39 variations found. LOC_Os03g56250 (LRR receptor-like protein kinase; putative; expressed), ranging from 32,043,842 bp to 32,048,414 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0332043913 (J) | chr03 | 32043913 | C | T | 65.20% | 0.00% | T -> C | NA |
LOC_Os03g56250.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56234.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56241.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.265; most accessible tissue: Minghui63 young leaf, score: 98.975 |
| vg0332043983 (J) | chr03 | 32043983 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g56250.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.542; most accessible tissue: Minghui63 young leaf, score: 98.842 |
| vg0332043988 (J) | chr03 | 32043988 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g56250.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g56234.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.124; most accessible tissue: Minghui63 young leaf, score: 98.808 |
| vg0332044006 (J) | chr03 | 32044006 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os03g56250.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g56234.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56241.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.253; most accessible tissue: Minghui63 young leaf, score: 98.795 |
| vg0332044031 (J) | chr03 | 32044031 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os03g56250.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.083; most accessible tissue: Minghui63 young leaf, score: 98.754 |
| vg0332044159 (J) | chr03 | 32044159 | C | T | 64.90% | 0.00% | T -> C | NA |
LOC_Os03g56250.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56234.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56241.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.361; most accessible tissue: Minghui63 young leaf, score: 98.502 |
| vg0332044209 (J) | chr03 | 32044209 | G | C | 64.90% | 0.00% | C -> G | NA |
LOC_Os03g56250.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.775; most accessible tissue: Minghui63 young leaf, score: 98.480 |
| vg0332044377 (J) | chr03 | 32044377 | A | G | 65.10% | 0.06% | G -> A | NA |
LOC_Os03g56250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g56250.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.324; most accessible tissue: Minghui63 young leaf, score: 98.029 |
| vg0332044378 (J) | chr03 | 32044378 | A | C | 65.10% | 0.06% | C -> A | NA |
LOC_Os03g56250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g56250.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.338; most accessible tissue: Minghui63 young leaf, score: 98.034 |
| vg0332044645 (J) | chr03 | 32044645 | G | A | 65.10% | 0.06% | A -> G | NA |
LOC_Os03g56250.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g56250.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.912; most accessible tissue: Minghui63 young leaf, score: 97.010 |
| vg0332044917 (J) | chr03 | 32044917 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g56250.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.523; most accessible tissue: Minghui63 young leaf, score: 94.332 |
| vg0332044938 (J) | chr03 | 32044938 | A | C | 92.30% | 2.90% | A -> C | NA |
LOC_Os03g56250.1 Alt: C| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g56250.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.173; most accessible tissue: Minghui63 young leaf, score: 94.332 |
| vg0332044984 (J) | chr03 | 32044984 | G | GATGTTC | 64.60% | 0.00% | GATGTTC -> G | NA |
LOC_Os03g56234.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56241.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56250.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.861; most accessible tissue: Minghui63 young leaf, score: 92.562 |
| vg0332045301 (J) | chr03 | 32045301 | T | TCA | 64.90% | 0.00% | TCA -> T | NA |
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56250.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.025; most accessible tissue: Minghui63 young leaf, score: 91.776 |
| vg0332045340 (J) | chr03 | 32045340 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56250.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.486; most accessible tissue: Minghui63 young leaf, score: 90.802 |
| vg0332045374 (J) | chr03 | 32045374 | C | A | 98.70% | 0.00% | C -> A | NA |
LOC_Os03g56234.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.931; most accessible tissue: Minghui63 young leaf, score: 90.449 |
| vg0332045399 (J) | chr03 | 32045399 | A | G | 64.90% | 0.00% | G -> A | NA |
LOC_Os03g56234.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.807; most accessible tissue: Minghui63 young leaf, score: 90.541 |
| vg0332045911 (J) | chr03 | 32045911 | T | TA | 65.20% | 0.00% | TA -> T | NA |
LOC_Os03g56234.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56234.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56250.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.586; most accessible tissue: Minghui63 young leaf, score: 87.373 |
| vg0332045972 (J) | chr03 | 32045972 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os03g56241.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g56250.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.798; most accessible tissue: Minghui63 young leaf, score: 85.826 |
| vg0332046056 (J) | chr03 | 32046056 | A | G | 65.20% | 0.00% | G -> A | NA |
LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.834; most accessible tissue: Minghui63 young leaf, score: 88.753 |
| vg0332046136 (J) | chr03 | 32046136 | G | C | 64.80% | 0.00% | C -> G | NA |
LOC_Os03g56241.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56250.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.313; most accessible tissue: Minghui63 young leaf, score: 88.992 |
| vg0332046169 (J) | chr03 | 32046169 | T | C | 95.50% | 0.00% | T -> C | NA |
LOC_Os03g56241.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56250.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.620; most accessible tissue: Minghui63 young leaf, score: 89.224 |
| vg0332046384 (J) | chr03 | 32046384 | A | G | 64.90% | 0.06% | G -> A | NA |
LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 72.561; most accessible tissue: Minghui63 young leaf, score: 91.776 |
| vg0332046481 (J) | chr03 | 32046481 | G | A | 93.50% | 0.00% | G -> A | NA |
LOC_Os03g56241.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.735; most accessible tissue: Minghui63 young leaf, score: 91.428 |
| vg0332046540 (J) | chr03 | 32046540 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os03g56241.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g56250.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.021; most accessible tissue: Minghui63 young leaf, score: 93.121 |
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