15 variations found. LOC_Os08g24670 (legume lectins beta domain containing protein; putative; expressed), ranging from 14,909,181 bp to 14,909,967 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0814909193 (J) | chr08 | 14909193 | T | C | 93.40% | 0.00% | T -> C | NA |
LOC_Os08g24670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.679; most accessible tissue: Callus, score: 92.846 |
| vg0814909242 (J) | chr08 | 14909242 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os08g24670.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g24680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g24660.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.256; most accessible tissue: Callus, score: 92.846 |
| vg0814909263 (J) | chr08 | 14909263 | G | T | 68.50% | 0.42% | T -> G |
LOC_Os08g24670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g24670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.546; most accessible tissue: Callus, score: 92.846 |
|
| vg0814909467 (J) | chr08 | 14909467 | A | G | 86.00% | 0.00% | A -> G |
LOC_Os08g24670.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.467; most accessible tissue: Minghui63 flag leaf, score: 89.905 |
|
| vg0814909506 (J) | chr08 | 14909506 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os08g24670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.269; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
| vg0814909551 (J) | chr08 | 14909551 | A | G | 60.90% | 0.55% | G -> A |
mr1238 (Ind_All); LR P-value: 8.72E-08;
mr1309 (Ind_All); LR P-value: 6.73E-06; mr1510 (All); LR P-value: 1.86E-06; mr1841 (Ind_All); LR P-value: 1.74E-08; mr1900 (Ind_All); LMM P-value: 9.16E-07; LR P-value: 9.16E-07; mr1146_2 (All); LR P-value: 2.57E-16; mr1150_2 (All); LR P-value: 1.28E-31; mr1595_2 (All); LR P-value: 1.88E-11; mr1600_2 (All); LR P-value: 1.87E-08 |
LOC_Os08g24670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g24670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.299; most accessible tissue: Minghui63 flag leaf, score: 90.086 |
| vg0814909612 (J) | chr08 | 14909612 | T | C | 97.10% | 0.00% | T -> C | NA |
LOC_Os08g24670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.029; most accessible tissue: Minghui63 flag leaf, score: 91.280 |
| vg0814909649 (J) | chr08 | 14909649 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os08g24670.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os08g24680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g24660.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.525; most accessible tissue: Zhenshan97 young leaf, score: 91.232 |
| vg0814909851 (J) | chr08 | 14909851 | G | C | 96.50% | 0.00% | G -> C | NA |
LOC_Os08g24670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.585; most accessible tissue: Zhenshan97 root, score: 94.300 |
| vg0814909856 (J) | chr08 | 14909856 | C | T | 98.70% | 0.00% | C -> T |
LOC_Os08g24670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.636; most accessible tissue: Zhenshan97 root, score: 94.976 |
|
| vg0814909863 (J) | chr08 | 14909863 | A | G | 54.10% | 0.08% | G -> A |
LOC_Os08g24670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g24670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.892; most accessible tissue: Zhenshan97 root, score: 95.096 |
|
| vg0814909913 (J) | chr08 | 14909913 | C | A | 97.10% | 0.00% | C -> A | NA |
LOC_Os08g24670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.237; most accessible tissue: Zhenshan97 root, score: 95.601 |
| vg0814909930 (J) | chr08 | 14909930 | C | A | 83.50% | 0.36% | C -> A |
mr1238 (Ind_All); LR P-value: 2.03E-07;
mr1309 (Ind_All); LR P-value: 9.47E-06; mr1746 (Jap_All); LR P-value: 9.56E-08; mr1841 (Ind_All); LR P-value: 1.06E-08; mr1900 (Ind_All); LMM P-value: 2.04E-06; LR P-value: 2.04E-06; mr1194_2 (Jap_All); LR P-value: 2.72E-06; mr1238_2 (Ind_All); LR P-value: 3.75E-07; mr1484_2 (Ind_All); LR P-value: 1.56E-06; mr1841_2 (Ind_All); LR P-value: 1.31E-07; mr1900_2 (Ind_All); LR P-value: 2.46E-06 |
LOC_Os08g24670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g24670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.143; most accessible tissue: Callus, score: 96.669 |
| vg0814909963 (J) | chr08 | 14909963 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os08g24670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.195; most accessible tissue: Callus, score: 96.669 |
| STR0814909905 (J) | chr08 | 14909905 | CGCCGCC GC | CGCCGCC GA | 98.40% | 0.00% | CGCCGCCGC -> CGCCGCCGA | NA |
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