11 variations found. LOC_Os04g46320 (inactive receptor kinase At2g26730 precursor; putative; expressed), ranging from 27,460,826 bp to 27,463,489 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0427461580 (J) | chr04 | 27461580 | G | T | 99.90% | 0.00% | G -> T,A | NA |
LOC_Os04g46320.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os04g46310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46320.1 Alt: T| synonymous_variant LOW(snpEff) LOC_Os04g46310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46310.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.645; most accessible tissue: Minghui63 flower, score: 90.298 |
| vg0427461721 (J) | chr04 | 27461721 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os04g46320.1 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)
LOC_Os04g46310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46310.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.647; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
| vg0427461787 (J) | chr04 | 27461787 | G | A | 79.80% | 0.06% | G -> A |
mr1031 (Ind_All); LR P-value: 1.40E-06;
mr1035 (Ind_All); LR P-value: 9.82E-06; mr1050 (Ind_All); LR P-value: 1.17E-07; mr1155 (Ind_All); LR P-value: 1.96E-06; mr1169 (Ind_All); LR P-value: 4.06E-06; mr1174 (Ind_All); LR P-value: 1.07E-07; mr1193 (All); LR P-value: 4.37E-08; mr1272 (Ind_All); LR P-value: 3.83E-07; mr1291 (All); LR P-value: 6.35E-07; mr1354 (Ind_All); LR P-value: 1.33E-08; mr1502 (Ind_All); LR P-value: 6.99E-06; mr1536 (Ind_All); LR P-value: 6.30E-06; mr1626 (Ind_All); LR P-value: 1.42E-06; mr1709 (All); LR P-value: 7.98E-07; mr1722 (All); LR P-value: 4.52E-10; mr1733 (Ind_All); LR P-value: 8.52E-07; mr1798 (Ind_All); LR P-value: 2.62E-07; mr1815 (All); LR P-value: 2.66E-06; mr1935 (Ind_All); LR P-value: 1.37E-09; mr1965 (Ind_All); LR P-value: 8.51E-06; mr1974 (Ind_All); LR P-value: 8.04E-06; mr1035_2 (Ind_All); LMM P-value: 2.27E-06; LR P-value: 2.27E-06; mr1158_2 (All); LR P-value: 6.67E-08; mr1167_2 (Ind_All); LR P-value: 4.46E-07; mr1170_2 (All); LR P-value: 3.05E-08; mr1174_2 (Ind_All); LR P-value: 3.87E-07; mr1272_2 (Ind_All); LR P-value: 2.60E-06; mr1354_2 (Ind_All); LR P-value: 1.81E-09; mr1355_2 (Ind_All); LR P-value: 8.42E-06; mr1439_2 (Ind_All); LR P-value: 3.59E-06; mr1478_2 (Ind_All); LR P-value: 3.43E-07; mr1631_2 (Ind_All); LR P-value: 6.80E-07; mr1706_2 (All); LR P-value: 4.28E-06; mr1709_2 (All); LR P-value: 2.86E-08; mr1715_2 (Ind_All); LR P-value: 8.46E-13; mr1719_2 (Ind_All); LR P-value: 8.16E-06; mr1720_2 (Ind_All); LR P-value: 1.31E-07; mr1733_2 (Ind_All); LR P-value: 9.98E-07; mr1895_2 (Ind_All); LR P-value: 4.02E-08; mr1904_2 (Ind_All); LR P-value: 5.28E-07; mr1931_2 (All); LR P-value: 3.48E-08; mr1931_2 (Ind_All); LR P-value: 4.65E-08; mr1942_2 (Ind_All); LR P-value: 6.16E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46320.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.175; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
| vg0427462098 (J) | chr04 | 27462098 | A | G | 53.40% | 0.38% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46320.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.948; most accessible tissue: Minghui63 flower, score: 80.968 |
|
| vg0427462344 (J) | chr04 | 27462344 | A | C | 53.40% | 0.00% | C -> A |
LOC_Os04g46310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46320.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.532; most accessible tissue: Minghui63 flower, score: 77.024 |
|
| vg0427462595 (J) | chr04 | 27462595 | T | C | 79.90% | 0.00% | T -> C |
mr1031 (Ind_All); LR P-value: 1.40E-06;
mr1035 (Ind_All); LR P-value: 9.82E-06; mr1050 (Ind_All); LR P-value: 1.17E-07; mr1155 (Ind_All); LR P-value: 1.96E-06; mr1169 (Ind_All); LR P-value: 4.06E-06; mr1174 (Ind_All); LR P-value: 1.07E-07; mr1193 (All); LR P-value: 4.37E-08; mr1272 (Ind_All); LR P-value: 3.83E-07; mr1291 (All); LR P-value: 6.35E-07; mr1354 (Ind_All); LR P-value: 1.33E-08; mr1502 (Ind_All); LR P-value: 6.99E-06; mr1536 (Ind_All); LR P-value: 6.30E-06; mr1626 (Ind_All); LR P-value: 1.42E-06; mr1709 (All); LR P-value: 7.98E-07; mr1722 (All); LR P-value: 4.52E-10; mr1733 (Ind_All); LR P-value: 8.52E-07; mr1798 (Ind_All); LR P-value: 2.62E-07; mr1815 (All); LR P-value: 2.66E-06; mr1935 (Ind_All); LR P-value: 1.37E-09; mr1965 (Ind_All); LR P-value: 8.51E-06; mr1974 (Ind_All); LR P-value: 8.04E-06; mr1035_2 (Ind_All); LMM P-value: 2.27E-06; LR P-value: 2.27E-06; mr1158_2 (All); LR P-value: 6.67E-08; mr1167_2 (Ind_All); LR P-value: 4.46E-07; mr1170_2 (All); LR P-value: 3.05E-08; mr1174_2 (Ind_All); LR P-value: 3.87E-07; mr1272_2 (Ind_All); LR P-value: 2.60E-06; mr1354_2 (Ind_All); LR P-value: 1.81E-09; mr1355_2 (Ind_All); LR P-value: 8.42E-06; mr1439_2 (Ind_All); LR P-value: 3.59E-06; mr1478_2 (Ind_All); LR P-value: 3.43E-07; mr1631_2 (Ind_All); LR P-value: 6.80E-07; mr1706_2 (All); LR P-value: 4.28E-06; mr1709_2 (All); LR P-value: 2.86E-08; mr1715_2 (Ind_All); LR P-value: 8.46E-13; mr1719_2 (Ind_All); LR P-value: 8.16E-06; mr1720_2 (Ind_All); LR P-value: 1.31E-07; mr1733_2 (Ind_All); LR P-value: 9.98E-07; mr1895_2 (Ind_All); LR P-value: 4.02E-08; mr1904_2 (Ind_All); LR P-value: 5.28E-07; mr1931_2 (All); LR P-value: 3.48E-08; mr1931_2 (Ind_All); LR P-value: 4.65E-08; mr1942_2 (Ind_All); LR P-value: 6.16E-07 |
LOC_Os04g46310.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46310.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46320.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.158; most accessible tissue: Minghui63 flower, score: 86.369 |
| vg0427462758 (J) | chr04 | 27462758 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os04g46310.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46310.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g46320.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.988; most accessible tissue: Zhenshan97 flag leaf, score: 88.022 |
| vg0427463091 (J) | chr04 | 27463091 | C | A | 67.20% | 0.00% | C -> A | NA |
LOC_Os04g46320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.589; most accessible tissue: Zhenshan97 flag leaf, score: 96.523 |
| vg0427463232 (J) | chr04 | 27463232 | G | A | 52.90% | 9.69% | G -> A | NA |
LOC_Os04g46320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.402; most accessible tissue: Zhenshan97 panicle, score: 97.039 |
| vg0427463294 (J) | chr04 | 27463294 | A | C | 36.10% | 19.89% | A -> C | NA |
LOC_Os04g46320.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os04g46320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.249; most accessible tissue: Zhenshan97 panicle, score: 97.039 |
| vg0427463444 (J) | chr04 | 27463444 | C | T | 77.80% | 10.92% | C -> T | NA |
LOC_Os04g46320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46320.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 94.934; most accessible tissue: Minghui63 flower, score: 97.920 |