33 variations found. LOC_Os06g41820 (SMP-30%2FGluconolaconase%2FLRE-like region containing protein; expressed), ranging from 25,080,892 bp to 25,081,930 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 |
---|---|---|---|---|---|---|---|---|---|
vg0625080926 (J) | chr06 | 25080926 | T | C | 58.10% | 0.36% | T -> C | NA |
LOC_Os06g41820.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41820.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.468; most accessible tissue: Callus, score: 77.910 |
vg0625080985 (J) | chr06 | 25080985 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os06g41810.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41830.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.509; most accessible tissue: Callus, score: 77.910 |
vg0625081025 (J) | chr06 | 25081025 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.175; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0625081034 (J) | chr06 | 25081034 | T | C | 98.70% | 0.00% | T -> C | NA |
LOC_Os06g41820.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.253; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0625081040 (J) | chr06 | 25081040 | T | A | 98.70% | 0.00% | T -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.223; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0625081053 (J) | chr06 | 25081053 | T | C | 98.60% | 0.00% | T -> C | NA |
LOC_Os06g41820.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.128; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
vg0625081055 (J) | chr06 | 25081055 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.158; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
vg0625081150 (J) | chr06 | 25081150 | A | G | 98.70% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.608; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
vg0625081154 (J) | chr06 | 25081154 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.621; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
vg0625081155 (J) | chr06 | 25081155 | A | G | 98.70% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.621; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
vg0625081166 (J) | chr06 | 25081166 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.159; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081169 (J) | chr06 | 25081169 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os06g41820.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.161; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081172 (J) | chr06 | 25081172 | A | G | 98.80% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.178; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081176 (J) | chr06 | 25081176 | A | G | 98.80% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.138; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081177 (J) | chr06 | 25081177 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os06g41820.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.138; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081200 (J) | chr06 | 25081200 | CTCA | C | 63.20% | 0.06% | C -> CTCA | NA |
LOC_Os06g41820.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os06g41820.1 Alt: CTCA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 73.268; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
vg0625081214 (J) | chr06 | 25081214 | G | C | 98.70% | 0.00% | G -> C | NA |
LOC_Os06g41820.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.421; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
vg0625081217 (J) | chr06 | 25081217 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os06g41810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41830.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.497; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
vg0625081223 (J) | chr06 | 25081223 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os06g41820.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.084; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
vg0625081234 (J) | chr06 | 25081234 | A | G | 98.70% | 0.00% | A -> G | NA |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.477; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
vg0625081292 (J) | chr06 | 25081292 | C | A | 59.50% | 0.00% | A -> C |
LOC_Os06g41820.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.356; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
|
vg0625081397 (J) | chr06 | 25081397 | G | A | 94.70% | 0.00% | G -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.529; most accessible tissue: Zhenshan97 flag leaf, score: 89.624 |
vg0625081400 (J) | chr06 | 25081400 | A | G | 52.00% | 0.42% | A -> G |
LOC_Os06g41820.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41820.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.314; most accessible tissue: Zhenshan97 flag leaf, score: 89.624 |
|
vg0625081409 (J) | chr06 | 25081409 | C | A | 57.80% | 0.02% | C -> A | NA |
LOC_Os06g41820.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41820.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.931; most accessible tissue: Zhenshan97 flag leaf, score: 90.791 |
vg0625081563 (J) | chr06 | 25081563 | A | T | 89.60% | 0.00% | A -> T | NA |
LOC_Os06g41820.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.726; most accessible tissue: Zhenshan97 flower, score: 92.539 |
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