13 variations found. LOC_Os05g51230 (phosphatidylinositol 3- and 4-kinase family protein; putative; expressed), ranging from 29,382,084 bp to 29,384,538 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0529382393 (J) | chr05 | 29382393 | G | C | 52.80% | 0.13% | G -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g51230.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51220.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.049; most accessible tissue: Zhenshan97 flag leaf, score: 95.508 |
|
| vg0529382421 (J) | chr05 | 29382421 | C | G | 60.40% | 0.02% | G -> C,A |
LOC_Os05g51230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g51230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os05g51230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 85.896; most accessible tissue: Zhenshan97 flag leaf, score: 95.681 |
|
| vg0529382516 (J) | chr05 | 29382516 | C | T | 80.60% | 0.00% | T -> C |
LOC_Os05g51230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.054; most accessible tissue: Zhenshan97 flag leaf, score: 94.870 |
|
| vg0529382884 (J) | chr05 | 29382884 | A | T | 60.90% | 0.11% | A -> T | NA |
LOC_Os05g51230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g51230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.507; most accessible tissue: Zhenshan97 flag leaf, score: 94.278 |
| vg0529383181 (J) | chr05 | 29383181 | C | G | 97.60% | 0.00% | C -> G | NA |
LOC_Os05g51230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.227; most accessible tissue: Minghui63 flag leaf, score: 95.107 |
| vg0529383300 (J) | chr05 | 29383300 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os05g51230.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g51220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g51240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.579; most accessible tissue: Minghui63 flag leaf, score: 95.398 |
| vg0529383560 (J) | chr05 | 29383560 | G | A | 64.30% | 0.08% | A -> G |
mr1072 (All); LR P-value: 1.36E-26;
mr1133 (All); LR P-value: 2.19E-17; mr1548 (All); LR P-value: 5.08E-22; mr1588 (All); LR P-value: 3.61E-22; mr1072_2 (All); LR P-value: 2.97E-40; mr1075_2 (All); LR P-value: 2.20E-38; mr1149_2 (All); LR P-value: 1.28E-26; mr1162_2 (All); LR P-value: 7.09E-16; mr1175_2 (All); LR P-value: 1.71E-21; mr1349_2 (Ind_All); LR P-value: 1.69E-06; mr1478_2 (Ind_All); LR P-value: 5.24E-07; mr1486_2 (All); LR P-value: 5.47E-46; mr1588_2 (All); LR P-value: 2.67E-30; mr1588_2 (Ind_All); LR P-value: 4.09E-10; mr1592_2 (All); LR P-value: 2.53E-16; mr1595_2 (All); LR P-value: 6.19E-10; mr1654_2 (All); LR P-value: 4.69E-07; mr1654_2 (Ind_All); LR P-value: 7.47E-06; mr1712_2 (All); LR P-value: 4.93E-17; mr1713_2 (All); LR P-value: 2.60E-12; mr1722_2 (All); LR P-value: 6.35E-12; mr1749_2 (All); LR P-value: 5.72E-08; mr1790_2 (All); LR P-value: 3.97E-14; mr1821_2 (All); LR P-value: 8.20E-08; mr1828_2 (Ind_All); LR P-value: 1.49E-07; mr1861_2 (All); LR P-value: 1.28E-47; mr1893_2 (All); LR P-value: 1.87E-10 |
LOC_Os05g51230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g51230.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.031; most accessible tissue: Minghui63 flag leaf, score: 95.107 |
| vg0529383947 (J) | chr05 | 29383947 | A | G | 86.50% | 0.13% | A -> G | NA |
LOC_Os05g51230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g51230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 82.417; most accessible tissue: Minghui63 flag leaf, score: 94.184 |
| vg0529384210 (J) | chr05 | 29384210 | GA | G | 58.00% | 0.19% | GA -> G,GAA | NA |
LOC_Os05g51230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g51230.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os05g51230.1 Alt: GAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 75.103; most accessible tissue: Minghui63 flag leaf, score: 91.949 |
| vg0529384250 (J) | chr05 | 29384250 | GC | G | 64.20% | 0.21% | G -> GC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g51230.1 Alt: GC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51220.1 Alt: GC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51240.1 Alt: GC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.695; most accessible tissue: Callus, score: 91.531 |
| vg0529384368 (J) | chr05 | 29384368 | A | G | 94.50% | 0.00% | A -> G | NA |
LOC_Os05g51230.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g51220.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.635; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
| vg0529384406 (J) | chr05 | 29384406 | T | A | 59.10% | 0.00% | T -> A | NA |
LOC_Os05g51230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g51220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g51240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.974; most accessible tissue: Minghui63 flag leaf, score: 89.325 |
| STR0529382392 (J) | chr05 | 29382392 | GG | GC | 46.50% | 0.00% | GG -> GC | NA |
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