13 variations found. Os12g0514300/LOC_Os12g32970 (membrane associated DUF588 domain containing protein; putative; expressed), ranging from 19,910,582 bp to 19,911,477 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g32970 | membrane associated DUF588 domain containing protein, putative, expressed; RAP ID: Os12g0514300; MSU ID: LOC_Os12g32970 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1219910582 (J) | chr12 | 19910582 | A | G | 61.70% | 0.00% | G -> A,C |
mr1084 (All); LR P-value: 8.27E-11;
mr1254 (All); LR P-value: 8.96E-21; mr1334 (Ind_All); LR P-value: 5.41E-08; mr1376 (All); LR P-value: 1.36E-15; mr1386 (All); LR P-value: 5.21E-12; mr1431 (All); LR P-value: 1.36E-15; mr1630 (All); LR P-value: 1.99E-10; mr1646 (All); LR P-value: 3.57E-06; mr1084_2 (All); LR P-value: 6.17E-08; mr1146_2 (All); LR P-value: 1.16E-16; mr1205_2 (All); LR P-value: 2.15E-07; mr1334_2 (All); LMM P-value: 5.47E-07; mr1334_2 (Ind_All); LMM P-value: 4.17E-10; LR P-value: 6.48E-13 |
LOC_Os12g32950.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32970.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960-LOC_Os12g32970 Alt: C| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32970.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960-LOC_Os12g32970 Alt: A| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.508; most accessible tissue: Minghui63 root, score: 97.041 |
| vg1219910584 (J) | chr12 | 19910584 | C | T | 78.20% | 0.00% | C -> T | NA |
LOC_Os12g32970.1 Alt: T| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g32970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.363; most accessible tissue: Minghui63 root, score: 97.013 |
| vg1219910610 (J) | chr12 | 19910610 | T | C | 97.50% | 0.00% | T -> C | NA |
LOC_Os12g32970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32950.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.530; most accessible tissue: Minghui63 root, score: 96.767 |
| vg1219910621 (J) | chr12 | 19910621 | A | C | 96.30% | 0.00% | A -> C | NA |
LOC_Os12g32970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32950.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.105; most accessible tissue: Minghui63 root, score: 96.737 |
| vg1219910629 (J) | chr12 | 19910629 | A | T | 73.40% | 0.00% | A -> T | NA |
LOC_Os12g32970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.777; most accessible tissue: Minghui63 root, score: 96.513 |
| vg1219910677 (J) | chr12 | 19910677 | T | A | 63.70% | 0.00% | A -> T |
mr1254 (All); LR P-value: 2.74E-21;
mr1334 (All); LMM P-value: 1.31E-06; mr1376 (All); LR P-value: 4.22E-15; mr1386 (All); LR P-value: 2.93E-12; mr1431 (All); LR P-value: 4.22E-15; mr1795 (All); LR P-value: 3.65E-51; mr1074_2 (All); LR P-value: 6.84E-29; mr1084_2 (All); LR P-value: 2.65E-08; mr1128_2 (All); LR P-value: 2.75E-12; mr1146_2 (All); LR P-value: 7.05E-17; mr1148_2 (All); LR P-value: 6.33E-16; mr1205_2 (All); LR P-value: 6.70E-08; mr1227_2 (All); LR P-value: 2.18E-06; mr1239_2 (All); LR P-value: 1.61E-19; mr1256_2 (All); LR P-value: 1.17E-33; mr1304_2 (All); LR P-value: 4.73E-22; mr1334_2 (All); LMM P-value: 5.27E-10; mr1575_2 (All); LR P-value: 3.11E-14; mr1835_2 (All); LR P-value: 4.96E-09; mr1904_2 (All); LR P-value: 1.67E-12; mr1922_2 (All); LR P-value: 1.29E-19; mr1944_2 (All); LR P-value: 2.29E-40 |
LOC_Os12g32970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.309; most accessible tissue: Minghui63 root, score: 96.429 |
| vg1219910743 (J) | chr12 | 19910743 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os12g32970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g32950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g32980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.879; most accessible tissue: Minghui63 root, score: 96.149 |
| vg1219910870 (J) | chr12 | 19910870 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os12g32970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.011; most accessible tissue: Minghui63 root, score: 95.288 |
| vg1219911152 (J) | chr12 | 19911152 | C | T | 64.20% | 0.00% | T -> C |
mr1018 (All); LR P-value: 1.10E-72;
mr1084 (All); LR P-value: 9.37E-11; mr1105 (All); LR P-value: 2.77E-34; mr1128 (All); LR P-value: 3.75E-10; mr1130 (All); LR P-value: 5.45E-26; mr1135 (All); LR P-value: 2.19E-73; mr1154 (All); LR P-value: 3.00E-50; mr1223 (All); LR P-value: 3.22E-28; mr1254 (All); LR P-value: 1.55E-21; mr1307 (All); LR P-value: 5.07E-10; mr1334 (All); LMM P-value: 2.92E-08; mr1376 (All); LR P-value: 8.74E-16; mr1383 (All); LR P-value: 1.28E-22; mr1386 (All); LR P-value: 5.30E-12; mr1414 (All); LR P-value: 4.24E-27; mr1431 (All); LR P-value: 8.74E-16; mr1553 (All); LR P-value: 1.10E-10; mr1630 (All); LR P-value: 1.69E-10; mr1641 (All); LR P-value: 6.91E-13; mr1698 (All); LR P-value: 2.86E-21; mr1711 (All); LR P-value: 5.93E-59; mr1719 (All); LR P-value: 1.40E-36; mr1775 (All); LR P-value: 4.81E-11; mr1779 (All); LR P-value: 3.83E-07; mr1838 (All); LR P-value: 3.70E-20; mr1846 (All); LR P-value: 6.82E-12; mr1987 (All); LR P-value: 9.22E-103; mr1024_2 (All); LR P-value: 2.77E-24; mr1074_2 (All); LR P-value: 4.95E-29; mr1084_2 (All); LR P-value: 6.08E-08; mr1092_2 (All); LR P-value: 7.89E-40; mr1097_2 (All); LR P-value: 8.46E-12; mr1146_2 (All); LR P-value: 6.73E-17; mr1148_2 (All); LR P-value: 1.24E-15; mr1152_2 (All); LR P-value: 4.13E-39; mr1154_2 (All); LR P-value: 2.63E-50; mr1205_2 (All); LR P-value: 1.57E-07; mr1227_2 (All); LR P-value: 3.22E-06; mr1239_2 (All); LR P-value: 4.75E-19; mr1256_2 (All); LR P-value: 2.97E-33; mr1334_2 (All); LMM P-value: 9.90E-11; mr1575_2 (All); LR P-value: 2.21E-14; mr1670_2 (All); LR P-value: 4.42E-47; mr1835_2 (All); LR P-value: 6.57E-09; mr1922_2 (All); LR P-value: 4.40E-20; mr1944_2 (All); LR P-value: 2.17E-40 |
LOC_Os12g32970.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.608; most accessible tissue: Minghui63 root, score: 92.361 |
| vg1219911194 (J) | chr12 | 19911194 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os12g32970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.037; most accessible tissue: Minghui63 root, score: 92.273 |
| vg1219911327 (J) | chr12 | 19911327 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os12g32970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.501; most accessible tissue: Minghui63 root, score: 93.544 |
| vg1219911343 (J) | chr12 | 19911343 | C | G | 71.60% | 0.00% | C -> G | NA |
LOC_Os12g32970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.253; most accessible tissue: Minghui63 root, score: 93.695 |
| vg1219911460 (J) | chr12 | 19911460 | T | A | 99.80% | 0.00% | T -> A | NA |
LOC_Os12g32970.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g32960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g32980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.960; most accessible tissue: Minghui63 root, score: 93.106 |