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Detailed information for vg1109584772:
| Variant ID: vg1109584772 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9584772 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGATAAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCC[C/T]
AGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATTACCATACCCGCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCA
Reverse complement sequence
TGCTAATGTGACCATTGGCAACACTGGAGATGGAAGCGGGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACT[G/A]
GGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTTATCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.60% | 0.40% | 52.98% | 45.05% | NA |
| All Indica | 2759 | 1.50% | 0.40% | 59.19% | 38.89% | NA |
| All Japonica | 1512 | 1.50% | 0.40% | 37.43% | 60.71% | NA |
| Aus | 269 | 1.90% | 0.40% | 66.91% | 30.86% | NA |
| Indica I | 595 | 0.70% | 0.20% | 30.76% | 68.40% | NA |
| Indica II | 465 | 0.60% | 1.10% | 47.10% | 51.18% | NA |
| Indica III | 913 | 2.70% | 0.40% | 88.83% | 8.00% | NA |
| Indica Intermediate | 786 | 1.10% | 0.30% | 53.44% | 45.17% | NA |
| Temperate Japonica | 767 | 0.50% | 0.50% | 22.56% | 76.40% | NA |
| Tropical Japonica | 504 | 3.20% | 0.20% | 53.97% | 42.66% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.40% | 50.21% | 48.55% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 78.12% | 16.67% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 55.56% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109584772 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Gly305Arg; MODERATE | nonsynonymous_codon ; G305R | Average:5.073; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
0.365 |
TOLERATED | 0.05 |
| vg1109584772 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:5.073; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |