGTACAACGAAGTTCTATGGTCCTCCAACATCTTGTCCAATTTATGGGCCTCCTTTTCACTTTCG[C/T]
AGTCTTCCCTGGCATCCTGCAACATCTGACCAAGATCATCCGCAACGTCGTTACCATCAACAGCTATTTCCTCCTCGCCCGTTTGATTTCCTTCAAATCC
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 | 34.70% | 0.10% | 2.07% | 63.14% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 3.12% | 94.67% | NA |
| All Japonica | 1512 | 96.30% | 0.30% | 0.13% | 3.24% | NA |
| Aus | 269 | 1.90% | 0.00% | 2.97% | 95.17% | NA |
| Indica I | 595 | 3.20% | 0.00% | 2.35% | 94.45% | NA |
| Indica II | 465 | 0.90% | 0.00% | 3.23% | 95.91% | NA |
| Indica III | 913 | 1.10% | 0.00% | 2.41% | 96.50% | NA |
| Indica Intermediate | 786 | 3.60% | 0.00% | 4.45% | 91.98% | NA |
| Temperate Japonica | 767 | 96.30% | 0.00% | 0.26% | 3.39% | NA |
| Tropical Japonica | 504 | 95.40% | 1.00% | 0.00% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 1.11% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114171761 | G -> A | LOC_Os11g24860.1 | missense_variant ; p.Cys131Tyr; MODERATE | nonsynonymous_codon ; C131Y | Average:4.406; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.442 |
DELETERIOUS | 0.02 |
| vg1114171761 | G -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:4.406; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |