22 variations found. LOC_Os11g02310 (pentatricopeptide; putative; expressed), ranging from 671,756 bp to 675,572 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100671856 (J) | chr11 | 671856 | T | TGCGCCG CTTCCCT CGCCGGA | 73.40% | 0.00% | T -> TGCGCCGCTT CCCTCGCCGG A | NA |
LOC_Os11g02310.1 Alt: TGCGCCGCTTCCCTCGCCGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: TGCGCCGCTTCCCTCGCCGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: TGCGCCGCTTCCCTCGCCGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: TGCGCCGCTTCCCTCGCCGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.663; most accessible tissue: Zhenshan97 panicle, score: 99.343 |
| vg1100671863 (J) | chr11 | 671863 | C | CTTCCCT | 99.70% | 0.00% | C -> CTTCCCT,CT TCCCTCG,CT TCCCTCGCCG GAG | NA |
LOC_Os11g02310.1 Alt: CTTCCCT| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g02320.1 Alt: CTTCCCT| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: CTTCCCT| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: CTTCCCT| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02310.1 Alt: CTTCCCTCGCCGGAG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os11g02320.1 Alt: CTTCCCTCGCCGGAG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: CTTCCCTCGCCGGAG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: CTTCCCTCGCCGGAG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02310.1 Alt: CTTCCCTCG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os11g02320.1 Alt: CTTCCCTCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: CTTCCCTCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: CTTCCCTCG| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.665; most accessible tissue: Zhenshan97 panicle, score: 99.353 |
| vg1100671874 (J) | chr11 | 671874 | CAGCTCC ACGCGCT GCTCGCC A | C | 99.70% | 0.00% | CAGCTCCACG CGCTGCTCGC CA -> C | NA |
LOC_Os11g02310.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.646; most accessible tissue: Zhenshan97 panicle, score: 99.339 |
| vg1100671962 (J) | chr11 | 671962 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g02310.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os11g02310.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os11g02320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.788; most accessible tissue: Zhenshan97 panicle, score: 98.811 |
| vg1100672538 (J) | chr11 | 672538 | T | G | 72.40% | 0.19% | T -> G | NA |
LOC_Os11g02310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g02310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 84.552; most accessible tissue: Minghui63 flag leaf, score: 91.692 |
| vg1100672596 (J) | chr11 | 672596 | T | A | 72.60% | 0.21% | T -> A | NA |
LOC_Os11g02310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g02310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.550; most accessible tissue: Minghui63 flower, score: 84.490 |
| vg1100672761 (J) | chr11 | 672761 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os11g02310.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.984; most accessible tissue: Minghui63 flag leaf, score: 82.289 |
| vg1100673167 (J) | chr11 | 673167 | G | T | 72.60% | 0.34% | G -> T | NA |
LOC_Os11g02310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g02310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 44.584; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg1100673679 (J) | chr11 | 673679 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os11g02310.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g02320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 37.945; most accessible tissue: Callus, score: 66.487 |
| vg1100674083 (J) | chr11 | 674083 | CTAAT | C | 95.70% | 0.00% | CTAAT -> C | NA |
LOC_Os11g02310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.794; most accessible tissue: Minghui63 flower, score: 63.841 |
| vg1100674220 (J) | chr11 | 674220 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os11g02310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 44.604; most accessible tissue: Callus, score: 62.682 |
| vg1100674296 (J) | chr11 | 674296 | CAA | C | 73.10% | 0.40% | CAA -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g02310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.756; most accessible tissue: Minghui63 flower, score: 65.900 |
| vg1100674535 (J) | chr11 | 674535 | C | A | 77.50% | 0.04% | C -> A | NA |
LOC_Os11g02310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 55.340; most accessible tissue: Callus, score: 71.150 |
| vg1100674538 (J) | chr11 | 674538 | G | A | 97.00% | 0.00% | G -> A | NA |
LOC_Os11g02310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.392; most accessible tissue: Callus, score: 71.150 |
| vg1100674728 (J) | chr11 | 674728 | T | C | 72.50% | 0.08% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g02310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.414; most accessible tissue: Minghui63 panicle, score: 76.913 |
| vg1100674740 (J) | chr11 | 674740 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os11g02310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g02320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.537; most accessible tissue: Minghui63 panicle, score: 78.920 |
| vg1100674823 (J) | chr11 | 674823 | C | A | 72.90% | 0.23% | C -> A | NA |
LOC_Os11g02320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.463; most accessible tissue: Minghui63 panicle, score: 88.893 |
| vg1100674903 (J) | chr11 | 674903 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g02310.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os11g02320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02320.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.408; most accessible tissue: Minghui63 panicle, score: 88.595 |
| vg1100675047 (J) | chr11 | 675047 | A | G | 72.50% | 0.06% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02330.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02310.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.297; most accessible tissue: Minghui63 panicle, score: 92.078 |
| vg1100675068 (J) | chr11 | 675068 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os11g02320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02330.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.413; most accessible tissue: Minghui63 panicle, score: 91.756 |
| vg1100675514 (J) | chr11 | 675514 | AG | A | 99.80% | 0.00% | AG -> A | NA |
LOC_Os11g02310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02320.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02330.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.741; most accessible tissue: Callus, score: 75.320 |
| STR1100675039 (J) | chr11 | 675039 | TGAAATT GA | TGAAATT GG | 76.50% | 0.00% | TGAAATTGA -> TGAAATTGG | NA |
|