7 variations found. LOC_Os02g25830 (expressed protein), ranging from 15,134,000 bp to 15,134,819 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0215134070 (J) | chr02 | 15134070 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os02g25830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.618; most accessible tissue: Minghui63 flag leaf, score: 87.594 |
| vg0215134347 (J) | chr02 | 15134347 | C | CCTT | 65.10% | 0.00% | CCTT -> C | NA |
LOC_Os02g25830.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 82.389; most accessible tissue: Minghui63 flag leaf, score: 92.011 |
| vg0215134455 (J) | chr02 | 15134455 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os02g25830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.045; most accessible tissue: Minghui63 flag leaf, score: 91.758 |
| vg0215134482 (J) | chr02 | 15134482 | C | A | 65.40% | 0.04% | A -> C | NA |
LOC_Os02g25830.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g25830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 86.375; most accessible tissue: Minghui63 flag leaf, score: 92.472 |
| vg0215134599 (J) | chr02 | 15134599 | C | G | 97.60% | 0.00% | C -> G | NA |
LOC_Os02g25830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.094; most accessible tissue: Minghui63 flag leaf, score: 90.430 |
| vg0215134812 (J) | chr02 | 15134812 | AC | A | 97.60% | 0.00% | AC -> A | NA |
LOC_Os02g25830.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.885; most accessible tissue: Zhenshan97 young leaf, score: 85.001 |
| STR0215134816 (J) | chr02 | 15134816 | ATGATGA TG | ATGATGA T | 98.20% | 0.00% | ATGATGATG -> ATGATGAT | NA |
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