11 variations found. LOC_Os04g44910 (receptor like protein kinase; putative; expressed), ranging from 26,576,091 bp to 26,578,766 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426576137 (J) | chr04 | 26576137 | GC | G | 95.30% | 0.00% | GC -> G | NA |
LOC_Os04g44910.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44920.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44890.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.360; most accessible tissue: Zhenshan97 root, score: 99.833 |
| vg0426576982 (J) | chr04 | 26576982 | G | A | 99.90% | 0.00% | G -> A,C | NA |
LOC_Os04g44910.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os04g44900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44910.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os04g44900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.814; most accessible tissue: Minghui63 flower, score: 96.918 |
| vg0426577292 (J) | chr04 | 26577292 | C | T | 95.30% | 0.00% | C -> T | NA |
LOC_Os04g44910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.723; most accessible tissue: Minghui63 flower, score: 97.204 |
| vg0426577470 (J) | chr04 | 26577470 | A | G | 95.30% | 0.00% | A -> G,T | NA |
LOC_Os04g44910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g44910.1 Alt: T| synonymous_variant LOW(snpEff) LOC_Os04g44900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.871; most accessible tissue: Minghui63 flower, score: 97.014 |
| vg0426577509 (J) | chr04 | 26577509 | A | C | 95.30% | 0.00% | A -> C | NA |
LOC_Os04g44910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.758; most accessible tissue: Minghui63 flower, score: 96.997 |
| vg0426577713 (J) | chr04 | 26577713 | G | C | 95.30% | 0.00% | G -> C | NA |
LOC_Os04g44910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.581; most accessible tissue: Minghui63 flower, score: 97.114 |
| vg0426577908 (J) | chr04 | 26577908 | C | T | 95.30% | 0.00% | C -> T | NA |
LOC_Os04g44910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.598; most accessible tissue: Minghui63 flower, score: 97.412 |
| vg0426577953 (J) | chr04 | 26577953 | C | T | 99.80% | 0.00% | C -> T,G | NA |
LOC_Os04g44910.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os04g44900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 93.297; most accessible tissue: Minghui63 flower, score: 97.440 |
| vg0426577956 (J) | chr04 | 26577956 | C | T | 98.50% | 0.00% | C -> T,G | NA |
LOC_Os04g44910.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os04g44900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 93.383; most accessible tissue: Minghui63 flower, score: 97.440 |
| vg0426578136 (J) | chr04 | 26578136 | C | T | 95.40% | 0.00% | C -> T | NA |
LOC_Os04g44910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.239; most accessible tissue: Zhenshan97 root, score: 98.540 |
| vg0426578552 (J) | chr04 | 26578552 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os04g44910.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44924.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.4 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44920.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.413; most accessible tissue: Zhenshan97 root, score: 99.653 |