41 variations found. LOC_Os03g48120 (BTB%2FPOZ domain containing protein; putative), ranging from 27,370,118 bp to 27,370,836 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 |
---|---|---|---|---|---|---|---|---|---|
vg0327370190 (J) | chr03 | 27370190 | C | T | 94.90% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.232; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
vg0327370193 (J) | chr03 | 27370193 | C | T | 65.30% | 0.15% | T -> C | NA |
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.494; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
vg0327370221 (J) | chr03 | 27370221 | T | C | 64.40% | 0.23% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
vg0327370239 (J) | chr03 | 27370239 | G | C | 66.00% | 0.00% | C -> G | NA |
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 78.061; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
vg0327370258 (J) | chr03 | 27370258 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.529; most accessible tissue: Zhenshan97 panicle, score: 87.764 |
vg0327370277 (J) | chr03 | 27370277 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.359; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
vg0327370301 (J) | chr03 | 27370301 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.861; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
vg0327370317 (J) | chr03 | 27370317 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.162; most accessible tissue: Zhenshan97 panicle, score: 89.846 |
vg0327370322 (J) | chr03 | 27370322 | G | A | 65.80% | 0.21% | A -> G | NA |
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 81.793; most accessible tissue: Zhenshan97 panicle, score: 90.061 |
vg0327370337 (J) | chr03 | 27370337 | A | C | 50.80% | 0.19% | C -> A |
LOC_Os03g48120.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.878; most accessible tissue: Zhenshan97 panicle, score: 90.268 |
|
vg0327370363 (J) | chr03 | 27370363 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.125; most accessible tissue: Zhenshan97 panicle, score: 90.661 |
vg0327370369 (J) | chr03 | 27370369 | T | C | 64.50% | 0.25% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.300; most accessible tissue: Zhenshan97 panicle, score: 90.661 |
vg0327370424 (J) | chr03 | 27370424 | C | T | 65.90% | 0.00% | T -> C | NA |
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g48120.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.264; most accessible tissue: Zhenshan97 panicle, score: 90.661 |
vg0327370425 (J) | chr03 | 27370425 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g48120.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.911; most accessible tissue: Zhenshan97 panicle, score: 90.661 |
vg0327370471 (J) | chr03 | 27370471 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.515; most accessible tissue: Zhenshan97 panicle, score: 91.030 |
vg0327370496 (J) | chr03 | 27370496 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.442; most accessible tissue: Zhenshan97 panicle, score: 90.061 |
vg0327370525 (J) | chr03 | 27370525 | C | G | 98.70% | 0.00% | C -> G | NA |
LOC_Os03g48120.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.166; most accessible tissue: Zhenshan97 panicle, score: 91.374 |
vg0327370526 (J) | chr03 | 27370526 | A | G | 64.50% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.124; most accessible tissue: Zhenshan97 panicle, score: 91.374 |
vg0327370540 (J) | chr03 | 27370540 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.207; most accessible tissue: Zhenshan97 panicle, score: 90.467 |
vg0327370551 (J) | chr03 | 27370551 | C | CAA | 99.80% | 0.00% | C -> CAA | NA |
The average chromatin accessibility score: 82.765; most accessible tissue: Zhenshan97 panicle, score: 90.467
|
vg0327370552 (J) | chr03 | 27370552 | G | GGAGCTC CATGGTG GACTCCG CCATGGA CCCA | 99.80% | 0.00% | G -> GGAGCTCCAT GGTGGACTCC GCCATGGACC CA | NA |
The average chromatin accessibility score: 82.765; most accessible tissue: Zhenshan97 panicle, score: 90.467
|
vg0327370572 (J) | chr03 | 27370572 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.969; most accessible tissue: Zhenshan97 panicle, score: 90.268 |
vg0327370583 (J) | chr03 | 27370583 | A | G | 65.30% | 0.23% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.160; most accessible tissue: Zhenshan97 panicle, score: 90.467 |
vg0327370585 (J) | chr03 | 27370585 | A | G | 64.40% | 0.23% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.295; most accessible tissue: Zhenshan97 panicle, score: 90.467 |
vg0327370609 (J) | chr03 | 27370609 | G | A | 65.50% | 0.23% | A -> G | NA |
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.641; most accessible tissue: Zhenshan97 panicle, score: 90.268 |
vg0327370621 (J) | chr03 | 27370621 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.049; most accessible tissue: Zhenshan97 panicle, score: 90.467 |
vg0327370626 (J) | chr03 | 27370626 | C | T | 91.60% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.967; most accessible tissue: Zhenshan97 panicle, score: 90.268 |
vg0327370634 (J) | chr03 | 27370634 | G | A | 65.80% | 0.23% | A -> G | NA |
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 79.520; most accessible tissue: Zhenshan97 panicle, score: 90.061 |
vg0327370639 (J) | chr03 | 27370639 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.938; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
vg0327370647 (J) | chr03 | 27370647 | T | C | 64.50% | 0.25% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.076; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
vg0327370655 (J) | chr03 | 27370655 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.058; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
vg0327370661 (J) | chr03 | 27370661 | A | G | 65.80% | 0.06% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.914; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
vg0327370669 (J) | chr03 | 27370669 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.451; most accessible tissue: Zhenshan97 panicle, score: 87.764 |
vg0327370671 (J) | chr03 | 27370671 | T | C | 65.30% | 0.06% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.369; most accessible tissue: Zhenshan97 panicle, score: 87.764 |
vg0327370685 (J) | chr03 | 27370685 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.159; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
vg0327370717 (J) | chr03 | 27370717 | A | G | 64.50% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.225; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
vg0327370726 (J) | chr03 | 27370726 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.232; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
vg0327370737 (J) | chr03 | 27370737 | T | C | 99.30% | 0.00% | T -> C | NA |
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.076; most accessible tissue: Zhenshan97 panicle, score: 84.374 |
vg0327370785 (J) | chr03 | 27370785 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.611; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0327370818 (J) | chr03 | 27370818 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.026; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
vg0327370831 (J) | chr03 | 27370831 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g48120.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.739; most accessible tissue: Zhenshan97 panicle, score: 77.482 |