15 variations found. Os09g0491612/LOC_Os09g31450 (polygalacturonase inhibitor 1 precursor; putative; expressed), ranging from 18,950,083 bp to 18,951,277 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g31450 | polygalacturonase inhibitor 1 precursor, putative, expressed; RAP ID: Os09g0491612; MSU ID: LOC_Os09g31450 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os09g31450 | Os09g0491612 | Ospgip7, pgip7, OsPGIP7 | Polygalacturonase-inhibiting protein 7, polygalacturonase inhibiting protein 7 | leucine-rich repeat (LRR) protein, inhibitor of fungal polygalacturonase. AC108762. EEE69955. | PGIP7 | POLYGALACTURONASE-INHIBITING PROTEIN 7 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0918950089 (J) | chr09 | 18950089 | T | C | 59.30% | 0.11% | C -> T |
mr1518 (Ind_All); LR P-value: 1.51E-07;
mr1676 (Ind_All); LR P-value: 5.32E-08; mr1713 (All); LR P-value: 2.94E-12; mr1064_2 (All); LR P-value: 2.09E-58; mr1299_2 (All); LR P-value: 4.46E-08; mr1342_2 (All); LR P-value: 1.45E-16; mr1676_2 (Ind_All); LR P-value: 1.48E-08; mr1700_2 (All); LR P-value: 2.33E-08; mr1713_2 (All); LR P-value: 2.64E-12; mr1938_2 (All); LR P-value: 1.52E-14 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g31450.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g31446.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g31454.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.679; most accessible tissue: Zhenshan97 panicle, score: 82.888 |
| vg0918950119 (J) | chr09 | 18950119 | C | A | 93.70% | 0.00% | C -> A |
mr1063 (Ind_All); LR P-value: 7.26E-06;
mr1177 (Ind_All); LR P-value: 4.04E-06; mr1246 (Ind_All); LR P-value: 3.49E-07; mr1740 (Ind_All); LR P-value: 1.04E-06; mr1063_2 (Ind_All); LR P-value: 7.72E-08; mr1180_2 (Ind_All); LR P-value: 9.96E-07; mr1360_2 (All); LR P-value: 2.03E-06; mr1378_2 (All); LR P-value: 1.62E-10; mr1707_2 (All); LR P-value: 3.52E-08; mr1729_2 (All); LR P-value: 3.53E-06; mr1743_2 (All); LR P-value: 6.16E-06; mr1792_2 (All); LR P-value: 1.16E-06; mr1794_2 (All); LR P-value: 4.52E-16; mr1870_2 (Ind_All); LR P-value: 3.15E-06 |
LOC_Os09g31450.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g31446.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g31454.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.057; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
| vg0918950133 (J) | chr09 | 18950133 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os09g31450.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g31446.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g31454.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.073; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
| vg0918950214 (J) | chr09 | 18950214 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os09g31450.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g31446.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g31454.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.326; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
| vg0918950258 (J) | chr09 | 18950258 | G | A | 95.40% | 0.00% | G -> A |
mr1138 (All); LMM P-value: 7.61E-06;
mr1138 (Ind_All); LR P-value: 1.81E-09; mr1707 (All); LR P-value: 6.90E-12; mr1707 (Ind_All); LR P-value: 9.49E-08; mr1728 (All); LR P-value: 2.22E-14; mr1728 (Ind_All); LR P-value: 2.22E-09; mr1860 (All); LR P-value: 1.75E-09; mr1860 (Ind_All); LR P-value: 1.45E-06; mr1138_2 (All); LMM P-value: 9.03E-09; mr1138_2 (Ind_All); LMM P-value: 1.23E-07; LR P-value: 2.28E-10; mr1354_2 (Ind_All); LR P-value: 4.19E-06; mr1707_2 (All); LMM P-value: 2.40E-07; LR P-value: 3.72E-15; mr1707_2 (Ind_All); LR P-value: 1.15E-09; mr1728_2 (All); LMM P-value: 4.46E-08; LR P-value: 1.86E-21; mr1728_2 (Ind_All); LMM P-value: 1.75E-06; LR P-value: 5.45E-13; mr1860_2 (All); LR P-value: 4.68E-13; mr1860_2 (Ind_All); LR P-value: 8.59E-09 |
LOC_Os09g31450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.430; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0918950291 (J) | chr09 | 18950291 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os09g31450.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g31446.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g31454.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.994; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0918950321 (J) | chr09 | 18950321 | G | A | 60.70% | 0.00% | A -> G,C |
mr1518 (All); LR P-value: 1.38E-19;
mr1518 (Ind_All); LMM P-value: 6.34E-06; LR P-value: 3.09E-10; mr1676 (Ind_All); LR P-value: 3.54E-10; mr1713 (All); LR P-value: 3.27E-11; mr1299_2 (All); LR P-value: 6.22E-08; mr1342_2 (All); LR P-value: 3.01E-16; mr1482_2 (Ind_All); LR P-value: 8.24E-06; mr1676_2 (All); LR P-value: 1.43E-21; mr1676_2 (Ind_All); LMM P-value: 2.76E-06; LR P-value: 1.99E-11; mr1700_2 (All); LR P-value: 3.43E-08; mr1938_2 (All); LR P-value: 7.13E-15 |
LOC_Os09g31450.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g31450.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os09g31446.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g31454.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.657; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0918950531 (J) | chr09 | 18950531 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os09g31450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.614; most accessible tissue: Zhenshan97 panicle, score: 91.374 |
| vg0918950552 (J) | chr09 | 18950552 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os09g31450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.799; most accessible tissue: Zhenshan97 panicle, score: 92.133 |
| vg0918950681 (J) | chr09 | 18950681 | T | C | 59.50% | 0.28% | C -> T |
mr1325 (All); LR P-value: 1.35E-10;
mr1326 (All); LR P-value: 1.29E-12; mr1518 (Ind_All); LR P-value: 7.72E-08; mr1676 (Ind_All); LR P-value: 1.30E-08; mr1713 (All); LR P-value: 1.20E-11; mr1159_2 (Ind_All); LR P-value: 2.45E-06; mr1299_2 (All); LR P-value: 3.87E-08; mr1342_2 (All); LR P-value: 1.05E-16; mr1676_2 (Ind_All); LR P-value: 2.21E-08; mr1700_2 (All); LR P-value: 2.06E-08; mr1733_2 (Ind_All); LR P-value: 2.83E-06; mr1938_2 (All); LR P-value: 1.01E-14 |
LOC_Os09g31450.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g31450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.838; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
| vg0918950730 (J) | chr09 | 18950730 | A | G | 99.30% | 0.00% | A -> G | NA |
LOC_Os09g31450.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.501; most accessible tissue: Zhenshan97 panicle, score: 93.558 |
| vg0918950924 (J) | chr09 | 18950924 | C | T | 51.70% | 0.00% | C -> T |
mr1138 (All); LR P-value: 8.91E-13;
mr1138 (Ind_All); LR P-value: 7.47E-06; mr1174 (All); LR P-value: 1.57E-08; mr1199 (All); LR P-value: 1.13E-14; mr1224 (All); LR P-value: 5.29E-31; mr1246 (Ind_All); LR P-value: 7.32E-07; mr1794 (All); LR P-value: 1.66E-09; mr1929 (All); LR P-value: 4.51E-08; mr1138_2 (All); LR P-value: 2.06E-13; mr1138_2 (Ind_All); LR P-value: 1.02E-06; mr1172_2 (All); LR P-value: 4.20E-09; mr1246_2 (Ind_All); LR P-value: 4.45E-07; mr1834_2 (All); LR P-value: 8.95E-08 |
LOC_Os09g31450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.187; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
| vg0918951185 (J) | chr09 | 18951185 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os09g31450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.236; most accessible tissue: Minghui63 young leaf, score: 89.337 |
| vg0918951226 (J) | chr09 | 18951226 | C | T | 93.70% | 0.00% | C -> T |
mr1063 (Ind_All); LR P-value: 7.26E-06;
mr1177 (Ind_All); LR P-value: 4.04E-06; mr1246 (Ind_All); LR P-value: 3.49E-07; mr1740 (Ind_All); LR P-value: 1.04E-06; mr1063_2 (Ind_All); LR P-value: 7.72E-08; mr1180_2 (Ind_All); LR P-value: 9.96E-07; mr1236_2 (All); LR P-value: 5.39E-06; mr1360_2 (All); LR P-value: 4.43E-06; mr1378_2 (All); LR P-value: 7.50E-11; mr1707_2 (All); LR P-value: 1.14E-08; mr1729_2 (All); LR P-value: 2.69E-07; mr1740_2 (All); LR P-value: 4.39E-06; mr1743_2 (All); LR P-value: 1.88E-06; mr1792_2 (All); LR P-value: 6.93E-07; mr1794_2 (All); LR P-value: 1.30E-15; mr1803_2 (All); LR P-value: 3.19E-12; mr1870_2 (Ind_All); LR P-value: 3.15E-06 |
LOC_Os09g31450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.267; most accessible tissue: Minghui63 young leaf, score: 88.240 |
| STR0918951215 (J) | chr09 | 18951215 | GACGACG ACGAC | GACGACG ACGAT | 92.80% | 0.00% | GACGACGACG AC -> GACGACGACG AT | NA |
|