38 variations found. LOC_Os01g41910 (receptor-like protein kinase 5 precursor; putative; expressed), ranging from 23,770,114 bp to 23,771,515 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0123770114 (J) | chr01 | 23770114 | C | T | 29.30% | 53.83% | C -> T,CT |
LOC_Os01g41910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: CT| frameshift_variant&start_lost HIGH(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.979; most accessible tissue: Zhenshan97 flag leaf, score: 96.182 |
|
| vg0123770117 (J) | chr01 | 23770117 | C | G | 25.00% | 53.75% | G -> C |
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: C| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.981; most accessible tissue: Zhenshan97 flag leaf, score: 96.182 |
|
| vg0123770122 (J) | chr01 | 23770122 | G | A | 43.80% | 54.15% | G -> A | NA |
LOC_Os01g41910.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.230; most accessible tissue: Zhenshan97 flag leaf, score: 96.245 |
| vg0123770124 (J) | chr01 | 23770124 | T | C | 43.80% | 55.48% | T -> C | NA |
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 87.230; most accessible tissue: Zhenshan97 flag leaf, score: 96.245 |
| vg0123770125 (J) | chr01 | 23770125 | C | CTAATCA GTTAAA | 42.40% | 55.99% | C -> CTAATCAGTT AAA | NA |
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: CTAATCAGTTAAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 87.231; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0123770129 (J) | chr01 | 23770129 | T | TCAGTTA | 28.20% | 55.44% | T -> TCAGTTA,TC AGTTACAAGT TA | NA |
LOC_Os01g41910.1 Alt: TCAGTTACAAGTTA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: TCAGTTA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.231; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0123770131 (J) | chr01 | 23770131 | A | AGTTACC | 90.30% | 2.62% | A -> AGTTACC | NA |
LOC_Os01g41910.1 Alt: AGTTACC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.254; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0123770132 (J) | chr01 | 23770132 | G | GTTAC | 41.10% | 57.19% | G -> GTTAC | NA |
LOC_Os01g41910.1 Alt: GTTAC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.256; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0123770133 (J) | chr01 | 23770133 | T | TC | 41.10% | 56.41% | T -> TC,TCAA,TC A | NA |
LOC_Os01g41910.1 Alt: TCA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: TC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: TCAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 87.256; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0123770134 (J) | chr01 | 23770134 | T | A | 41.10% | 55.82% | T -> A,C | NA |
LOC_Os01g41910.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 87.257; most accessible tissue: Zhenshan97 flag leaf, score: 96.266 |
| vg0123770136 (J) | chr01 | 23770136 | A | T | 40.60% | 55.95% | A -> T,C | NA |
LOC_Os01g41910.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 87.259; most accessible tissue: Zhenshan97 flag leaf, score: 96.286 |
| vg0123770138 (J) | chr01 | 23770138 | G | A | 41.00% | 56.09% | G -> A | NA |
LOC_Os01g41910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.259; most accessible tissue: Zhenshan97 flag leaf, score: 96.286 |
| vg0123770146 (J) | chr01 | 23770146 | T | C | 99.10% | 0.00% | T -> C | NA |
LOC_Os01g41910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.897; most accessible tissue: Zhenshan97 flag leaf, score: 95.878 |
| vg0123770161 (J) | chr01 | 23770161 | T | C | 38.70% | 57.19% | T -> C | NA |
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 85.292; most accessible tissue: Zhenshan97 flag leaf, score: 95.396 |
| vg0123770165 (J) | chr01 | 23770165 | C | T | 29.10% | 56.37% | C -> T |
LOC_Os01g41910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.140; most accessible tissue: Zhenshan97 flag leaf, score: 95.262 |
|
| vg0123770173 (J) | chr01 | 23770173 | T | G | 28.80% | 60.09% | T -> G | NA |
LOC_Os01g41910.1 Alt: G| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.523; most accessible tissue: Zhenshan97 flag leaf, score: 94.782 |
| vg0123770176 (J) | chr01 | 23770176 | C | G | 99.30% | 0.36% | C -> G,T | NA |
LOC_Os01g41910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g41910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.786; most accessible tissue: Zhenshan97 flag leaf, score: 94.459 |
| vg0123770180 (J) | chr01 | 23770180 | GGAC | GATTTTG AC | 99.50% | 0.04% | GGAC -> GATTTTGAC, GATTTTGAGA C,G | NA |
LOC_Os01g41910.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g41910.1 Alt: GATTTTGAC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g41910.1 Alt: GATTTTGAGAC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 84.717; most accessible tissue: Zhenshan97 flag leaf, score: 94.439 |
| vg0123770195 (J) | chr01 | 23770195 | C | T | 62.40% | 0.00% | C -> T |
mr1174 (All); LR P-value: 8.55E-08;
mr1794 (All); LR P-value: 3.15E-09; mr1265_2 (Ind_All); LR P-value: 4.29E-06; mr1352_2 (All); LR P-value: 4.67E-17; mr1376_2 (All); LR P-value: 1.36E-07; mr1431_2 (All); LR P-value: 5.55E-08; mr1528_2 (Ind_All); LR P-value: 4.66E-06; mr1550_2 (Ind_All); LR P-value: 1.00E-05; mr1758_2 (Ind_All); LR P-value: 2.73E-08 |
LOC_Os01g41910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.105; most accessible tissue: Callus, score: 94.426 |
| vg0123770253 (J) | chr01 | 23770253 | C | A | 98.60% | 0.00% | C -> A | NA |
LOC_Os01g41910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.980; most accessible tissue: Callus, score: 94.426 |
| vg0123770388 (J) | chr01 | 23770388 | G | T | 81.30% | 0.00% | G -> T | NA |
LOC_Os01g41910.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 66.070; most accessible tissue: Minghui63 flower, score: 75.455 |
| vg0123770487 (J) | chr01 | 23770487 | T | A | 88.50% | 0.00% | T -> A |
LOC_Os01g41910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 64.795; most accessible tissue: Callus, score: 89.698 |
|
| vg0123770514 (J) | chr01 | 23770514 | G | C | 74.40% | 0.00% | C -> G |
mr1484 (All); LMM P-value: 4.02E-06; LR P-value: 9.95E-18;
mr1815 (All); LR P-value: 1.54E-06; mr1925 (Jap_All); LR P-value: 2.91E-06; mr1945 (All); LR P-value: 4.42E-12; mr1013_2 (All); LR P-value: 2.14E-15; mr1268_2 (Jap_All); LR P-value: 5.42E-06; mr1808_2 (Jap_All); LR P-value: 1.73E-07; mr1870_2 (Jap_All); LR P-value: 5.67E-06 |
LOC_Os01g41910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 63.849; most accessible tissue: Callus, score: 89.698 |
| vg0123770525 (J) | chr01 | 23770525 | G | A | 89.80% | 0.00% | G -> A |
mr1068 (Ind_All); LR P-value: 1.59E-09;
mr1094 (Ind_All); LR P-value: 2.42E-07; mr1096 (Ind_All); LR P-value: 4.40E-07; mr1111 (Ind_All); LR P-value: 8.15E-07; mr1121 (Ind_All); LR P-value: 2.22E-06; mr1125 (Ind_All); LR P-value: 5.26E-07; mr1144 (Ind_All); LR P-value: 1.20E-08; mr1155 (Ind_All); LR P-value: 5.04E-08; mr1244 (Ind_All); LR P-value: 6.25E-11; mr1561 (All); LR P-value: 3.72E-06; mr1798 (Ind_All); LR P-value: 2.26E-08; mr1068_2 (Ind_All); LR P-value: 2.63E-08; mr1121_2 (Ind_All); LR P-value: 9.56E-06; mr1144_2 (Ind_All); LR P-value: 5.36E-07; mr1155_2 (Ind_All); LR P-value: 1.06E-09; mr1220_2 (Ind_All); LR P-value: 7.99E-06; mr1244_2 (Ind_All); LR P-value: 5.23E-09; mr1380_2 (All); LR P-value: 5.71E-07; mr1380_2 (Ind_All); LR P-value: 3.75E-06; mr1458_2 (Ind_All); LR P-value: 3.66E-07; mr1561_2 (All); LR P-value: 1.37E-06; mr1653_2 (Ind_All); LR P-value: 2.10E-07; mr1798_2 (Ind_All); LR P-value: 9.44E-10; mr1996_2 (All); LR P-value: 1.69E-07; mr1996_2 (Ind_All); LR P-value: 8.66E-07 |
LOC_Os01g41910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 61.785; most accessible tissue: Callus, score: 89.698 |
| vg0123770567 (J) | chr01 | 23770567 | G | C | 62.80% | 0.00% | G -> C |
mr1174 (All); LR P-value: 5.54E-08;
mr1794 (All); LR P-value: 3.13E-09; mr1352_2 (All); LR P-value: 5.21E-17; mr1376_2 (All); LR P-value: 1.66E-07; mr1431_2 (All); LR P-value: 7.06E-08; mr1528_2 (Ind_All); LR P-value: 6.90E-06; mr1550_2 (Ind_All); LR P-value: 8.29E-06; mr1739_2 (Ind_All); LR P-value: 6.67E-09; mr1758_2 (Ind_All); LR P-value: 2.15E-08 |
LOC_Os01g41910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.240; most accessible tissue: Callus, score: 89.698 |
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