20 variations found. LOC_Os04g44900 (lectin-like receptor kinase; putative; expressed), ranging from 26,572,699 bp to 26,575,257 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426572973 (J) | chr04 | 26572973 | T | C | 95.30% | 0.00% | T -> C | NA |
LOC_Os04g44900.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.103; most accessible tissue: Zhenshan97 root, score: 99.178 |
| vg0426573609 (J) | chr04 | 26573609 | T | G | 95.30% | 0.00% | T -> G | NA |
LOC_Os04g44900.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 92.966; most accessible tissue: Minghui63 flower, score: 98.088 |
| vg0426573642 (J) | chr04 | 26573642 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os04g44900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.778; most accessible tissue: Minghui63 flower, score: 98.064 |
| vg0426573948 (J) | chr04 | 26573948 | C | A | 96.90% | 0.00% | C -> A | NA |
LOC_Os04g44900.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.426; most accessible tissue: Minghui63 flower, score: 97.123 |
| vg0426574227 (J) | chr04 | 26574227 | A | G | 95.30% | 0.00% | A -> G | NA |
LOC_Os04g44900.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.759; most accessible tissue: Zhenshan97 flag leaf, score: 96.394 |
| vg0426574230 (J) | chr04 | 26574230 | A | G | 95.30% | 0.00% | A -> G | NA |
LOC_Os04g44900.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.748; most accessible tissue: Zhenshan97 flag leaf, score: 96.375 |
| vg0426574346 (J) | chr04 | 26574346 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os04g44900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.428; most accessible tissue: Minghui63 flower, score: 95.960 |
| vg0426574711 (J) | chr04 | 26574711 | C | G | 95.30% | 0.00% | C -> G | NA |
LOC_Os04g44900.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.865; most accessible tissue: Zhenshan97 root, score: 95.956 |
| vg0426574716 (J) | chr04 | 26574716 | C | G | 95.30% | 0.00% | C -> G | NA |
LOC_Os04g44900.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.961; most accessible tissue: Zhenshan97 root, score: 96.077 |
| vg0426574733 (J) | chr04 | 26574733 | A | C | 95.30% | 0.00% | A -> C | NA |
LOC_Os04g44900.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.860; most accessible tissue: Zhenshan97 root, score: 96.192 |
| vg0426574796 (J) | chr04 | 26574796 | A | G | 95.30% | 0.00% | A -> G | NA |
LOC_Os04g44900.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 95.449; most accessible tissue: Zhenshan97 root, score: 97.967 |
| vg0426574806 (J) | chr04 | 26574806 | T | C | 95.30% | 0.00% | T -> C | NA |
LOC_Os04g44900.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.433; most accessible tissue: Zhenshan97 root, score: 98.052 |
| vg0426574809 (J) | chr04 | 26574809 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os04g44900.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g44910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g44890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g44890.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.509; most accessible tissue: Zhenshan97 root, score: 98.172 |
| vg0426574858 (J) | chr04 | 26574858 | C | T | 95.30% | 0.00% | C -> T | NA |
LOC_Os04g44900.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.634; most accessible tissue: Zhenshan97 root, score: 98.715 |
| vg0426574868 (J) | chr04 | 26574868 | T | C | 95.30% | 0.00% | T -> C | NA |
LOC_Os04g44900.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.916; most accessible tissue: Zhenshan97 root, score: 98.919 |
| vg0426574998 (J) | chr04 | 26574998 | G | GC | 95.30% | 0.00% | G -> GC | NA |
LOC_Os04g44900.1 Alt: GC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44910.1 Alt: GC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: GC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: GC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: GC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.134; most accessible tissue: Zhenshan97 root, score: 99.494 |
| vg0426575003 (J) | chr04 | 26575003 | A | T | 95.30% | 0.00% | A -> T | NA |
LOC_Os04g44900.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g44900.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.114; most accessible tissue: Zhenshan97 root, score: 99.495 |
| vg0426575036 (J) | chr04 | 26575036 | C | A | 95.30% | 0.00% | C -> A | NA |
LOC_Os04g44900.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g44900.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.101; most accessible tissue: Zhenshan97 root, score: 99.545 |
| vg0426575078 (J) | chr04 | 26575078 | CTT | C | 95.30% | 0.00% | CTT -> C | NA |
LOC_Os04g44900.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.183; most accessible tissue: Zhenshan97 root, score: 99.648 |
| vg0426575254 (J) | chr04 | 26575254 | T | C | 95.30% | 0.00% | T -> C | NA |
LOC_Os04g44900.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.4 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.170; most accessible tissue: Zhenshan97 root, score: 99.886 |