12 variations found. LOC_Os03g56400 (pentatricopeptide; putative; expressed), ranging from 32,150,803 bp to 32,153,382 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0332150873 (J) | chr03 | 32150873 | A | T | 93.60% | 0.00% | A -> T | NA |
LOC_Os03g56400.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56410.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56390.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247 |
| vg0332151205 (J) | chr03 | 32151205 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g56400.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g56410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56410.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g56390.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.281; most accessible tissue: Minghui63 flag leaf, score: 90.909 |
| vg0332151972 (J) | chr03 | 32151972 | C | T | 64.90% | 0.15% | T -> C | NA |
LOC_Os03g56400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g56400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.048; most accessible tissue: Minghui63 flag leaf, score: 90.593 |
| vg0332152067 (J) | chr03 | 32152067 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os03g56400.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g56410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56410.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.706; most accessible tissue: Callus, score: 90.554 |
| vg0332152590 (J) | chr03 | 32152590 | C | T | 53.60% | 0.00% | T -> C |
mr1063 (All); LR P-value: 3.67E-51;
mr1065 (All); LR P-value: 1.46E-55; mr1068 (All); LR P-value: 1.36E-53; mr1078 (All); LR P-value: 4.42E-52; mr1091 (All); LR P-value: 2.00E-40; mr1094 (All); LR P-value: 2.50E-37; mr1096 (All); LR P-value: 4.23E-52; mr1110 (All); LR P-value: 4.38E-36; mr1121 (All); LR P-value: 2.82E-47; mr1125 (All); LR P-value: 3.68E-48; mr1144 (All); LR P-value: 5.09E-44; mr1161 (All); LR P-value: 2.33E-32; mr1200 (All); LR P-value: 1.21E-41; mr1221 (All); LR P-value: 3.71E-29; mr1234 (All); LR P-value: 1.35E-46; mr1244 (All); LR P-value: 8.50E-22; mr1422 (All); LR P-value: 8.17E-20; mr1426 (All); LR P-value: 3.58E-28; mr1526 (All); LR P-value: 3.05E-42; mr1583 (All); LR P-value: 1.53E-17; mr1798 (All); LR P-value: 4.63E-56; mr1870 (All); LR P-value: 7.27E-16; mr1877 (All); LR P-value: 1.13E-25; mr1929 (All); LR P-value: 4.13E-09; mr1943 (All); LR P-value: 5.90E-22; mr1037_2 (All); LR P-value: 1.97E-30; mr1063_2 (All); LR P-value: 3.57E-54; mr1065_2 (All); LR P-value: 6.84E-65; mr1068_2 (All); LR P-value: 1.48E-64; mr1078_2 (All); LR P-value: 1.42E-66; mr1091_2 (All); LR P-value: 7.96E-52; mr1094_2 (All); LR P-value: 4.84E-47; mr1096_2 (All); LR P-value: 1.38E-61; mr1110_2 (All); LR P-value: 1.57E-39; mr1111_2 (All); LR P-value: 5.63E-51; mr1112_2 (All); LR P-value: 8.00E-63; mr1121_2 (All); LR P-value: 8.50E-51; mr1138_2 (All); LR P-value: 1.33E-11; mr1144_2 (All); LR P-value: 1.90E-51; mr1218_2 (All); LR P-value: 4.83E-19; mr1221_2 (All); LR P-value: 1.13E-36; mr1234_2 (All); LR P-value: 1.49E-56; mr1244_2 (All); LR P-value: 4.03E-27; mr1260_2 (All); LR P-value: 8.94E-18; mr1422_2 (All); LR P-value: 2.57E-25; mr1457_2 (All); LR P-value: 1.07E-16; mr1580_2 (All); LR P-value: 7.93E-31; mr1583_2 (All); LR P-value: 1.14E-14; mr1798_2 (All); LR P-value: 3.78E-76; mr1825_2 (All); LR P-value: 2.57E-30; mr1870_2 (All); LR P-value: 5.43E-19; mr1877_2 (All); LR P-value: 1.18E-21; mr1932_2 (All); LR P-value: 2.16E-31; mr1943_2 (All); LR P-value: 4.56E-27; mr1970_2 (All); LR P-value: 3.31E-61 |
LOC_Os03g56400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.497; most accessible tissue: Minghui63 flag leaf, score: 90.909 |
| vg0332152707 (J) | chr03 | 32152707 | C | G | 65.00% | 0.13% | G -> C | NA |
LOC_Os03g56400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g56400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.728; most accessible tissue: Zhenshan97 flag leaf, score: 93.606 |
| vg0332152720 (J) | chr03 | 32152720 | C | A | 65.00% | 0.15% | A -> C | NA |
LOC_Os03g56400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g56400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.029; most accessible tissue: Zhenshan97 flag leaf, score: 93.831 |
| vg0332152896 (J) | chr03 | 32152896 | G | C | 94.10% | 0.00% | G -> C | NA |
LOC_Os03g56400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.885; most accessible tissue: Zhenshan97 flag leaf, score: 97.880 |
| vg0332152934 (J) | chr03 | 32152934 | G | T | 98.70% | 0.00% | G -> T | NA |
LOC_Os03g56400.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g56410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56410.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56390.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.438; most accessible tissue: Zhenshan97 flag leaf, score: 97.927 |
| vg0332153141 (J) | chr03 | 32153141 | GGT | AGT | 98.50% | 0.00% | GGT -> AGT,G | NA |
LOC_Os03g56400.1 Alt: AGT| synonymous_variant LOW(snpEff)
LOC_Os03g56410.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56410.2 Alt: AGT| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56390.1 Alt: AGT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g56400.1 Alt: G| frameshift_variant HIGH(snpEff) LOC_Os03g56410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56410.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.525; most accessible tissue: Zhenshan97 flag leaf, score: 98.647 |
| vg0332153329 (J) | chr03 | 32153329 | T | C | 58.40% | 0.02% | C -> T | NA |
LOC_Os03g56400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g56400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 97.305; most accessible tissue: Zhenshan97 flag leaf, score: 98.999 |
| vg0332153336 (J) | chr03 | 32153336 | C | G | 58.40% | 0.02% | G -> C | NA |
LOC_Os03g56400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g56400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 97.297; most accessible tissue: Zhenshan97 flag leaf, score: 98.995 |