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Detailed information for vg0802669982:
| Variant ID: vg0802669982 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2669982 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
AATAATGCCACTTGCCACAAACTTGTCCGGCAACTCACAGTTGTTGTTCTCAAGTTCCTTAGCCAGCATCTGAATCTCATGAGCTTGTTCAACTACAGAA[C/T]
GGTCATCGACCATCTTGTAGTCATAGAACTGCTCCATAACATACAGCTCACTGCCGGCGTCAGAAACTCCGAACTTGGCCTCAAGTGCATCCCACATGTC
Reverse complement sequence
GACATGTGGGATGCACTTGAGGCCAAGTTCGGAGTTTCTGACGCCGGCAGTGAGCTGTATGTTATGGAGCAGTTCTATGACTACAAGATGGTCGATGACC[G/A]
TTCTGTAGTTGAACAAGCTCATGAGATTCAGATGCTGGCTAAGGAACTTGAGAACAACAACTGTGAGTTGCCGGACAAGTTTGTGGCAAGTGGCATTATT
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 | 71.30% | 3.40% | 2.52% | 22.75% | NA |
| All Indica | 2759 | 67.80% | 0.10% | 2.21% | 29.90% | NA |
| All Japonica | 1512 | 87.80% | 10.60% | 1.26% | 0.33% | NA |
| Aus | 269 | 3.70% | 0.00% | 11.90% | 84.39% | NA |
| Indica I | 595 | 96.10% | 0.20% | 0.84% | 2.86% | NA |
| Indica II | 465 | 83.90% | 0.00% | 0.86% | 15.27% | NA |
| Indica III | 913 | 43.80% | 0.00% | 2.19% | 54.00% | NA |
| Indica Intermediate | 786 | 64.80% | 0.10% | 4.07% | 31.04% | NA |
| Temperate Japonica | 767 | 78.60% | 18.80% | 2.35% | 0.26% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802669982 | C -> T | LOC_Os08g05150.1 | missense_variant ; p.Arg233His; MODERATE | nonsynonymous_codon ; R233H | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.862 |
TOLERATED | 0.05 |
| vg0802669982 | C -> DEL | LOC_Os08g05150.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |