7 variations found. LOC_Os04g56380 (transposon protein; putative; unclassified; expressed), ranging from 33,614,943 bp to 33,621,407 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0433619465 (J) | chr04 | 33619465 | C | G | 44.60% | 51.52% | C -> G | NA |
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g56380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.332; most accessible tissue: Callus, score: 10.801 |
| vg0433619584 (J) | chr04 | 33619584 | T | C | 24.90% | 59.61% | T -> C | NA |
LOC_Os04g56380.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.218; most accessible tissue: Callus, score: 9.547 |
| vg0433620169 (J) | chr04 | 33620169 | G | A | 48.00% | 50.04% | G -> A | NA |
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g56380.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.681; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0433620178 (J) | chr04 | 33620178 | C | T | 48.10% | 50.21% | C -> T | NA |
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g56380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.685; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0433620195 (J) | chr04 | 33620195 | C | T | 48.30% | 50.36% | C -> T | NA |
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g56380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.685; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0433620756 (J) | chr04 | 33620756 | C | T | 49.30% | 48.37% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g56390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g56400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g56380.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0433621392 (J) | chr04 | 33621392 | C | T | 48.20% | 50.72% | C -> T | NA |
LOC_Os04g56380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g56380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 63.394; most accessible tissue: Minghui63 root, score: 88.642 |