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Detailed information for vg1120598096:
| Variant ID: vg1120598096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20598096 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
AACAGGCCACAAGGATGATCCATGGGTTTTAGCAGAGCGTGTGGCTCAAGTGTTTTATGTGAAGGACCCTTCAGATGAAAGAAAAACTATTGTCATATCC[G/A]
GAAAGCAACAGATCGTCGGCATCGACAACATCGAAGACCCCAATGATTACAACCAGTTCGATGATGTACCATTGTTTACTGATCTTCCTATGCGAATTAA
Reverse complement sequence
TTAATTCGCATAGGAAGATCAGTAAACAATGGTACATCATCGAACTGGTTGTAATCATTGGGGTCTTCGATGTTGTCGATGCCGACGATCTGTTGCTTTC[C/T]
GGATATGACAATAGTTTTTCTTTCATCTGAAGGGTCCTTCACATAAAACACTTGAGCCACACGCTCTGCTAAAACCCATGGATCATCCTTGTGGCCTGTT
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 | 33.30% | 0.10% | 7.62% | 58.93% | NA |
| All Indica | 2759 | 19.90% | 0.00% | 8.70% | 71.40% | NA |
| All Japonica | 1512 | 57.40% | 0.30% | 5.69% | 36.64% | NA |
| Aus | 269 | 12.30% | 0.00% | 8.18% | 79.55% | NA |
| Indica I | 595 | 52.10% | 0.00% | 2.86% | 45.04% | NA |
| Indica II | 465 | 6.50% | 0.00% | 7.31% | 86.24% | NA |
| Indica III | 913 | 10.70% | 0.00% | 11.94% | 77.33% | NA |
| Indica Intermediate | 786 | 14.10% | 0.00% | 10.18% | 75.70% | NA |
| Temperate Japonica | 767 | 72.60% | 0.30% | 3.78% | 23.34% | NA |
| Tropical Japonica | 504 | 44.80% | 0.20% | 7.54% | 47.42% | NA |
| Japonica Intermediate | 241 | 35.30% | 0.40% | 7.88% | 56.43% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 8.33% | 7.29% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 4.44% | 44.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120598096 | G -> A | LOC_Os11g35130.1 | missense_variant ; p.Gly904Arg; MODERATE | nonsynonymous_codon ; G904R | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.747 |
DELETERIOUS | 0.01 |
| vg1120598096 | G -> DEL | LOC_Os11g35130.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |