16 variations found. LOC_Os02g16380 (retrotransposon protein; putative; unclassified), ranging from 9,333,331 bp to 9,334,745 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333385 (J) | chr02 | 9333385 | G | A | 40.40% | 50.55% | G -> A | NA |
LOC_Os02g16380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g16380.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.927; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333433 (J) | chr02 | 9333433 | C | T | 41.20% | 50.59% | C -> T | NA |
LOC_Os02g16380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g16380.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.134; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333855 (J) | chr02 | 9333855 | G | A | 42.50% | 53.96% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333893 (J) | chr02 | 9333893 | G | A | 51.50% | 45.56% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333899 (J) | chr02 | 9333899 | C | T | 51.20% | 45.05% | C -> T | NA |
LOC_Os02g16390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333915 (J) | chr02 | 9333915 | T | A | 51.70% | 45.32% | T -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333917 (J) | chr02 | 9333917 | A | G | 51.60% | 45.45% | A -> G | NA |
LOC_Os02g16390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209333926 (J) | chr02 | 9333926 | G | A | 41.60% | 49.07% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.363; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0209334207 (J) | chr02 | 9334207 | T | A | 41.50% | 56.90% | T -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334246 (J) | chr02 | 9334246 | G | A | 51.00% | 44.77% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334283 (J) | chr02 | 9334283 | G | A | 52.50% | 44.54% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334291 (J) | chr02 | 9334291 | G | A | 51.70% | 44.94% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334295 (J) | chr02 | 9334295 | C | T | 51.80% | 44.79% | C -> T | NA |
LOC_Os02g16390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334297 (J) | chr02 | 9334297 | G | A | 45.50% | 37.52% | G -> A | NA |
LOC_Os02g16390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334298 (J) | chr02 | 9334298 | G | T | 51.70% | 45.20% | G -> T | NA |
LOC_Os02g16390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16380.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0209334614 (J) | chr02 | 9334614 | A | C | 43.20% | 50.08% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g16390.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16380.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |