27 variations found. LOC_Os02g57560 (tyrosine protein kinase domain containing protein; putative; expressed), ranging from 35,263,165 bp to 35,265,393 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0235263181 (J) | chr02 | 35263181 | G | A | 89.80% | 0.00% | G -> A | NA |
LOC_Os02g57560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.728; most accessible tissue: Callus, score: 85.023 |
| vg0235263192 (J) | chr02 | 35263192 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g57560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g57540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.891; most accessible tissue: Callus, score: 85.023 |
| vg0235263221 (J) | chr02 | 35263221 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os02g57560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g57540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.412; most accessible tissue: Callus, score: 85.023 |
| vg0235263261 (J) | chr02 | 35263261 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os02g57560.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g57550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.743; most accessible tissue: Callus, score: 85.023 |
| vg0235263275 (J) | chr02 | 35263275 | T | C | 62.70% | 0.08% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g57560.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57570.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.199; most accessible tissue: Callus, score: 85.023 |
|
| vg0235263336 (J) | chr02 | 35263336 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os02g57560.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g57550.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.461; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 |
| vg0235263403 (J) | chr02 | 35263403 | T | C | 83.60% | 0.00% | C -> T |
mr1575 (All); LR P-value: 4.44E-09;
mr1010_2 (All); LR P-value: 3.10E-20; mr1011_2 (All); LR P-value: 1.91E-09; mr1013_2 (All); LR P-value: 6.18E-18; mr1013_2 (Jap_All); LR P-value: 6.96E-08; mr1031_2 (All); LR P-value: 1.19E-16; mr1031_2 (Jap_All); LR P-value: 1.43E-09; mr1087_2 (Jap_All); LR P-value: 6.03E-11; mr1096_2 (Jap_All); LR P-value: 1.80E-06; mr1125_2 (Jap_All); LR P-value: 1.94E-08; mr1268_2 (Jap_All); LR P-value: 2.40E-06; mr1350_2 (Jap_All); LR P-value: 1.96E-08; mr1526_2 (Jap_All); LR P-value: 5.08E-08; mr1543_2 (Jap_All); LR P-value: 5.03E-09; mr1853_2 (All); LR P-value: 4.31E-12 |
LOC_Os02g57560.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57570.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.746; most accessible tissue: Zhenshan97 flag leaf, score: 91.286 |
| vg0235263423 (J) | chr02 | 35263423 | A | G | 96.60% | 0.00% | A -> G | NA |
LOC_Os02g57560.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57550.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57570.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.510; most accessible tissue: Zhenshan97 flag leaf, score: 92.310 |
| vg0235263508 (J) | chr02 | 35263508 | C | T | 85.20% | 0.00% | C -> T | NA |
LOC_Os02g57560.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.186; most accessible tissue: Zhenshan97 flag leaf, score: 94.459 |
| vg0235263538 (J) | chr02 | 35263538 | G | C | 83.60% | 0.00% | C -> G |
mr1031 (All); LR P-value: 3.57E-13;
mr1056 (All); LR P-value: 3.89E-13; mr1563 (All); LR P-value: 1.53E-43; mr1010_2 (All); LR P-value: 3.32E-22; mr1011_2 (All); LR P-value: 1.22E-09; mr1013_2 (All); LR P-value: 1.20E-18; mr1013_2 (Jap_All); LR P-value: 6.67E-08; mr1031_2 (All); LR P-value: 5.58E-17; mr1031_2 (Jap_All); LR P-value: 1.71E-09; mr1047_2 (Jap_All); LR P-value: 5.29E-07; mr1087_2 (Jap_All); LR P-value: 1.13E-10; mr1096_2 (Jap_All); LR P-value: 1.67E-06; mr1125_2 (Jap_All); LR P-value: 2.87E-08; mr1268_2 (Jap_All); LR P-value: 5.18E-06; mr1310_2 (All); LR P-value: 1.23E-31; mr1350_2 (Jap_All); LR P-value: 8.68E-09; mr1526_2 (Jap_All); LR P-value: 5.11E-08; mr1543_2 (Jap_All); LR P-value: 3.55E-09; mr1844_2 (All); LR P-value: 4.67E-11; mr1853_2 (All); LR P-value: 5.76E-12 |
LOC_Os02g57560.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.662; most accessible tissue: Zhenshan97 flag leaf, score: 94.708 |
| vg0235263607 (J) | chr02 | 35263607 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g57560.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g57550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.322; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 |
| vg0235263623 (J) | chr02 | 35263623 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os02g57560.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.790; most accessible tissue: Zhenshan97 flag leaf, score: 95.842 |
| vg0235263949 (J) | chr02 | 35263949 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os02g57560.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os02g57550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.640; most accessible tissue: Zhenshan97 flag leaf, score: 96.849 |
| vg0235264051 (J) | chr02 | 35264051 | G | A | 75.40% | 0.00% | A -> G |
Grain_width (All); LR P-value: 3.53E-53;
mr1136 (All); LR P-value: 3.53E-43; mr1188 (All); LMM P-value: 1.17E-07; LR P-value: 3.65E-12; mr1188 (Jap_All); LMM P-value: 5.10E-06; LR P-value: 4.10E-07; mr1448 (All); LR P-value: 2.17E-37; mr1448 (Jap_All); LR P-value: 2.40E-06; mr1636 (All); LR P-value: 2.76E-12; mr1653 (All); LR P-value: 4.11E-14; mr1698 (All); LR P-value: 1.22E-22; mr1125_2 (All); LMM P-value: 9.71E-07; LR P-value: 4.21E-64; mr1125_2 (Jap_All); LMM P-value: 5.23E-06; LR P-value: 1.38E-09; mr1188_2 (All); LR P-value: 1.32E-11; mr1188_2 (Jap_All); LR P-value: 3.89E-07; mr1448_2 (All); LR P-value: 1.57E-37; mr1695_2 (All); LR P-value: 1.84E-58 |
LOC_Os02g57560.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.200; most accessible tissue: Zhenshan97 flag leaf, score: 96.568 |
| vg0235264072 (J) | chr02 | 35264072 | C | T | 96.60% | 0.00% | C -> T | NA |
LOC_Os02g57560.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.847; most accessible tissue: Zhenshan97 flag leaf, score: 96.326 |
| vg0235264113 (J) | chr02 | 35264113 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os02g57560.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.490; most accessible tissue: Zhenshan97 flag leaf, score: 96.040 |
| vg0235264329 (J) | chr02 | 35264329 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os02g57560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.210; most accessible tissue: Zhenshan97 flag leaf, score: 95.562 |
| vg0235264607 (J) | chr02 | 35264607 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os02g57560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.471; most accessible tissue: Zhenshan97 flag leaf, score: 92.878 |
| vg0235264739 (J) | chr02 | 35264739 | C | T | 71.60% | 0.00% | T -> C |
LOC_Os02g57550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57570.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57580.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.092; most accessible tissue: Zhenshan97 flag leaf, score: 91.045 |
|
| vg0235264842 (J) | chr02 | 35264842 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os02g57550.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g57570.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57580.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57560.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.699; most accessible tissue: Zhenshan97 flag leaf, score: 88.280 |
| vg0235264870 (J) | chr02 | 35264870 | T | A | 98.70% | 0.00% | T -> A | NA |
LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.112; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 |
| vg0235264873 (J) | chr02 | 35264873 | T | A | 87.50% | 0.00% | T -> A | NA |
LOC_Os02g57550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57570.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.847; most accessible tissue: Zhenshan97 flag leaf, score: 91.771 |
| vg0235264971 (J) | chr02 | 35264971 | G | T | 85.20% | 0.00% | G -> T | NA |
LOC_Os02g57550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57570.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57580.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.128; most accessible tissue: Zhenshan97 flag leaf, score: 93.341 |
| vg0235264997 (J) | chr02 | 35264997 | T | C | 98.80% | 0.00% | T -> C | NA |
LOC_Os02g57550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g57570.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57580.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g57560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.006; most accessible tissue: Zhenshan97 flag leaf, score: 94.746 |
| vg0235265038 (J) | chr02 | 35265038 | T | C | 96.60% | 0.00% | T -> C | NA |
LOC_Os02g57560.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.157; most accessible tissue: Zhenshan97 flag leaf, score: 96.442 |
| vg0235265106 (J) | chr02 | 35265106 | C | G | 71.60% | 0.00% | G -> C |
mr1188 (Jap_All); LMM P-value: 5.10E-06; LR P-value: 4.10E-07;
mr1448 (All); LMM P-value: 2.90E-06; LR P-value: 1.34E-37; mr1448 (Jap_All); LR P-value: 2.40E-06; mr1125_2 (All); LR P-value: 7.59E-64; mr1125_2 (Jap_All); LMM P-value: 5.23E-06; LR P-value: 1.38E-09; mr1188_2 (Jap_All); LR P-value: 3.89E-07 |
LOC_Os02g57560.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.702; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 |
| vg0235265205 (J) | chr02 | 35265205 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g57560.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g57550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57570.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g57580.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.260; most accessible tissue: Zhenshan97 flag leaf, score: 98.561 |