20 variations found. LOC_Os11g03340 (hypothetical protein), ranging from 1,254,747 bp to 1,256,914 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101254918 (J) | chr11 | 1254918 | G | A | 36.70% | 55.01% | G -> A | NA |
LOC_Os11g03340.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os11g03330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1101255057 (J) | chr11 | 1255057 | C | G | 33.50% | 55.65% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g03340.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os11g03330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.678; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1101255243 (J) | chr11 | 1255243 | G | A | 73.80% | 18.83% | G -> A | NA |
LOC_Os11g03330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g03340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.679; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1101255292 (J) | chr11 | 1255292 | C | T | 40.60% | 51.33% | C -> T | NA |
LOC_Os11g03340.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.679; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1101255313 (J) | chr11 | 1255313 | C | T | 42.80% | 53.62% | C -> T | NA |
LOC_Os11g03340.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.086; most accessible tissue: Minghui63 young leaf, score: 8.301 |
| vg1101255389 (J) | chr11 | 1255389 | T | A | 69.10% | 29.28% | T -> A | NA |
LOC_Os11g03340.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os11g03330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.723; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg1101255544 (J) | chr11 | 1255544 | G | A | 36.60% | 36.50% | G -> A | NA |
LOC_Os11g03340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
| vg1101255550 (J) | chr11 | 1255550 | G | A | 67.70% | 28.76% | G -> A | NA |
LOC_Os11g03340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
| vg1101255638 (J) | chr11 | 1255638 | C | T | 44.10% | 51.40% | C -> T | NA |
LOC_Os11g03330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g03340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
| vg1101255640 (J) | chr11 | 1255640 | A | G | 44.20% | 50.91% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g03330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g03340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
| vg1101255641 (J) | chr11 | 1255641 | T | C | 36.50% | 41.13% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g03330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g03340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
| vg1101255723 (J) | chr11 | 1255723 | G | A | 64.50% | 29.45% | G -> A | NA |
LOC_Os11g03340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.762; most accessible tissue: Callus, score: 12.962 |
| vg1101255731 (J) | chr11 | 1255731 | A | C | 68.50% | 23.85% | A -> C | NA |
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g03340.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.762; most accessible tissue: Callus, score: 12.962 |
| vg1101255823 (J) | chr11 | 1255823 | C | T | 65.10% | 27.80% | C -> T | NA |
LOC_Os11g03340.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.546; most accessible tissue: Callus, score: 12.962 |
| vg1101255944 (J) | chr11 | 1255944 | T | A | 63.50% | 29.35% | T -> A | NA |
LOC_Os11g03340.1 Alt: A| splice_donor_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar)
LOC_Os11g03340.1 Alt: DEL/splice_donor_variant(CooVar) The average chromatin accessibility score: 5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 |
| vg1101256004 (J) | chr11 | 1256004 | G | A | 67.70% | 28.02% | G -> A | NA |
LOC_Os11g03330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g03340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 |
| vg1101256047 (J) | chr11 | 1256047 | C | G | 70.50% | 28.73% | C -> G | NA |
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g03340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.744; most accessible tissue: Callus, score: 7.517 |
| vg1101256060 (J) | chr11 | 1256060 | G | A | 44.80% | 30.77% | G -> A | NA |
LOC_Os11g03340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.744; most accessible tissue: Callus, score: 7.517 |
| vg1101256105 (J) | chr11 | 1256105 | C | T | 70.30% | 28.73% | C -> T | NA |
LOC_Os11g03340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g03340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.464; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1101256336 (J) | chr11 | 1256336 | A | G | 37.00% | 54.99% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g03330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g03340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.534; most accessible tissue: Callus, score: 16.207 |