25 variations found. Os01g0874800/LOC_Os01g65400 (DNA polymerase I; putative; expressed), ranging from 37,955,087 bp to 37,959,001 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g65400 | DNA polymerase I, putative, expressed; RAP ID: Os01g0874800; MSU ID: LOC_Os01g65400 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137955114 (J) | chr01 | 37955114 | AT | A | 94.50% | 0.00% | AT -> A | NA |
LOC_Os01g65400.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.805; most accessible tissue: Minghui63 flower, score: 96.800 |
| vg0137955620 (J) | chr01 | 37955620 | T | TTAGACA GTAAAAC | 64.60% | 0.11% | TTAGACAGTA AAAC -> T | NA |
LOC_Os01g65400.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 78.557; most accessible tissue: Callus, score: 92.080 |
| vg0137955832 (J) | chr01 | 37955832 | T | G | 64.70% | 0.13% | G -> T |
Yield (All); LR P-value: 7.72E-19;
mr1008 (All); LR P-value: 2.63E-105; mr1009 (All); LR P-value: 3.60E-103; mr1014 (All); LR P-value: 1.05E-69; mr1024 (All); LR P-value: 7.80E-29; mr1092 (All); LR P-value: 4.68E-46; mr1097 (All); LR P-value: 1.35E-09; mr1134 (All); LMM P-value: 1.33E-24; LR P-value: 2.25E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.90E-25; LR P-value: 5.03E-115; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.34E-46; mr1154 (All); LR P-value: 4.51E-51; mr1375 (All); LMM P-value: 3.09E-06; LR P-value: 2.30E-31; mr1504 (All); LMM P-value: 1.63E-21; LR P-value: 2.50E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.49E-13; LR P-value: 6.20E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 4.12E-13; LR P-value: 1.47E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 6.59E-21; mr1594 (All); LR P-value: 2.20E-57; mr1630 (All); LR P-value: 1.42E-10; mr1645 (All); LR P-value: 8.67E-39; mr1647 (All); LR P-value: 1.07E-31; mr1670 (All); LMM P-value: 1.58E-11; LR P-value: 9.50E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.83E-19; LR P-value: 9.38E-116; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.38E-31; mr1758 (All); LR P-value: 1.96E-89; mr1891 (All); LR P-value: 2.25E-40; mr1024_2 (All); LR P-value: 3.61E-24; mr1092_2 (All); LR P-value: 1.76E-39; mr1134_2 (All); LMM P-value: 4.73E-25; LR P-value: 4.23E-130; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 8.21E-40; mr1154_2 (All); LR P-value: 2.90E-50; mr1416_2 (All); LR P-value: 7.71E-16; mr1504_2 (All); LMM P-value: 2.18E-19; LR P-value: 4.14E-118; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 9.79E-17; LR P-value: 3.04E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.59E-17; LR P-value: 3.29E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.15E-06; LR P-value: 8.61E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.49E-15; LR P-value: 2.31E-64; mr1672_2 (All); LMM P-value: 9.60E-21; LR P-value: 1.10E-155; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 74.621; most accessible tissue: Callus, score: 93.642 |
| vg0137955881 (J) | chr01 | 37955881 | A | AC | 64.80% | 0.00% | AC -> A | NA |
LOC_Os01g65400.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.511; most accessible tissue: Callus, score: 93.642 |
| vg0137955897 (J) | chr01 | 37955897 | T | C | 64.70% | 0.06% | C -> T |
mr1008 (All); LR P-value: 2.73E-103;
mr1009 (All); LR P-value: 6.82E-101; mr1024 (All); LR P-value: 1.73E-28; mr1092 (All); LR P-value: 3.50E-46; mr1097 (All); LR P-value: 2.79E-09; mr1134 (All); LMM P-value: 3.57E-23; LR P-value: 1.82E-115; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 1.80E-23; LR P-value: 4.51E-113; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.54E-46; mr1154 (All); LR P-value: 2.87E-50; mr1375 (All); LMM P-value: 3.62E-06; LR P-value: 1.91E-31; mr1504 (All); LMM P-value: 3.00E-20; LR P-value: 1.93E-125; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 7.85E-13; LR P-value: 2.42E-112; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 2.93E-12; LR P-value: 1.76E-85; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 7.84E-21; mr1630 (All); LR P-value: 2.05E-10; mr1647 (All); LR P-value: 4.66E-31; mr1670 (All); LMM P-value: 8.78E-10; LR P-value: 7.59E-46; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 4.44E-18; LR P-value: 5.40E-114; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 2.81E-31; mr1758 (All); LR P-value: 4.95E-90; mr1891 (All); LR P-value: 1.17E-38; mr1024_2 (All); LR P-value: 1.89E-24; mr1092_2 (All); LR P-value: 7.98E-40; mr1134_2 (All); LMM P-value: 1.24E-24; LR P-value: 9.70E-129; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 4.73E-40; mr1154_2 (All); LR P-value: 1.22E-50; mr1217_2 (All); LR P-value: 1.16E-12; mr1416_2 (All); LR P-value: 8.21E-16; mr1504_2 (All); LMM P-value: 8.07E-19; LR P-value: 6.15E-117; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 3.33E-15; LR P-value: 2.90E-169; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.27E-16; LR P-value: 3.34E-131; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.99E-06; LR P-value: 2.07E-43; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 7.12E-14; LR P-value: 6.61E-63; mr1672_2 (All); LMM P-value: 6.54E-22; LR P-value: 7.16E-157; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.125; most accessible tissue: Callus, score: 93.642 |
| vg0137956053 (J) | chr01 | 37956053 | G | T | 64.70% | 0.00% | T -> G |
Yield (All); LR P-value: 7.72E-19;
mr1008 (All); LR P-value: 2.63E-105; mr1009 (All); LR P-value: 3.60E-103; mr1014 (All); LR P-value: 1.05E-69; mr1024 (All); LR P-value: 7.80E-29; mr1092 (All); LR P-value: 4.68E-46; mr1097 (All); LR P-value: 1.35E-09; mr1134 (All); LMM P-value: 1.33E-24; LR P-value: 2.25E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.90E-25; LR P-value: 5.03E-115; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.34E-46; mr1154 (All); LR P-value: 4.51E-51; mr1375 (All); LMM P-value: 3.09E-06; LR P-value: 2.30E-31; mr1504 (All); LMM P-value: 1.63E-21; LR P-value: 2.50E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.49E-13; LR P-value: 6.20E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 4.12E-13; LR P-value: 1.47E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 6.59E-21; mr1594 (All); LR P-value: 2.20E-57; mr1630 (All); LR P-value: 1.42E-10; mr1645 (All); LR P-value: 8.67E-39; mr1647 (All); LR P-value: 1.07E-31; mr1670 (All); LMM P-value: 1.58E-11; LR P-value: 9.50E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.83E-19; LR P-value: 9.38E-116; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.38E-31; mr1758 (All); LR P-value: 1.96E-89; mr1891 (All); LR P-value: 2.25E-40; mr1024_2 (All); LR P-value: 3.61E-24; mr1092_2 (All); LR P-value: 1.76E-39; mr1134_2 (All); LMM P-value: 4.73E-25; LR P-value: 4.23E-130; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 8.21E-40; mr1154_2 (All); LR P-value: 2.90E-50; mr1416_2 (All); LR P-value: 7.71E-16; mr1504_2 (All); LMM P-value: 2.18E-19; LR P-value: 4.14E-118; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 9.79E-17; LR P-value: 3.04E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.59E-17; LR P-value: 3.29E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.15E-06; LR P-value: 8.61E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.49E-15; LR P-value: 2.31E-64; mr1672_2 (All); LMM P-value: 9.60E-21; LR P-value: 1.10E-155; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.511; most accessible tissue: Callus, score: 96.193 |
| vg0137956146 (J) | chr01 | 37956146 | C | T | 64.80% | 0.00% | T -> C |
mr1008 (All); LR P-value: 2.73E-103;
mr1009 (All); LR P-value: 6.82E-101; mr1024 (All); LR P-value: 1.73E-28; mr1092 (All); LR P-value: 3.50E-46; mr1097 (All); LR P-value: 2.79E-09; mr1134 (All); LMM P-value: 3.57E-23; LR P-value: 1.82E-115; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 1.80E-23; LR P-value: 4.51E-113; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.54E-46; mr1154 (All); LR P-value: 2.87E-50; mr1375 (All); LMM P-value: 3.62E-06; LR P-value: 1.91E-31; mr1504 (All); LMM P-value: 3.00E-20; LR P-value: 1.93E-125; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 7.85E-13; LR P-value: 2.42E-112; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 2.93E-12; LR P-value: 1.76E-85; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 7.84E-21; mr1630 (All); LR P-value: 2.05E-10; mr1647 (All); LR P-value: 4.66E-31; mr1670 (All); LMM P-value: 8.78E-10; LR P-value: 7.59E-46; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 4.44E-18; LR P-value: 5.40E-114; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 2.81E-31; mr1758 (All); LR P-value: 4.95E-90; mr1891 (All); LR P-value: 1.17E-38; mr1024_2 (All); LR P-value: 1.89E-24; mr1092_2 (All); LR P-value: 7.98E-40; mr1134_2 (All); LMM P-value: 1.24E-24; LR P-value: 9.70E-129; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 4.73E-40; mr1154_2 (All); LR P-value: 1.22E-50; mr1217_2 (All); LR P-value: 1.16E-12; mr1416_2 (All); LR P-value: 8.21E-16; mr1504_2 (All); LMM P-value: 8.07E-19; LR P-value: 6.15E-117; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 3.33E-15; LR P-value: 2.90E-169; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.27E-16; LR P-value: 3.34E-131; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.99E-06; LR P-value: 2.07E-43; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 7.12E-14; LR P-value: 6.61E-63; mr1672_2 (All); LMM P-value: 6.54E-22; LR P-value: 7.16E-157; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.954; most accessible tissue: Callus, score: 70.744 |
| vg0137956203 (J) | chr01 | 37956203 | C | T | 64.80% | 0.00% | T -> C |
Yield (All); LR P-value: 7.72E-19;
mr1008 (All); LR P-value: 2.63E-105; mr1009 (All); LR P-value: 3.60E-103; mr1014 (All); LR P-value: 1.05E-69; mr1024 (All); LR P-value: 7.80E-29; mr1092 (All); LR P-value: 4.68E-46; mr1097 (All); LR P-value: 1.35E-09; mr1134 (All); LMM P-value: 1.33E-24; LR P-value: 2.25E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.90E-25; LR P-value: 5.03E-115; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.34E-46; mr1154 (All); LR P-value: 4.51E-51; mr1375 (All); LMM P-value: 3.09E-06; LR P-value: 2.30E-31; mr1504 (All); LMM P-value: 1.63E-21; LR P-value: 2.50E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.49E-13; LR P-value: 6.20E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 4.12E-13; LR P-value: 1.47E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 6.59E-21; mr1594 (All); LR P-value: 2.20E-57; mr1630 (All); LR P-value: 1.42E-10; mr1645 (All); LR P-value: 8.67E-39; mr1647 (All); LR P-value: 1.07E-31; mr1670 (All); LMM P-value: 1.58E-11; LR P-value: 9.50E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.83E-19; LR P-value: 9.38E-116; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.38E-31; mr1758 (All); LR P-value: 1.96E-89; mr1891 (All); LR P-value: 2.25E-40; mr1024_2 (All); LR P-value: 3.61E-24; mr1092_2 (All); LR P-value: 1.76E-39; mr1134_2 (All); LMM P-value: 4.73E-25; LR P-value: 4.23E-130; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 8.21E-40; mr1154_2 (All); LR P-value: 2.90E-50; mr1416_2 (All); LR P-value: 7.71E-16; mr1504_2 (All); LMM P-value: 2.18E-19; LR P-value: 4.14E-118; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 9.79E-17; LR P-value: 3.04E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.59E-17; LR P-value: 3.29E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.15E-06; LR P-value: 8.61E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.49E-15; LR P-value: 2.31E-64; mr1672_2 (All); LMM P-value: 9.60E-21; LR P-value: 1.10E-155; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.539; most accessible tissue: Callus, score: 85.604 |
| vg0137956250 (J) | chr01 | 37956250 | T | C | 64.70% | 0.00% | C -> T |
mr1008 (All); LR P-value: 5.29E-104;
mr1009 (All); LR P-value: 7.90E-102; mr1014 (All); LR P-value: 8.07E-70; mr1024 (All); LR P-value: 3.50E-28; mr1092 (All); LR P-value: 2.66E-45; mr1097 (All); LR P-value: 2.15E-09; mr1134 (All); LMM P-value: 1.85E-22; LR P-value: 4.69E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 9.02E-23; LR P-value: 4.80E-114; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 2.76E-45; mr1154 (All); LR P-value: 1.10E-50; mr1375 (All); LMM P-value: 3.67E-06; LR P-value: 8.47E-32; mr1504 (All); LMM P-value: 9.13E-21; LR P-value: 1.68E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 1.82E-11; LR P-value: 8.56E-110; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 1.03E-11; LR P-value: 1.18E-84; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 4.00E-20; mr1594 (All); LR P-value: 1.54E-56; mr1630 (All); LR P-value: 2.89E-10; mr1670 (All); LMM P-value: 1.64E-11; LR P-value: 6.66E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 2.81E-18; LR P-value: 1.78E-114; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 2.40E-30; mr1758 (All); LR P-value: 3.29E-88; mr1891 (All); LR P-value: 1.55E-39; mr1134_2 (All); LMM P-value: 6.28E-19; LR P-value: 4.55E-128; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1416_2 (All); LR P-value: 9.89E-16; mr1504_2 (All); LMM P-value: 9.34E-17; LR P-value: 9.41E-117; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 5.31E-16; LR P-value: 1.24E-168; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 1.86E-18; LR P-value: 5.50E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 2.43E-07; LR P-value: 3.29E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 1.22E-12; LR P-value: 1.53E-62; mr1672_2 (All); LMM P-value: 2.80E-18; LR P-value: 1.69E-152; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.231; most accessible tissue: Callus, score: 85.604 |
| vg0137956510 (J) | chr01 | 37956510 | G | T | 82.10% | 0.00% | G -> T |
mr1375 (Ind_All); LR P-value: 6.23E-06;
mr1517 (All); LMM P-value: 2.34E-09; mr1517 (Ind_All); LMM P-value: 2.10E-13; LR P-value: 2.18E-15; mr1538 (All); LMM P-value: 1.15E-08; mr1538 (Ind_All); LMM P-value: 5.75E-11; LR P-value: 3.82E-12; mr1134_2 (Ind_All); LR P-value: 2.04E-06; mr1517_2 (All); LMM P-value: 1.40E-09; mr1517_2 (Ind_All); LMM P-value: 1.20E-15; LR P-value: 5.90E-15; mr1538_2 (All); LMM P-value: 3.72E-08; mr1538_2 (Ind_All); LMM P-value: 5.03E-12; LR P-value: 3.74E-15 |
LOC_Os01g65400.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.5 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.659; most accessible tissue: Callus, score: 90.465 |
| vg0137957155 (J) | chr01 | 37957155 | G | C | 64.70% | 0.00% | C -> G |
Yield (All); LR P-value: 2.50E-19;
mr1008 (All); LR P-value: 4.20E-102; mr1009 (All); LR P-value: 9.15E-100; mr1024 (All); LR P-value: 3.50E-28; mr1092 (All); LR P-value: 6.48E-45; mr1134 (All); LMM P-value: 1.06E-19; LR P-value: 1.50E-111; mr1134 (Jap_All); LMM P-value: 8.59E-09; LR P-value: 6.37E-13; mr1135 (All); LMM P-value: 2.20E-20; LR P-value: 1.76E-109; mr1135 (Jap_All); LMM P-value: 4.75E-08; LR P-value: 1.81E-11; mr1152 (All); LR P-value: 1.55E-44; mr1154 (All); LR P-value: 1.62E-49; mr1375 (All); LR P-value: 1.29E-29; mr1504 (All); LMM P-value: 1.59E-17; LR P-value: 5.73E-121; mr1504 (Jap_All); LMM P-value: 7.73E-08; LR P-value: 8.41E-13; mr1517 (All); LMM P-value: 7.35E-13; LR P-value: 5.04E-112; mr1517 (Jap_All); LR P-value: 1.70E-07; mr1538 (All); LMM P-value: 7.02E-11; LR P-value: 4.43E-84; mr1538 (Jap_All); LMM P-value: 7.44E-08; LR P-value: 1.19E-12; mr1541 (All); LR P-value: 3.36E-20; mr1630 (All); LR P-value: 2.22E-10; mr1670 (All); LMM P-value: 7.33E-09; LR P-value: 4.51E-45; mr1672 (All); LMM P-value: 1.11E-16; LR P-value: 3.21E-112; mr1672 (Jap_All); LR P-value: 5.60E-07; mr1737 (All); LR P-value: 2.61E-31; mr1758 (All); LR P-value: 5.64E-90; mr1134_2 (All); LMM P-value: 1.55E-20; LR P-value: 3.09E-124; mr1134_2 (Jap_All); LMM P-value: 1.13E-13; LR P-value: 2.84E-24; mr1154_2 (All); LR P-value: 9.92E-50; mr1504_2 (All); LMM P-value: 5.28E-16; LR P-value: 1.14E-112; mr1504_2 (Jap_All); LMM P-value: 9.63E-13; LR P-value: 6.47E-23; mr1517_2 (All); LMM P-value: 1.42E-16; LR P-value: 3.97E-169; mr1517_2 (Jap_All); LMM P-value: 5.24E-07; LR P-value: 1.29E-10; mr1538_2 (All); LMM P-value: 1.56E-14; LR P-value: 4.33E-127; mr1538_2 (Jap_All); LMM P-value: 2.91E-09; LR P-value: 3.00E-15; mr1541_2 (All); LMM P-value: 3.79E-06; LR P-value: 4.46E-43; mr1541_2 (Jap_All); LMM P-value: 7.63E-06; LR P-value: 7.63E-06; mr1670_2 (All); LMM P-value: 8.78E-12; LR P-value: 6.75E-61; mr1672_2 (All); LMM P-value: 9.71E-19; LR P-value: 1.16E-151; mr1672_2 (Jap_All); LR P-value: 4.96E-11 |
LOC_Os01g65400.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.4 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.130; most accessible tissue: Callus, score: 62.544 |
| vg0137957193 (J) | chr01 | 37957193 | C | A | 64.80% | 0.00% | A -> C |
Yield (All); LR P-value: 7.72E-19;
mr1008 (All); LR P-value: 2.63E-105; mr1009 (All); LR P-value: 3.60E-103; mr1014 (All); LR P-value: 1.05E-69; mr1024 (All); LR P-value: 7.80E-29; mr1092 (All); LR P-value: 4.68E-46; mr1097 (All); LR P-value: 1.35E-09; mr1134 (All); LMM P-value: 1.33E-24; LR P-value: 2.25E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.90E-25; LR P-value: 5.03E-115; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.34E-46; mr1154 (All); LR P-value: 4.51E-51; mr1375 (All); LMM P-value: 3.09E-06; LR P-value: 2.30E-31; mr1504 (All); LMM P-value: 1.63E-21; LR P-value: 2.50E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.49E-13; LR P-value: 6.20E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 4.12E-13; LR P-value: 1.47E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 6.59E-21; mr1594 (All); LR P-value: 2.20E-57; mr1630 (All); LR P-value: 1.42E-10; mr1645 (All); LR P-value: 8.67E-39; mr1647 (All); LR P-value: 1.07E-31; mr1670 (All); LMM P-value: 1.58E-11; LR P-value: 9.50E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.83E-19; LR P-value: 9.38E-116; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.38E-31; mr1758 (All); LR P-value: 1.96E-89; mr1891 (All); LR P-value: 2.25E-40; mr1024_2 (All); LR P-value: 3.61E-24; mr1092_2 (All); LR P-value: 1.76E-39; mr1134_2 (All); LMM P-value: 4.73E-25; LR P-value: 4.23E-130; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 8.21E-40; mr1154_2 (All); LR P-value: 2.90E-50; mr1416_2 (All); LR P-value: 7.71E-16; mr1504_2 (All); LMM P-value: 2.18E-19; LR P-value: 4.14E-118; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 9.79E-17; LR P-value: 3.04E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.59E-17; LR P-value: 3.29E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.15E-06; LR P-value: 8.61E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.49E-15; LR P-value: 2.31E-64; mr1672_2 (All); LMM P-value: 9.60E-21; LR P-value: 1.10E-155; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.4 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.650; most accessible tissue: Callus, score: 88.366 |
| vg0137957217 (J) | chr01 | 37957217 | GA | GAA | 57.50% | 0.00% | GAA -> GA,G,GAAA | NA |
LOC_Os01g65400.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.4 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.4 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.2 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.4 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.006; most accessible tissue: Callus, score: 88.366 |
| vg0137957228 (J) | chr01 | 37957228 | TA | T | 64.70% | 0.00% | T -> TA | NA |
LOC_Os01g65400.2 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.4 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.070; most accessible tissue: Callus, score: 88.366 |
| vg0137957497 (J) | chr01 | 37957497 | C | T | 64.60% | 0.08% | T -> C |
Yield (All); LR P-value: 7.38E-19;
mr1008 (All); LR P-value: 1.86E-103; mr1009 (All); LR P-value: 1.52E-101; mr1014 (All); LR P-value: 3.04E-68; mr1024 (All); LR P-value: 1.14E-28; mr1092 (All); LR P-value: 8.87E-45; mr1134 (All); LMM P-value: 8.17E-21; LR P-value: 1.86E-115; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 2.47E-23; LR P-value: 3.02E-114; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.37E-45; mr1154 (All); LR P-value: 1.72E-49; mr1375 (All); LR P-value: 3.62E-31; mr1504 (All); LMM P-value: 5.77E-18; LR P-value: 1.17E-124; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 7.95E-13; LR P-value: 2.61E-112; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 1.54E-12; LR P-value: 5.71E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 5.02E-21; mr1594 (All); LR P-value: 1.99E-57; mr1630 (All); LR P-value: 1.07E-10; mr1647 (All); LR P-value: 1.43E-31; mr1670 (All); LMM P-value: 4.36E-10; LR P-value: 1.28E-46; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.18E-17; LR P-value: 1.50E-113; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 4.82E-31; mr1758 (All); LR P-value: 4.50E-88; mr1891 (All); LR P-value: 2.43E-40; mr1024_2 (All); LR P-value: 2.22E-24; mr1092_2 (All); LR P-value: 1.57E-39; mr1134_2 (All); LMM P-value: 3.12E-20; LR P-value: 1.73E-128; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 6.88E-40; mr1154_2 (All); LR P-value: 5.93E-50; mr1217_2 (All); LR P-value: 3.22E-13; mr1504_2 (All); LMM P-value: 3.14E-18; LR P-value: 1.78E-117; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 8.19E-15; LR P-value: 5.79E-168; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 3.74E-14; LR P-value: 1.16E-128; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LR P-value: 2.72E-42; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1657_2 (All); LR P-value: 1.84E-18; mr1670_2 (All); LMM P-value: 2.52E-12; LR P-value: 2.68E-62; mr1672_2 (All); LMM P-value: 4.21E-20; LR P-value: 2.92E-154; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g65400.2 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.4 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.297; most accessible tissue: Callus, score: 92.093 |
| vg0137957899 (J) | chr01 | 37957899 | C | T | 64.70% | 0.17% | T -> C |
Yield (All); LR P-value: 7.72E-19;
mr1008 (All); LR P-value: 2.63E-105; mr1009 (All); LR P-value: 3.60E-103; mr1014 (All); LR P-value: 1.05E-69; mr1024 (All); LR P-value: 7.80E-29; mr1092 (All); LR P-value: 4.68E-46; mr1097 (All); LR P-value: 1.35E-09; mr1134 (All); LMM P-value: 1.33E-24; LR P-value: 2.25E-117; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.90E-25; LR P-value: 5.03E-115; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.34E-46; mr1154 (All); LR P-value: 4.51E-51; mr1375 (All); LMM P-value: 3.09E-06; LR P-value: 2.30E-31; mr1504 (All); LMM P-value: 1.63E-21; LR P-value: 2.50E-127; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.49E-13; LR P-value: 6.20E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 4.12E-13; LR P-value: 1.47E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 6.59E-21; mr1594 (All); LR P-value: 2.20E-57; mr1630 (All); LR P-value: 1.42E-10; mr1645 (All); LR P-value: 8.67E-39; mr1647 (All); LR P-value: 1.07E-31; mr1670 (All); LMM P-value: 1.58E-11; LR P-value: 9.50E-48; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 1.83E-19; LR P-value: 9.38E-116; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.38E-31; mr1758 (All); LR P-value: 1.96E-89; mr1891 (All); LR P-value: 2.25E-40; mr1024_2 (All); LR P-value: 3.61E-24; mr1092_2 (All); LR P-value: 1.76E-39; mr1134_2 (All); LMM P-value: 4.73E-25; LR P-value: 4.23E-130; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 8.21E-40; mr1154_2 (All); LR P-value: 2.90E-50; mr1416_2 (All); LR P-value: 7.71E-16; mr1504_2 (All); LMM P-value: 2.18E-19; LR P-value: 4.14E-118; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 9.79E-17; LR P-value: 3.04E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.59E-17; LR P-value: 3.29E-132; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.15E-06; LR P-value: 8.61E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.49E-15; LR P-value: 2.31E-64; mr1672_2 (All); LMM P-value: 9.60E-21; LR P-value: 1.10E-155; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65400.4 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.5 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.4 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.5 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.3 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 70.573; most accessible tissue: Minghui63 flower, score: 82.637 |
| vg0137958048 (J) | chr01 | 37958048 | C | G | 64.60% | 0.00% | G -> C |
Yield (All); LR P-value: 3.79E-19;
mr1008 (All); LR P-value: 5.74E-104; mr1009 (All); LR P-value: 9.40E-102; mr1014 (All); LR P-value: 1.92E-69; mr1024 (All); LR P-value: 8.99E-29; mr1092 (All); LR P-value: 9.35E-46; mr1134 (All); LMM P-value: 2.17E-22; LR P-value: 4.65E-114; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 3.12E-23; LR P-value: 3.04E-112; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 1.24E-45; mr1154 (All); LR P-value: 3.62E-50; mr1375 (All); LR P-value: 1.57E-30; mr1504 (All); LMM P-value: 2.28E-19; LR P-value: 2.25E-123; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 3.42E-13; LR P-value: 5.63E-113; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 2.89E-12; LR P-value: 1.76E-85; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 1.69E-20; mr1630 (All); LR P-value: 2.05E-10; mr1670 (All); LMM P-value: 2.39E-11; LR P-value: 2.12E-47; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 6.29E-18; LR P-value: 1.17E-113; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 3.66E-31; mr1758 (All); LR P-value: 4.01E-90; mr1891 (All); LR P-value: 3.80E-40; mr1134_2 (All); LMM P-value: 3.43E-23; LR P-value: 6.30E-127; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 7.44E-39; mr1154_2 (All); LR P-value: 4.10E-50; mr1504_2 (All); LMM P-value: 2.36E-17; LR P-value: 1.47E-114; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 4.36E-17; LR P-value: 3.81E-172; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.26E-16; LR P-value: 9.50E-130; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 1.02E-06; LR P-value: 8.03E-44; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 2.24E-14; LR P-value: 2.56E-63; mr1672_2 (All); LMM P-value: 2.79E-19; LR P-value: 3.28E-153; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65400.4 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65400.5 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65400.3 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 78.720; most accessible tissue: Callus, score: 90.041 |
| vg0137958531 (J) | chr01 | 37958531 | G | T | 64.70% | 0.08% | T -> G |
Yield (All); LR P-value: 9.53E-19;
mr1008 (All); LR P-value: 2.91E-103; mr1009 (All); LR P-value: 3.27E-101; mr1014 (All); LR P-value: 1.40E-68; mr1024 (All); LR P-value: 2.17E-28; mr1092 (All); LR P-value: 3.50E-45; mr1097 (All); LR P-value: 1.62E-09; mr1134 (All); LMM P-value: 6.04E-21; LR P-value: 8.31E-118; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 7.19E-22; LR P-value: 1.84E-112; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 5.54E-46; mr1154 (All); LR P-value: 3.93E-50; mr1375 (All); LR P-value: 2.37E-30; mr1504 (All); LMM P-value: 3.25E-18; LR P-value: 1.24E-124; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 5.11E-12; LR P-value: 6.60E-112; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 6.17E-12; LR P-value: 6.08E-86; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 5.02E-21; mr1594 (All); LR P-value: 1.31E-57; mr1630 (All); LR P-value: 1.01E-10; mr1647 (All); LR P-value: 1.91E-31; mr1670 (All); LMM P-value: 2.55E-09; LR P-value: 9.75E-46; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 9.14E-17; LR P-value: 7.29E-114; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 2.33E-31; mr1758 (All); LR P-value: 3.96E-88; mr1891 (All); LR P-value: 1.02E-40; mr1024_2 (All); LR P-value: 3.91E-24; mr1092_2 (All); LR P-value: 1.22E-39; mr1134_2 (All); LMM P-value: 5.65E-20; LR P-value: 4.14E-133; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1152_2 (All); LR P-value: 6.22E-40; mr1154_2 (All); LR P-value: 2.97E-50; mr1217_2 (All); LR P-value: 1.15E-12; mr1504_2 (All); LMM P-value: 3.39E-16; LR P-value: 2.87E-116; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 1.15E-13; LR P-value: 8.20E-169; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 4.32E-14; LR P-value: 2.93E-129; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LMM P-value: 9.91E-06; LR P-value: 1.17E-42; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1670_2 (All); LMM P-value: 1.21E-13; LR P-value: 4.56E-63; mr1672_2 (All); LMM P-value: 5.30E-18; LR P-value: 2.18E-154; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.4 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 90.952; most accessible tissue: Zhenshan97 flag leaf, score: 96.129 |
| vg0137958582 (J) | chr01 | 37958582 | T | TG | 64.50% | 0.11% | TG -> T | NA |
LOC_Os01g65410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65400.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.4 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.5 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65400.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.325; most accessible tissue: Zhenshan97 flag leaf, score: 97.906 |
| vg0137958622 (J) | chr01 | 37958622 | C | T | 94.60% | 0.00% | C -> T |
mr1317 (All); LR P-value: 9.27E-09;
mr1348 (All); LR P-value: 2.87E-08; mr1415 (All); LR P-value: 7.70E-07; mr1446 (All); LR P-value: 5.40E-08; mr1504 (All); LMM P-value: 8.52E-06; mr1567 (All); LR P-value: 7.70E-07; mr1608 (All); LR P-value: 1.36E-09; mr1612 (All); LR P-value: 5.99E-13; mr1855_2 (All); LR P-value: 8.18E-22 |
LOC_Os01g65400.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g65400.4 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os01g65400.5 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os01g65400.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os01g65400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 93.270; most accessible tissue: Zhenshan97 flag leaf, score: 98.509 |
| vg0137958733 (J) | chr01 | 37958733 | T | A | 58.90% | 0.00% | T -> A |
mr1375 (All); LMM P-value: 9.60E-07; LR P-value: 8.46E-23;
mr1375 (Ind_All); LR P-value: 6.98E-07; mr1517 (All); LMM P-value: 9.20E-18; mr1517 (Ind_All); LMM P-value: 7.95E-15; LR P-value: 3.40E-18; mr1538 (All); LMM P-value: 2.29E-16; LR P-value: 5.52E-70; mr1538 (Ind_All); LMM P-value: 3.07E-10; LR P-value: 4.51E-12; mr1517_2 (All); LMM P-value: 3.97E-22; mr1517_2 (Ind_All); LMM P-value: 3.76E-18; LR P-value: 1.63E-19; mr1538_2 (All); LMM P-value: 2.14E-17; mr1538_2 (Ind_All); LMM P-value: 6.64E-12; LR P-value: 1.35E-15 |
LOC_Os01g65400.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65400.4 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.5 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 96.776; most accessible tissue: Zhenshan97 flag leaf, score: 98.658 |
| vg0137958805 (J) | chr01 | 37958805 | G | A | 94.60% | 0.00% | G -> A |
mr1317 (All); LR P-value: 9.27E-09;
mr1348 (All); LR P-value: 2.87E-08; mr1415 (All); LR P-value: 7.70E-07; mr1446 (All); LR P-value: 5.40E-08; mr1504 (All); LMM P-value: 8.52E-06; mr1567 (All); LR P-value: 7.70E-07; mr1608 (All); LR P-value: 1.36E-09; mr1612 (All); LR P-value: 5.99E-13; mr1855_2 (All); LR P-value: 8.18E-22 |
LOC_Os01g65400.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65400.4 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.5 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 97.527; most accessible tissue: Zhenshan97 flag leaf, score: 99.049 |
| vg0137958818 (J) | chr01 | 37958818 | C | T | 83.10% | 0.00% | C -> T | NA |
LOC_Os01g65400.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65400.4 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.5 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 97.902; most accessible tissue: Zhenshan97 flag leaf, score: 99.217 |
| vg0137958819 (J) | chr01 | 37958819 | C | G | 64.70% | 0.02% | G -> C |
mr1008 (All); LR P-value: 6.21E-102;
mr1009 (All); LR P-value: 1.29E-99; mr1014 (All); LR P-value: 4.65E-69; mr1024 (All); LR P-value: 3.53E-27; mr1092 (All); LR P-value: 3.25E-46; mr1097 (All); LR P-value: 1.02E-09; mr1134 (All); LMM P-value: 6.10E-19; LR P-value: 3.42E-114; mr1134 (Jap_All); LMM P-value: 9.60E-11; LR P-value: 1.69E-15; mr1135 (All); LMM P-value: 2.94E-19; LR P-value: 1.58E-110; mr1135 (Jap_All); LMM P-value: 4.21E-10; LR P-value: 4.78E-14; mr1152 (All); LR P-value: 2.08E-46; mr1154 (All); LR P-value: 1.70E-50; mr1375 (All); LR P-value: 2.89E-30; mr1504 (All); LMM P-value: 7.97E-17; LR P-value: 6.27E-123; mr1504 (Jap_All); LMM P-value: 2.65E-09; LR P-value: 5.97E-15; mr1517 (All); LMM P-value: 1.92E-10; LR P-value: 4.20E-107; mr1517 (Jap_All); LMM P-value: 7.43E-06; LR P-value: 9.93E-08; mr1538 (All); LMM P-value: 1.03E-09; LR P-value: 1.67E-81; mr1538 (Jap_All); LMM P-value: 7.27E-10; LR P-value: 8.40E-15; mr1541 (All); LR P-value: 2.98E-20; mr1647 (All); LR P-value: 5.88E-32; mr1670 (All); LMM P-value: 6.42E-10; LR P-value: 1.87E-46; mr1670 (Jap_All); LMM P-value: 7.47E-06; LR P-value: 7.47E-06; mr1672 (All); LMM P-value: 2.80E-15; LR P-value: 1.43E-109; mr1672 (Jap_All); LMM P-value: 7.59E-06; LR P-value: 1.48E-07; mr1737 (All); LR P-value: 1.10E-29; mr1758 (All); LR P-value: 3.23E-86; mr1891 (All); LR P-value: 1.96E-39; mr1134_2 (All); LMM P-value: 2.12E-18; LR P-value: 2.74E-126; mr1134_2 (Jap_All); LMM P-value: 2.80E-16; LR P-value: 9.79E-30; mr1504_2 (All); LMM P-value: 1.04E-15; LR P-value: 4.16E-114; mr1504_2 (Jap_All); LMM P-value: 4.99E-15; LR P-value: 2.02E-27; mr1517_2 (All); LMM P-value: 1.23E-11; LR P-value: 3.79E-161; mr1517_2 (Jap_All); LMM P-value: 2.48E-07; LR P-value: 1.32E-11; mr1538_2 (All); LMM P-value: 2.01E-12; LR P-value: 1.08E-124; mr1538_2 (Jap_All); LMM P-value: 2.58E-11; LR P-value: 2.77E-18; mr1541_2 (All); LR P-value: 6.99E-42; mr1541_2 (Jap_All); LMM P-value: 6.51E-07; LR P-value: 6.51E-07; mr1657_2 (All); LR P-value: 1.81E-18; mr1670_2 (All); LMM P-value: 1.79E-14; LR P-value: 5.83E-64; mr1672_2 (All); LMM P-value: 3.35E-16; LR P-value: 8.04E-148; mr1672_2 (Jap_All); LR P-value: 1.22E-11 |
LOC_Os01g65400.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65400.4 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.5 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65400.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.4 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.5 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os01g65400.3 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g65400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 97.948; most accessible tissue: Zhenshan97 flag leaf, score: 99.236 |
| STR0137957218 (J) | chr01 | 37957218 | AA | AAA | 97.00% | 0.00% | AA -> AAA | NA |
|