30 variations found. LOC_Os07g48310 (inactive receptor kinase At2g26730 precursor; putative; expressed), ranging from 28,863,556 bp to 28,868,629 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0728863557 (J) | chr07 | 28863557 | G | A | 57.60% | 0.19% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48310.1 Alt: A| splice_region_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48290.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.556; most accessible tissue: Callus, score: 98.165 |
| vg0728863678 (J) | chr07 | 28863678 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os07g48310.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g48310.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os07g48300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g48290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g48290.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.886; most accessible tissue: Zhenshan97 flag leaf, score: 96.007 |
| vg0728863844 (J) | chr07 | 28863844 | C | T | 57.40% | 0.51% | C -> T |
LOC_Os07g48310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g48310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g48310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os07g48310.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 88.627; most accessible tissue: Zhenshan97 flag leaf, score: 97.013 |
|
| vg0728864259 (J) | chr07 | 28864259 | C | G | 54.10% | 0.44% | G -> C |
mr1548 (All); LR P-value: 4.27E-22;
mr1609 (All); LR P-value: 3.17E-11; mr1771 (Ind_All); LR P-value: 1.92E-06; mr1837 (All); LR P-value: 6.29E-06; mr1902 (All); LR P-value: 1.16E-11; mr1299_2 (All); LR P-value: 6.11E-08; mr1537_2 (All); LR P-value: 3.60E-11; mr1609_2 (All); LR P-value: 6.01E-24; mr1700_2 (All); LR P-value: 2.83E-08; mr1713_2 (All); LR P-value: 2.29E-12; mr1727_2 (All); LR P-value: 8.49E-07; mr1756_2 (All); LR P-value: 5.47E-10; mr1783_2 (All); LR P-value: 9.88E-08; mr1785_2 (All); LR P-value: 2.52E-07; mr1804_2 (All); LR P-value: 4.09E-08; mr1837_2 (All); LR P-value: 8.34E-09; mr1844_2 (All); LR P-value: 2.32E-11; mr1905_2 (All); LR P-value: 1.59E-08; mr1915_2 (All); LR P-value: 3.06E-07; mr1938_2 (All); LR P-value: 5.49E-14 |
LOC_Os07g48310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g48310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g48310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os07g48310.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 89.458; most accessible tissue: Zhenshan97 flag leaf, score: 96.887 |
| vg0728864269 (J) | chr07 | 28864269 | A | G | 90.60% | 0.00% | A -> G | NA |
LOC_Os07g48310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os07g48310.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 89.343; most accessible tissue: Zhenshan97 flag leaf, score: 96.856 |
| vg0728864800 (J) | chr07 | 28864800 | T | C | 98.40% | 0.00% | T -> C | NA |
LOC_Os07g48300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48290.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.440; most accessible tissue: Zhenshan97 flag leaf, score: 92.274 |
| vg0728864918 (J) | chr07 | 28864918 | A | G | 94.90% | 0.00% | A -> G |
LOC_Os07g48310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os07g48310.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 75.955; most accessible tissue: Zhenshan97 flag leaf, score: 91.333 |
|
| vg0728865284 (J) | chr07 | 28865284 | C | T | 98.40% | 0.00% | C -> T | NA |
LOC_Os07g48310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os07g48310.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 77.163; most accessible tissue: Zhenshan97 flag leaf, score: 90.123 |
| vg0728865668 (J) | chr07 | 28865668 | A | G | 94.90% | 0.00% | A -> G |
LOC_Os07g48310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g48310.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 71.215; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 |
|
| vg0728865735 (J) | chr07 | 28865735 | A | G | 52.20% | 0.15% | A -> G | NA |
LOC_Os07g48310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g48310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g48310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g48310.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.815; most accessible tissue: Zhenshan97 flag leaf, score: 87.378 |
| vg0728865817 (J) | chr07 | 28865817 | G | A | 94.90% | 0.00% | G -> A |
LOC_Os07g48310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os07g48310.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 73.208; most accessible tissue: Zhenshan97 flag leaf, score: 87.378 |
|
| vg0728865888 (J) | chr07 | 28865888 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os07g48310.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g48310.2 Alt: T| synonymous_variant LOW(snpEff) LOC_Os07g48300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.124; most accessible tissue: Zhenshan97 flag leaf, score: 88.526 |
| vg0728866029 (J) | chr07 | 28866029 | G | T | 94.90% | 0.00% | G -> T |
LOC_Os07g48310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g48310.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.502; most accessible tissue: Zhenshan97 flag leaf, score: 86.230 |
|
| vg0728866079 (J) | chr07 | 28866079 | T | C | 52.20% | 0.34% | T -> C | NA |
LOC_Os07g48310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g48310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g48310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os07g48310.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 69.278; most accessible tissue: Zhenshan97 flag leaf, score: 84.726 |
| vg0728866141 (J) | chr07 | 28866141 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os07g48310.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g48310.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.914; most accessible tissue: Minghui63 flower, score: 82.109 |
| vg0728866206 (J) | chr07 | 28866206 | C | T | 57.40% | 0.49% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48310.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.587; most accessible tissue: Callus, score: 83.517 |
| vg0728866275 (J) | chr07 | 28866275 | G | A | 57.40% | 0.28% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.925; most accessible tissue: Callus, score: 83.517 |
| vg0728866532 (J) | chr07 | 28866532 | C | A | 57.30% | 0.25% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.093; most accessible tissue: Minghui63 flower, score: 82.507 |
| vg0728866617 (J) | chr07 | 28866617 | T | A | 94.90% | 0.00% | T -> A |
LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.013; most accessible tissue: Minghui63 flower, score: 78.798 |
|
| vg0728866676 (J) | chr07 | 28866676 | T | C | 57.50% | 0.40% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.717; most accessible tissue: Callus, score: 84.028 |
| vg0728866724 (J) | chr07 | 28866724 | A | T | 57.50% | 0.40% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.641; most accessible tissue: Minghui63 flower, score: 84.384 |
| vg0728866762 (J) | chr07 | 28866762 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g48300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g48310.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os07g48310.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.896; most accessible tissue: Minghui63 flower, score: 85.480 |
| vg0728867073 (J) | chr07 | 28867073 | G | A | 52.30% | 0.40% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48310.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.086; most accessible tissue: Callus, score: 89.223 |
|
| vg0728867121 (J) | chr07 | 28867121 | G | C | 52.10% | 0.51% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g48310.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.564; most accessible tissue: Zhenshan97 flower, score: 87.365 |
| vg0728867560 (J) | chr07 | 28867560 | T | A | 94.90% | 0.00% | T -> A |
LOC_Os07g48300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48310.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.289; most accessible tissue: Callus, score: 92.521 |
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