23 variations found. LOC_Os12g44320 (carbohydrate binding protein; putative; expressed), ranging from 27,474,467 bp to 27,477,302 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1227474732 (J) | chr12 | 27474732 | G | T | 81.30% | 0.00% | G -> T,A | NA |
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g44310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44320.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 94.495; most accessible tissue: Minghui63 root, score: 98.180 |
| vg1227474734 (J) | chr12 | 27474734 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os12g44320.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.492; most accessible tissue: Minghui63 root, score: 98.180 |
| vg1227474791 (J) | chr12 | 27474791 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os12g44320.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.281; most accessible tissue: Minghui63 root, score: 97.870 |
| vg1227474939 (J) | chr12 | 27474939 | A | G | 62.30% | 0.00% | G -> A |
mr1020 (All); LR P-value: 6.13E-22;
mr1021 (All); LR P-value: 5.82E-21; mr1170 (All); LR P-value: 5.56E-12; mr1326 (All); LR P-value: 3.43E-13; mr1477 (All); LR P-value: 8.20E-21; mr1541 (All); LR P-value: 8.10E-20; mr1558 (All); LR P-value: 3.67E-46; mr1580 (All); LR P-value: 1.56E-19; mr1591 (All); LR P-value: 4.74E-44; mr1718 (All); LR P-value: 2.19E-77; mr1793 (All); LR P-value: 3.72E-29; mr1890 (All); LR P-value: 1.40E-38; mr1916 (All); LR P-value: 7.00E-15; mr1323_2 (All); LR P-value: 4.82E-26; mr1325_2 (All); LR P-value: 1.54E-12; mr1326_2 (All); LR P-value: 7.31E-14; mr1558_2 (All); LR P-value: 8.70E-58; mr1671_2 (All); LR P-value: 2.57E-82; mr1686_2 (All); LR P-value: 4.30E-15; mr1721_2 (All); LR P-value: 1.05E-47; mr1913_2 (All); LR P-value: 4.70E-31; mr1916_2 (All); LR P-value: 3.49E-24 |
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.134; most accessible tissue: Zhenshan97 flag leaf, score: 97.697 |
| vg1227474964 (J) | chr12 | 27474964 | G | A | 64.80% | 0.00% | A -> G | NA |
LOC_Os12g44320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.228; most accessible tissue: Zhenshan97 flag leaf, score: 97.692 |
| vg1227474982 (J) | chr12 | 27474982 | T | A | 99.70% | 0.00% | T -> A | NA |
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g44310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.250; most accessible tissue: Zhenshan97 flag leaf, score: 97.678 |
| vg1227475031 (J) | chr12 | 27475031 | C | A | 97.50% | 0.00% | C -> A | NA |
LOC_Os12g44320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.818; most accessible tissue: Zhenshan97 flag leaf, score: 97.504 |
| vg1227475445 (J) | chr12 | 27475445 | C | A | 99.30% | 0.00% | C -> A | NA |
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.069; most accessible tissue: Zhenshan97 flag leaf, score: 97.078 |
| vg1227475472 (J) | chr12 | 27475472 | G | T | 64.90% | 0.00% | T -> G | NA |
LOC_Os12g44320.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.037; most accessible tissue: Zhenshan97 flag leaf, score: 97.166 |
| vg1227475712 (J) | chr12 | 27475712 | G | T | 64.90% | 0.00% | T -> G,C | NA |
LOC_Os12g44320.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os12g44310.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44320.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.662; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg1227475940 (J) | chr12 | 27475940 | CAAGAAG AAG | C | 58.00% | 0.00% | C -> CAAGAAGAAG ,CAAGAAG,C AAG,CAAGAA GAAGAAG | NA |
LOC_Os12g44320.1 Alt: CAAGAAGAAG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g44320.1 Alt: CAAGAAGAAGAAG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os12g44320.1 Alt: CAAG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os12g44320.1 Alt: CAAGAAG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 91.254; most accessible tissue: Zhenshan97 flag leaf, score: 96.203 |
| vg1227476006 (J) | chr12 | 27476006 | G | A | 96.70% | 0.00% | G -> A | NA |
LOC_Os12g44320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.925; most accessible tissue: Zhenshan97 flag leaf, score: 97.166 |
| vg1227476198 (J) | chr12 | 27476198 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os12g44320.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g44310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.762; most accessible tissue: Zhenshan97 flag leaf, score: 97.854 |
| vg1227476244 (J) | chr12 | 27476244 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g44310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.415; most accessible tissue: Zhenshan97 flag leaf, score: 98.188 |
| vg1227476480 (J) | chr12 | 27476480 | T | C | 62.30% | 0.00% | C -> T,G |
mr1021 (All); LR P-value: 2.25E-20;
mr1170 (All); LR P-value: 3.07E-12; mr1326 (All); LR P-value: 6.20E-13; mr1477 (All); LR P-value: 1.86E-20; mr1541 (All); LR P-value: 4.83E-20; mr1580 (All); LR P-value: 1.03E-19; mr1591 (All); LR P-value: 8.11E-45; mr1671 (All); LR P-value: 1.08E-57; mr1718 (All); LR P-value: 9.96E-79; mr1793 (All); LR P-value: 2.17E-28; mr1890 (All); LR P-value: 8.79E-39; mr1891 (All); LR P-value: 6.82E-39; mr1325_2 (All); LR P-value: 2.65E-12; mr1326_2 (All); LR P-value: 1.71E-13; mr1558_2 (All); LR P-value: 6.12E-57; mr1671_2 (All); LR P-value: 3.95E-83; mr1721_2 (All); LR P-value: 1.62E-47 |
LOC_Os12g44320.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os12g44310.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44320.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.975; most accessible tissue: Zhenshan97 flag leaf, score: 98.360 |
| vg1227476532 (J) | chr12 | 27476532 | G | A | 64.80% | 0.02% | A -> G | NA |
LOC_Os12g44320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g44320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 95.072; most accessible tissue: Zhenshan97 flag leaf, score: 98.467 |
| vg1227476783 (J) | chr12 | 27476783 | C | A | 96.70% | 0.00% | C -> A | NA |
LOC_Os12g44320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.704; most accessible tissue: Minghui63 root, score: 98.369 |
| vg1227476993 (J) | chr12 | 27476993 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g44320.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g44310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.476; most accessible tissue: Minghui63 root, score: 98.918 |
| vg1227477001 (J) | chr12 | 27477001 | A | T | 62.30% | 0.02% | T -> A |
mr1021 (All); LR P-value: 2.83E-20;
mr1170 (All); LR P-value: 4.26E-12; mr1326 (All); LR P-value: 8.61E-13; mr1477 (All); LR P-value: 3.86E-20; mr1509 (All); LR P-value: 4.46E-41; mr1541 (All); LR P-value: 1.11E-19; mr1558 (All); LR P-value: 8.71E-47; mr1580 (All); LR P-value: 6.47E-20; mr1591 (All); LR P-value: 5.51E-45; mr1671 (All); LR P-value: 4.49E-58; mr1718 (All); LR P-value: 9.90E-78; mr1793 (All); LR P-value: 1.77E-28; mr1890 (All); LR P-value: 2.55E-38; mr1326_2 (All); LR P-value: 1.74E-13; mr1558_2 (All); LR P-value: 3.19E-58; mr1671_2 (All); LR P-value: 5.67E-84; mr1721_2 (All); LR P-value: 2.14E-47; mr1913_2 (All); LR P-value: 7.83E-31 |
LOC_Os12g44320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g44320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 97.468; most accessible tissue: Minghui63 root, score: 98.916 |
| vg1227477222 (J) | chr12 | 27477222 | TGA | T | 64.30% | 0.02% | T -> TGA,TGATAG | NA |
LOC_Os12g44320.1 Alt: TGATAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44330.1 Alt: TGATAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44330.2 Alt: TGATAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44320.1 Alt: TGA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44330.1 Alt: TGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44330.2 Alt: TGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.669; most accessible tissue: Zhenshan97 root, score: 99.146 |
| vg1227477224 (J) | chr12 | 27477224 | AG | A | 64.80% | 0.02% | A -> AG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g44320.1 Alt: AG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44330.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44330.2 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.664; most accessible tissue: Zhenshan97 root, score: 99.149 |
| vg1227477280 (J) | chr12 | 27477280 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os12g44320.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g44330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.344; most accessible tissue: Zhenshan97 root, score: 99.198 |
| STR1227476003 (J) | chr12 | 27476003 | GCAGCAG GCGT | GCAACAG GCGT | 98.80% | 0.00% | GCAGCAGGCG T -> GCAACAGGCG T | NA |
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