Variant ID: vg0910657665 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 10657665 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTCCACCCGCTCCGTGCGGAAGTTGGCGGAA[T/C]
CACCGATGGTGACCGGGAGGTCGATATGACCCAGCGGCCAGGTGTGCCCCGGCGTCACACCGATGATCGGCTGGGACGGCCGGAGCACCATCCCTGGGGC
GCCCCAGGGATGGTGCTCCGGCCGTCCCAGCCGATCATCGGTGTGACGCCGGGGCACACCTGGCCGCTGGGTCATATCGACCTCCCGGTCACCATCGGTG[A/G]
TTCCGCCAACTTCCGCACGGAGCGGGTGGACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATG
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 | 38.00% | 0.60% | 13.46% | 47.86% | NA |
All Indica | 2759 | 29.00% | 0.20% | 19.83% | 50.96% | NA |
All Japonica | 1512 | 54.80% | 1.60% | 1.52% | 42.13% | NA |
Aus | 269 | 37.90% | 0.00% | 21.56% | 40.52% | NA |
Indica I | 595 | 42.50% | 0.30% | 10.42% | 46.72% | NA |
Indica II | 465 | 22.40% | 0.00% | 12.90% | 64.73% | NA |
Indica III | 913 | 21.90% | 0.10% | 32.20% | 45.78% | NA |
Indica Intermediate | 786 | 30.90% | 0.40% | 16.67% | 52.04% | NA |
Temperate Japonica | 767 | 76.90% | 0.10% | 0.65% | 22.29% | NA |
Tropical Japonica | 504 | 27.20% | 4.60% | 2.38% | 65.87% | NA |
Japonica Intermediate | 241 | 41.90% | 0.00% | 2.49% | 55.60% | NA |
VI/Aromatic | 96 | 32.30% | 0.00% | 4.17% | 63.54% | NA |
Intermediate | 90 | 41.10% | 0.00% | 4.44% | 54.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0910657665 | T -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:10.919; most accessible tissue: Callus, score: 20.752 | N | N | N | N |
vg0910657665 | T -> C | LOC_Os09g17420.1 | missense_variant ; p.Asp69Gly; MODERATE | nonsynonymous_codon ; D69G | Average:10.919; most accessible tissue: Callus, score: 20.752 | benign | -0.159 | TOLERATED | 1.00 |