15 variations found. LOC_Os01g37660 (hypothetical protein), ranging from 21,065,460 bp to 21,065,910 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065460 (J) | chr01 | 21065460 | G | T | 96.00% | 1.95% | G -> T | NA |
LOC_Os01g37650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g37660.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g37670.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g37650-LOC_Os01g37660 Alt: T| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 50.743; most accessible tissue: Zhenshan97 flag leaf, score: 79.935 |
| vg0121065536 (J) | chr01 | 21065536 | G | A | 96.20% | 2.03% | G -> A | NA |
LOC_Os01g37660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 49.703; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 |
| vg0121065560 (J) | chr01 | 21065560 | TG | T | 97.40% | 2.09% | TG -> T | NA |
LOC_Os01g37660.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.167; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 |
| vg0121065562 (J) | chr01 | 21065562 | G | A | 97.40% | 2.29% | G -> A | NA |
LOC_Os01g37660.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.219; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 |
| vg0121065564 (J) | chr01 | 21065564 | GGAA | AGAA | 96.40% | 2.16% | GGAA -> AGAA,G | NA |
LOC_Os01g37660.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g37660.1 Alt: AGAA| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.328; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 |
| vg0121065569 (J) | chr01 | 21065569 | A | G | 97.00% | 2.16% | A -> G | NA |
LOC_Os01g37660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.724; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 |
| vg0121065598 (J) | chr01 | 21065598 | G | A | 96.50% | 2.09% | G -> A | NA |
LOC_Os01g37660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 45.175; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 |
| vg0121065602 (J) | chr01 | 21065602 | C | T | 96.00% | 2.09% | C -> T | NA |
LOC_Os01g37660.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 44.981; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 |
| vg0121065635 (J) | chr01 | 21065635 | C | T | 97.60% | 1.97% | C -> T | NA |
LOC_Os01g37660.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 42.878; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 |
| vg0121065693 (J) | chr01 | 21065693 | C | CTGA | 97.60% | 1.99% | C -> CTGA | NA |
LOC_Os01g37660.1 Alt: CTGA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 45.887; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 |
| vg0121065713 (J) | chr01 | 21065713 | T | C | 97.60% | 1.97% | T -> C | NA |
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g37660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 46.405; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 |
| vg0121065777 (J) | chr01 | 21065777 | A | G | 97.60% | 2.03% | A -> G | NA |
LOC_Os01g37660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 42.285; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 |
| vg0121065810 (J) | chr01 | 21065810 | G | T | 97.50% | 1.95% | G -> T | NA |
LOC_Os01g37660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.376; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 |
| vg0121065811 (J) | chr01 | 21065811 | G | A | 94.80% | 1.95% | G -> A | NA |
LOC_Os01g37660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.376; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 |
| vg0121065884 (J) | chr01 | 21065884 | A | G | 96.30% | 2.14% | A -> G | NA |
LOC_Os01g37660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g37660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 42.368; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 |