231 variations found. LOC_Os04g53000 (NBS-LRR disease resistance protein; putative; expressed), ranging from 31,565,143 bp to 31,566,271 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0431565162 (J) | chr04 | 31565162 | TCGCAGT CTCCGCG CCAC | T | 44.50% | 45.47% | TCGCAGTCTC CGCGCCAC -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 24.239; most accessible tissue: Callus, score: 54.383 |
| vg0431565179 (J) | chr04 | 31565179 | C | T | 42.20% | 52.45% | C -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 28.025; most accessible tissue: Callus, score: 85.988 |
| vg0431565239 (J) | chr04 | 31565239 | G | A | 95.80% | 1.23% | G -> A | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 33.027; most accessible tissue: Callus, score: 85.988 |
| vg0431565278 (J) | chr04 | 31565278 | CATCCAT | C | 58.00% | 6.94% | CATCCAT -> C | NA |
LOC_Os04g53000.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 36.289; most accessible tissue: Callus, score: 85.988 |
| vg0431565289 (J) | chr04 | 31565289 | T | G | 48.40% | 17.54% | T -> G | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 42.185; most accessible tissue: Callus, score: 85.988 |
| vg0431565295 (J) | chr04 | 31565295 | A | T | 46.90% | 19.09% | A -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 42.535; most accessible tissue: Callus, score: 85.988 |
| vg0431565296 (J) | chr04 | 31565296 | G | T | 69.10% | 15.02% | G -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 42.651; most accessible tissue: Callus, score: 85.988 |
| vg0431565300 (J) | chr04 | 31565300 | G | T | 44.90% | 21.43% | G -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 42.945; most accessible tissue: Callus, score: 85.988 |
| vg0431565301 (J) | chr04 | 31565301 | T | A | 43.10% | 23.19% | T -> A | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os04g53000.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 42.945; most accessible tissue: Callus, score: 85.988 |
| vg0431565309 (J) | chr04 | 31565309 | A | G | 99.70% | 0.17% | A -> G | NA |
LOC_Os04g53000.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os04g52990.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g53010.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 43.144; most accessible tissue: Callus, score: 85.988 |
| vg0431565314 (J) | chr04 | 31565314 | T | C | 40.40% | 19.91% | T -> C | NA |
LOC_Os04g53000.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.708; most accessible tissue: Callus, score: 85.988 |
| vg0431565317 (J) | chr04 | 31565317 | T | A | 97.70% | 1.10% | T -> A | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 43.890; most accessible tissue: Callus, score: 85.988 |
| vg0431565329 (J) | chr04 | 31565329 | C | A | 42.90% | 19.59% | C -> A,T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os04g53000.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 50.260; most accessible tissue: Callus, score: 73.976 |
| vg0431565338 (J) | chr04 | 31565338 | A | G | 97.50% | 0.40% | A -> G | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 50.413; most accessible tissue: Callus, score: 73.976 |
| vg0431565357 (J) | chr04 | 31565357 | TAC | T | 96.70% | 0.00% | TAC -> T | NA |
LOC_Os04g53000.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 52.975; most accessible tissue: Callus, score: 73.976 |
| vg0431565362 (J) | chr04 | 31565362 | C | T | 99.60% | 0.06% | C -> T | NA |
LOC_Os04g53000.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os04g52990.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g53010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.337; most accessible tissue: Callus, score: 73.976 |
| vg0431565369 (J) | chr04 | 31565369 | G | A | 57.00% | 0.00% | A -> G,C | NA |
LOC_Os04g53000.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g53000.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 53.838; most accessible tissue: Callus, score: 73.976 |
| vg0431565371 (J) | chr04 | 31565371 | GTC | G | 99.90% | 0.00% | GTC -> G | NA |
LOC_Os04g53000.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os04g52990.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.838; most accessible tissue: Callus, score: 73.976 |
| vg0431565373 (J) | chr04 | 31565373 | T | C | 57.00% | 0.02% | C -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 53.824; most accessible tissue: Callus, score: 73.976 |
| vg0431565376 (J) | chr04 | 31565376 | T | TCTTC | 99.90% | 0.00% | T -> TCTTC | NA |
LOC_Os04g53000.1 Alt: TCTTC| frameshift_variant HIGH(snpEff)
LOC_Os04g52990.1 Alt: TCTTC| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.151; most accessible tissue: Callus, score: 73.976 |
| vg0431565378 (J) | chr04 | 31565378 | A | C | 99.10% | 0.57% | A -> C | NA |
LOC_Os04g53000.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os04g52990.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g53010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.151; most accessible tissue: Callus, score: 73.976 |
| vg0431565379 (J) | chr04 | 31565379 | AAG | A | 99.10% | 0.55% | AAG -> A | NA |
LOC_Os04g53000.1 Alt: A| frameshift_variant HIGH(snpEff)
LOC_Os04g52990.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.316; most accessible tissue: Callus, score: 73.976 |
| vg0431565383 (J) | chr04 | 31565383 | T | C | 99.50% | 0.08% | T -> C | NA |
LOC_Os04g53000.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os04g52990.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g53010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.565; most accessible tissue: Callus, score: 73.976 |
| vg0431565387 (J) | chr04 | 31565387 | G | C | 97.40% | 0.34% | G -> C | NA |
LOC_Os04g53000.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.866; most accessible tissue: Callus, score: 73.976 |
| vg0431565393 (J) | chr04 | 31565393 | C | T | 97.40% | 0.32% | C -> T | NA |
LOC_Os04g53000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g53000.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 54.946; most accessible tissue: Callus, score: 73.976 |
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