14 variations found. LOC_Os01g66020 (protein kinase family protein; putative; expressed), ranging from 38,319,059 bp to 38,321,000 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138319090 (J) | chr01 | 38319090 | G | Unkown | 90.50% | 2.88% | G -> C | NA |
LOC_Os01g66020.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g66030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.470; most accessible tissue: Minghui63 flag leaf, score: 99.528 |
| vg0138319093 (J) | chr01 | 38319093 | G | Unkown | 90.70% | 2.69% | G -> C | NA |
LOC_Os01g66020.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g66030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.414; most accessible tissue: Minghui63 flag leaf, score: 99.507 |
| vg0138319512 (J) | chr01 | 38319512 | G | T | 99.40% | 0.00% | G -> T | NA |
LOC_Os01g66020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.320; most accessible tissue: Zhenshan97 flower, score: 97.819 |
| vg0138319621 (J) | chr01 | 38319621 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os01g66020.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g66040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.679; most accessible tissue: Zhenshan97 flower, score: 97.364 |
| vg0138319704 (J) | chr01 | 38319704 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g66020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.421; most accessible tissue: Minghui63 flag leaf, score: 96.689 |
| vg0138319900 (J) | chr01 | 38319900 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g66020.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g66040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.174; most accessible tissue: Zhenshan97 flower, score: 96.440 |
| vg0138320259 (J) | chr01 | 38320259 | G | T | 82.50% | 0.13% | G -> T | NA |
LOC_Os01g66020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g66020.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.637; most accessible tissue: Zhenshan97 flower, score: 96.696 |
| vg0138320382 (J) | chr01 | 38320382 | C | G | 65.30% | 0.00% | G -> C |
Yield (All); LR P-value: 4.17E-19;
mr1024 (All); LR P-value: 3.70E-26; mr1027 (All); LR P-value: 3.43E-66; mr1134 (All); LMM P-value: 7.83E-18; LR P-value: 2.18E-108; mr1134 (Jap_All); LMM P-value: 6.62E-08; LR P-value: 1.12E-12; mr1135 (All); LMM P-value: 1.07E-18; LR P-value: 3.16E-107; mr1135 (Jap_All); LMM P-value: 4.52E-07; LR P-value: 9.24E-11; mr1152 (All); LR P-value: 2.01E-43; mr1309 (All); LR P-value: 5.46E-27; mr1375 (All); LR P-value: 5.47E-29; mr1504 (All); LMM P-value: 4.85E-16; LR P-value: 7.73E-118; mr1504 (Jap_All); LMM P-value: 4.84E-07; LR P-value: 1.58E-12; mr1517 (All); LMM P-value: 1.83E-07; LR P-value: 1.57E-101; mr1538 (All); LMM P-value: 1.37E-08; LR P-value: 3.22E-80; mr1538 (Jap_All); LMM P-value: 5.51E-06; LR P-value: 1.51E-09; mr1630 (All); LR P-value: 2.37E-10; mr1670 (All); LMM P-value: 2.73E-09; LR P-value: 1.02E-44; mr1672 (All); LMM P-value: 6.69E-14; LR P-value: 1.37E-108; mr1672 (Jap_All); LR P-value: 8.37E-07; mr1758 (All); LR P-value: 3.77E-86; mr1891 (All); LR P-value: 1.00E-40; mr1134_2 (All); LMM P-value: 4.84E-17; LR P-value: 1.19E-119; mr1134_2 (Jap_All); LMM P-value: 1.31E-11; LR P-value: 2.03E-25; mr1504_2 (All); LMM P-value: 2.31E-15; LR P-value: 6.82E-110; mr1504_2 (Jap_All); LMM P-value: 1.19E-13; LR P-value: 3.83E-27; mr1517_2 (All); LMM P-value: 9.53E-09; LR P-value: 1.16E-151; mr1517_2 (Jap_All); LR P-value: 7.08E-07; mr1538_2 (All); LMM P-value: 2.33E-09; LR P-value: 3.52E-121; mr1538_2 (Jap_All); LR P-value: 3.96E-11; mr1541_2 (All); LR P-value: 4.56E-42; mr1670_2 (All); LMM P-value: 1.59E-11; LR P-value: 1.58E-58; mr1672_2 (All); LMM P-value: 1.20E-15; LR P-value: 5.11E-148; mr1672_2 (Jap_All); LR P-value: 2.63E-13; mr1767_2 (All); LR P-value: 8.65E-15; mr1946_2 (Jap_All); LR P-value: 1.21E-07; mr1948_2 (Jap_All); LR P-value: 1.21E-07 |
LOC_Os01g66020.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.312; most accessible tissue: Zhenshan97 flower, score: 97.138 |
| vg0138320502 (J) | chr01 | 38320502 | C | T | 65.30% | 0.00% | T -> C |
Yield (All); LR P-value: 4.17E-19;
mr1024 (All); LR P-value: 3.70E-26; mr1027 (All); LR P-value: 3.43E-66; mr1134 (All); LMM P-value: 7.83E-18; LR P-value: 2.18E-108; mr1134 (Jap_All); LMM P-value: 6.62E-08; LR P-value: 1.12E-12; mr1135 (All); LMM P-value: 1.07E-18; LR P-value: 3.16E-107; mr1135 (Jap_All); LMM P-value: 4.52E-07; LR P-value: 9.24E-11; mr1152 (All); LR P-value: 2.01E-43; mr1309 (All); LR P-value: 5.46E-27; mr1375 (All); LR P-value: 5.47E-29; mr1504 (All); LMM P-value: 4.85E-16; LR P-value: 7.73E-118; mr1504 (Jap_All); LMM P-value: 4.84E-07; LR P-value: 1.58E-12; mr1517 (All); LMM P-value: 1.83E-07; LR P-value: 1.57E-101; mr1538 (All); LMM P-value: 1.37E-08; LR P-value: 3.22E-80; mr1538 (Jap_All); LMM P-value: 5.51E-06; LR P-value: 1.51E-09; mr1630 (All); LR P-value: 2.37E-10; mr1670 (All); LMM P-value: 2.73E-09; LR P-value: 1.02E-44; mr1672 (All); LMM P-value: 6.69E-14; LR P-value: 1.37E-108; mr1672 (Jap_All); LR P-value: 8.37E-07; mr1758 (All); LR P-value: 3.77E-86; mr1891 (All); LR P-value: 1.00E-40; mr1134_2 (All); LMM P-value: 4.84E-17; LR P-value: 1.19E-119; mr1134_2 (Jap_All); LMM P-value: 1.31E-11; LR P-value: 2.03E-25; mr1504_2 (All); LMM P-value: 2.31E-15; LR P-value: 6.82E-110; mr1504_2 (Jap_All); LMM P-value: 1.19E-13; LR P-value: 3.83E-27; mr1517_2 (All); LMM P-value: 9.53E-09; LR P-value: 1.16E-151; mr1517_2 (Jap_All); LR P-value: 7.08E-07; mr1538_2 (All); LMM P-value: 2.33E-09; LR P-value: 3.52E-121; mr1538_2 (Jap_All); LR P-value: 3.96E-11; mr1541_2 (All); LR P-value: 4.56E-42; mr1670_2 (All); LMM P-value: 1.59E-11; LR P-value: 1.58E-58; mr1672_2 (All); LMM P-value: 1.20E-15; LR P-value: 5.11E-148; mr1672_2 (Jap_All); LR P-value: 2.63E-13; mr1767_2 (All); LR P-value: 8.65E-15; mr1946_2 (Jap_All); LR P-value: 1.21E-07; mr1948_2 (Jap_All); LR P-value: 1.21E-07 |
LOC_Os01g66020.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.911; most accessible tissue: Zhenshan97 flower, score: 98.442 |
| vg0138320608 (J) | chr01 | 38320608 | C | T | 52.40% | 0.08% | C -> T |
mr1134 (Jap_All); LMM P-value: 9.35E-07; LR P-value: 5.32E-11;
mr1135 (Jap_All); LMM P-value: 2.38E-06; LR P-value: 1.31E-09; mr1375 (All); LR P-value: 1.53E-24; mr1504 (Jap_All); LR P-value: 2.08E-10; mr1517 (All); LMM P-value: 1.93E-09; mr1517 (Ind_All); LMM P-value: 3.21E-07; LR P-value: 3.72E-09; mr1538 (All); LMM P-value: 2.69E-10; mr1538 (Ind_All); LMM P-value: 4.80E-06; LR P-value: 8.47E-06; mr1538 (Jap_All); LR P-value: 9.54E-08; mr1672 (Jap_All); LR P-value: 8.15E-06; mr1693 (All); LR P-value: 4.26E-09; mr1134_2 (Jap_All); LMM P-value: 5.13E-10; LR P-value: 3.06E-22; mr1504_2 (Jap_All); LMM P-value: 3.38E-12; LR P-value: 1.10E-24; mr1517_2 (All); LMM P-value: 1.39E-08; mr1517_2 (Ind_All); LMM P-value: 2.27E-06; LR P-value: 1.01E-07; mr1517_2 (Jap_All); LR P-value: 1.14E-06; mr1538_2 (All); LMM P-value: 2.02E-08; mr1538_2 (Ind_All); LR P-value: 3.81E-06; mr1538_2 (Jap_All); LR P-value: 2.30E-09; mr1600_2 (All); LR P-value: 8.80E-09; mr1672_2 (Jap_All); LR P-value: 5.87E-13; mr1767_2 (Jap_All); LMM P-value: 5.88E-06; LR P-value: 5.88E-06; mr1870_2 (Jap_All); LR P-value: 1.00E-05; mr1946_2 (Jap_All); LR P-value: 9.65E-09; mr1948_2 (Jap_All); LR P-value: 9.65E-09 |
LOC_Os01g66020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g66020.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.281; most accessible tissue: Zhenshan97 flower, score: 98.436 |
| vg0138320820 (J) | chr01 | 38320820 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g66020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.329; most accessible tissue: Zhenshan97 flower, score: 98.645 |
| vg0138320877 (J) | chr01 | 38320877 | C | A | 53.20% | 0.00% | C -> A |
mr1134 (Jap_All); LR P-value: 1.23E-09;
mr1135 (Jap_All); LR P-value: 2.26E-08; mr1375 (All); LR P-value: 1.43E-24; mr1504 (Jap_All); LR P-value: 4.57E-09; mr1517 (All); LMM P-value: 1.12E-08; mr1517 (Ind_All); LMM P-value: 1.34E-06; LR P-value: 1.57E-08; mr1538 (All); LMM P-value: 4.41E-09; mr1538 (Jap_All); LR P-value: 1.23E-06; mr1134_2 (Jap_All); LMM P-value: 3.79E-08; LR P-value: 7.71E-19; mr1504_2 (Jap_All); LMM P-value: 4.34E-09; LR P-value: 6.27E-20; mr1517_2 (All); LMM P-value: 2.53E-08; mr1517_2 (Ind_All); LMM P-value: 9.15E-06; LR P-value: 3.28E-07; mr1517_2 (Jap_All); LR P-value: 2.12E-07; mr1538_2 (All); LMM P-value: 7.55E-09; mr1538_2 (Jap_All); LR P-value: 1.92E-09; mr1541_2 (All); LMM P-value: 4.72E-06; mr1600_2 (All); LR P-value: 2.18E-09; mr1672_2 (Jap_All); LR P-value: 1.86E-11; mr1946_2 (Jap_All); LR P-value: 2.36E-07; mr1948_2 (Jap_All); LR P-value: 2.36E-07 |
LOC_Os01g66020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.008; most accessible tissue: Zhenshan97 flower, score: 98.227 |
| vg0138320963 (J) | chr01 | 38320963 | G | GCCC | 94.90% | 0.00% | GCCC -> G | NA |
LOC_Os01g66020.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 86.789; most accessible tissue: Zhenshan97 flower, score: 97.656 |
| STR0138320599 (J) | chr01 | 38320599 | GTGCTGG TGT | GTGCTGG TGC | 49.60% | 0.00% | GTGCTGGTGC -> GTGCTGGTGT | NA |
|