7 variations found. LOC_Os01g11450 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 6,163,186 bp to 6,166,385 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0106163187 (J) | chr01 | 6163187 | T | C | 22.50% | 74.99% | T -> C | NA |
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g11450.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar) The average chromatin accessibility score: 5.697; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0106164798 (J) | chr01 | 6164798 | G | C | 23.10% | 60.43% | G -> C | NA |
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g11450.1 Alt: C/stop_gained(CooVar) The average chromatin accessibility score: 4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 |
| vg0106164859 (J) | chr01 | 6164859 | G | A | 22.40% | 62.53% | G -> A | NA |
LOC_Os01g11450.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 |
| vg0106165093 (J) | chr01 | 6165093 | T | C | 23.20% | 73.09% | T -> C | NA |
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g11450.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.784; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0106165263 (J) | chr01 | 6165263 | C | T | 22.90% | 73.76% | C -> T | NA |
LOC_Os01g11450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.909; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0106165875 (J) | chr01 | 6165875 | C | T | 0.70% | 96.47% | C -> T | NA |
LOC_Os01g11450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.658; most accessible tissue: Minghui63 flag leaf, score: 13.491 |
| vg0106165909 (J) | chr01 | 6165909 | A | G | 0.70% | 97.38% | A -> G | NA |
LOC_Os01g11450.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g11450.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.557; most accessible tissue: Minghui63 flag leaf, score: 12.986 |