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Detailed information for vg0614258037:
| Variant ID: vg0614258037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14258037 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
GGAATCCATTTCACTACGGACAGCCTCCTTCCAGTAGTCTGCATCAGGAGATGCATATGCTTCTGAAATTGACTTAGGAGTGTCATCCACGAGGTACACA[G/A]
TGAAATCATCACCAAAAGACTTAGCCGTCCTTTGTCTCTTACTCCTTCGAGGAGCTTCACTGACATCCTCCTCAGAGACAAGTTCATGTGTATGTTCAGT
Reverse complement sequence
ACTGAACATACACATGAACTTGTCTCTGAGGAGGATGTCAGTGAAGCTCCTCGAAGGAGTAAGAGACAAAGGACGGCTAAGTCTTTTGGTGATGATTTCA[C/T]
TGTGTACCTCGTGGATGACACTCCTAAGTCAATTTCAGAAGCATATGCATCTCCTGATGCAGACTACTGGAAGGAGGCTGTCCGTAGTGAAATGGATTCC
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 | 32.10% | 0.10% | 3.11% | 64.73% | NA |
| All Indica | 2759 | 3.40% | 0.00% | 1.38% | 95.25% | NA |
| All Japonica | 1512 | 90.80% | 0.30% | 1.72% | 7.14% | NA |
| Aus | 269 | 1.90% | 0.00% | 25.65% | 72.49% | NA |
| Indica I | 595 | 5.50% | 0.00% | 0.67% | 93.78% | NA |
| Indica II | 465 | 1.30% | 0.00% | 1.08% | 97.63% | NA |
| Indica III | 913 | 1.10% | 0.00% | 2.30% | 96.60% | NA |
| Indica Intermediate | 786 | 5.60% | 0.00% | 1.02% | 93.38% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.00% | 3.52% | NA |
| Tropical Japonica | 504 | 81.50% | 1.00% | 4.56% | 12.90% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.00% | 1.24% | 6.64% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 5.21% | 84.38% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 10.00% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614258037 | G -> A | LOC_Os06g24360.1 | missense_variant ; p.Thr623Ile; MODERATE | nonsynonymous_codon ; T623I | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.266 |
TOLERATED | 0.82 |
| vg0614258037 | G -> DEL | LOC_Os06g24360.1 | N | frameshift_variant | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |