25 variations found. LOC_Os05g38770 (protein kinase APK1B; chloroplast precursor; putative; expressed), ranging from 22,745,075 bp to 22,747,649 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522745101 (J) | chr05 | 22745101 | G | T | 96.20% | 0.00% | G -> T | NA |
LOC_Os05g38770.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.587; most accessible tissue: Zhenshan97 young leaf, score: 53.314 |
| vg0522745124 (J) | chr05 | 22745124 | A | G | 66.30% | 0.02% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.144; most accessible tissue: Zhenshan97 young leaf, score: 52.657 |
| vg0522745226 (J) | chr05 | 22745226 | C | CA | 94.60% | 0.00% | C -> CA | NA |
LOC_Os05g38770.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.024; most accessible tissue: Zhenshan97 young leaf, score: 66.320 |
| vg0522745422 (J) | chr05 | 22745422 | G | A | 97.50% | 0.00% | G -> A |
LOC_Os05g38770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 43.526; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
|
| vg0522745440 (J) | chr05 | 22745440 | G | T | 95.30% | 0.00% | G -> T | NA |
LOC_Os05g38770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 48.236; most accessible tissue: Zhenshan97 young leaf, score: 80.056 |
| vg0522745487 (J) | chr05 | 22745487 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os05g38770.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g38760.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 49.232; most accessible tissue: Zhenshan97 young leaf, score: 81.841 |
| vg0522745784 (J) | chr05 | 22745784 | C | CATAATG CTATTGC T | 65.20% | 0.13% | CATAATGCTA TTGCT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38770.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.946; most accessible tissue: Callus, score: 77.168 |
| vg0522746045 (J) | chr05 | 22746045 | C | T | 96.20% | 0.00% | C -> T | NA |
LOC_Os05g38770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 58.406; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0522746267 (J) | chr05 | 22746267 | G | A | 97.50% | 0.00% | G -> A |
LOC_Os05g38770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.020; most accessible tissue: Minghui63 young leaf, score: 83.166 |
|
| vg0522746315 (J) | chr05 | 22746315 | C | A | 98.10% | 0.00% | C -> A | NA |
LOC_Os05g38770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.731; most accessible tissue: Minghui63 young leaf, score: 82.907 |
| vg0522746391 (J) | chr05 | 22746391 | G | A | 96.20% | 0.00% | G -> A | NA |
LOC_Os05g38760.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.742; most accessible tissue: Minghui63 young leaf, score: 80.883 |
| vg0522746463 (J) | chr05 | 22746463 | G | A | 97.60% | 0.00% | G -> A |
LOC_Os05g38760.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.450; most accessible tissue: Zhenshan97 young leaf, score: 82.763 |
|
| vg0522746654 (J) | chr05 | 22746654 | C | CAA | 99.60% | 0.00% | C -> CAA | NA |
LOC_Os05g38770.1 Alt: CAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.750; most accessible tissue: Zhenshan97 young leaf, score: 76.440 |
| vg0522746655 (J) | chr05 | 22746655 | TGC | T | 99.60% | 0.00% | TGC -> T | NA |
LOC_Os05g38770.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.883; most accessible tissue: Zhenshan97 young leaf, score: 76.440 |
| vg0522746678 (J) | chr05 | 22746678 | A | G | 94.60% | 0.00% | A -> G | NA |
LOC_Os05g38770.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.349; most accessible tissue: Callus, score: 76.633 |
| vg0522746683 (J) | chr05 | 22746683 | C | CA | 99.10% | 0.00% | C -> CA | NA |
LOC_Os05g38760.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38780.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38770.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.332; most accessible tissue: Callus, score: 76.633 |
| vg0522746957 (J) | chr05 | 22746957 | G | C | 94.60% | 0.00% | G -> C | NA |
LOC_Os05g38770.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.320; most accessible tissue: Zhenshan97 flower, score: 84.964 |
| vg0522747094 (J) | chr05 | 22747094 | A | C | 62.90% | 0.00% | C -> A |
mr1064 (All); LR P-value: 3.71E-36;
mr1125 (All); LR P-value: 1.39E-47; mr1309 (All); LR P-value: 8.31E-27; mr1448 (All); LR P-value: 3.43E-31; mr1534 (All); LR P-value: 1.49E-40; mr1594 (All); LR P-value: 1.73E-56; mr1718 (All); LR P-value: 8.19E-85; mr1737 (All); LR P-value: 2.47E-29; mr1795 (All); LR P-value: 2.65E-51; mr1841 (All); LR P-value: 6.14E-23; mr1890 (All); LR P-value: 2.42E-38; mr1064_2 (All); LR P-value: 6.12E-58; mr1125_2 (All); LR P-value: 2.63E-62; mr1377_2 (All); LR P-value: 1.05E-11; mr1609_2 (All); LR P-value: 1.47E-22; mr1718_2 (All); LR P-value: 1.59E-109; mr1888_2 (All); LR P-value: 2.01E-34 |
LOC_Os05g38770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.205; most accessible tissue: Zhenshan97 flower, score: 86.041 |
| vg0522747249 (J) | chr05 | 22747249 | TCCGCCG CCG | T | 87.80% | 0.70% | TCCGCCGCCG -> T | NA |
LOC_Os05g38770.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 76.470; most accessible tissue: Zhenshan97 flower, score: 87.730 |
| vg0522747319 (J) | chr05 | 22747319 | C | A | 65.40% | 1.02% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.725; most accessible tissue: Zhenshan97 flower, score: 86.908 |
| vg0522747460 (J) | chr05 | 22747460 | C | G | 84.50% | 3.43% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.451; most accessible tissue: Zhenshan97 flower, score: 85.807 |
| vg0522747495 (J) | chr05 | 22747495 | G | GCGAT | 82.90% | 3.53% | G -> GCGAT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g38770.1 Alt: GCGAT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: GCGAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: GCGAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.726; most accessible tissue: Zhenshan97 flower, score: 88.571 |
| vg0522747537 (J) | chr05 | 22747537 | A | AG | 28.40% | 56.18% | A -> AG,AGG,AGG G | NA |
LOC_Os05g38770.1 Alt: AG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os05g38770.1 Alt: AGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: AGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: AGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38770.1 Alt: AGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38760.1 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 |
| vg0522747581 (J) | chr05 | 22747581 | G | T | 17.60% | 57.58% | G -> T | NA |
LOC_Os05g38770.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g38760.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g38780.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.563; most accessible tissue: Zhenshan97 flower, score: 89.409 |
| STR0522746384 (J) | chr05 | 22746384 | CGACGAC GACGAT | CGACGAC AACGAT | 96.90% | 0.00% | CGACGACGAC GAT -> CGACGACAAC GAT | NA |
|