Variant ID: vg0125112007 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 25112007 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACCGAGCTCCCAC[G/A]
TTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATGACCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTGCAAATCTTCACCCATTAATGAAGGAA
TTCCTTCATTAATGGGTGAAGATTTGCAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGGTCATATCTACCTCCACTCCGCCGGAAGCAGATGCAA[C/T]
GTGGGAGCTCGGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCT
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 | 51.00% | 0.30% | 5.29% | 43.42% | NA |
All Indica | 2759 | 39.80% | 0.60% | 8.37% | 51.29% | NA |
All Japonica | 1512 | 74.70% | 0.00% | 0.66% | 24.67% | NA |
Aus | 269 | 16.40% | 0.00% | 1.12% | 82.53% | NA |
Indica I | 595 | 34.50% | 0.00% | 14.45% | 51.09% | NA |
Indica II | 465 | 60.20% | 0.00% | 5.16% | 34.62% | NA |
Indica III | 913 | 30.30% | 1.50% | 7.34% | 60.79% | NA |
Indica Intermediate | 786 | 42.60% | 0.30% | 6.87% | 50.25% | NA |
Temperate Japonica | 767 | 98.20% | 0.00% | 0.13% | 1.69% | NA |
Tropical Japonica | 504 | 44.00% | 0.00% | 0.99% | 54.96% | NA |
Japonica Intermediate | 241 | 63.90% | 0.00% | 1.66% | 34.44% | NA |
VI/Aromatic | 96 | 86.50% | 0.00% | 2.08% | 11.46% | NA |
Intermediate | 90 | 61.10% | 0.00% | 4.44% | 34.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0125112007 | G -> A | LOC_Os01g43830.1 | synonymous_variant ; p.Asn14Asn; LOW | synonymous_codon | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |
vg0125112007 | G -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |