9 variations found. LOC_Os03g24970 (SWIM zinc finger family protein; putative), ranging from 14,253,792 bp to 14,254,884 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0314254349 (J) | chr03 | 14254349 | G | A | 97.10% | 0.00% | G -> A | NA |
LOC_Os03g24970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.991; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0314254371 (J) | chr03 | 14254371 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os03g24970.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 4.991; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0314254436 (J) | chr03 | 14254436 | G | T | 70.10% | 0.30% | G -> T | NA |
LOC_Os03g24970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.462; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0314254509 (J) | chr03 | 14254509 | T | C | 32.40% | 64.66% | T -> C | NA |
LOC_Os03g24970.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.462; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0314254696 (J) | chr03 | 14254696 | C | T | 80.80% | 1.67% | C -> T | NA |
LOC_Os03g24970.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.655; most accessible tissue: Callus, score: 16.966 |
| vg0314254707 (J) | chr03 | 14254707 | C | A | 98.00% | 0.51% | C -> A | NA |
LOC_Os03g24970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.655; most accessible tissue: Callus, score: 16.966 |
| vg0314254710 (J) | chr03 | 14254710 | G | C | 45.50% | 2.54% | C -> G | NA |
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g24970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.655; most accessible tissue: Callus, score: 16.966 |
| vg0314254857 (J) | chr03 | 14254857 | G | A | 19.60% | 52.35% | A -> G | NA |
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g24970.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.794; most accessible tissue: Callus, score: 16.602 |
| vg0314254860 (J) | chr03 | 14254860 | G | A | 34.10% | 51.33% | G -> A | NA |
LOC_Os03g24970.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g24970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.794; most accessible tissue: Callus, score: 16.602 |