11 variations found. LOC_Os04g17920 (retrotransposon protein; putative; unclassified; expressed), ranging from 9,852,670 bp to 9,854,775 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409852831 (J) | chr04 | 9852831 | A | G | 0.10% | 98.96% | G -> A | NA |
LOC_Os04g17920.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g17910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g17900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.231; most accessible tissue: Zhenshan97 root, score: 23.888 |
| vg0409854362 (J) | chr04 | 9854362 | C | T | 7.00% | 79.71% | C -> T | NA |
LOC_Os04g17920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17920.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854364 (J) | chr04 | 9854364 | C | T | 10.40% | 71.29% | C -> T | NA |
LOC_Os04g17920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854378 (J) | chr04 | 9854378 | GC | G | 29.80% | 65.72% | GC -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17920.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os04g17910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854386 (J) | chr04 | 9854386 | G | A | 30.10% | 65.70% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854400 (J) | chr04 | 9854400 | G | C | 23.20% | 71.27% | G -> C | NA |
LOC_Os04g17910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854402 (J) | chr04 | 9854402 | T | A | 23.20% | 71.16% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854412 (J) | chr04 | 9854412 | C | T | 32.90% | 63.42% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854434 (J) | chr04 | 9854434 | G | A | 32.70% | 61.87% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854438 (J) | chr04 | 9854438 | T | A | 27.10% | 64.01% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0409854752 (J) | chr04 | 9854752 | G | A | 22.70% | 72.49% | G -> A | NA |
LOC_Os04g17920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 19.623; most accessible tissue: Minghui63 panicle, score: 25.313 |