79 variations found. Os01g0872600/LOC_Os01g65210 (proton-dependent oligopeptide transport; putative; expressed), ranging from 37,837,136 bp to 37,843,664 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g65210 | proton-dependent oligopeptide transport, putative, expressed; RAP ID: Os01g0872600; MSU ID: LOC_Os01g65210 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0137837235 (J) | chr01 | 37837235 | GCCGGAG | G | 63.00% | 0.00% | GCCGGAG -> G | NA |
|
| STR0137838170 (J) | chr01 | 37838170 | AGTAGAG TG | AGTAGAG TA | 61.20% | 0.00% | AGTAGAGTA -> AGTAGAGTG | NA |
|
| vg0137837234 (J) | chr01 | 37837234 | TGCCGGA | T | 77.70% | 0.00% | TGCCGGA -> T | NA |
LOC_Os01g65210.1 Alt: T| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 85.533; most accessible tissue: Callus, score: 94.523 |
| vg0137837368 (J) | chr01 | 37837368 | C | CT | 77.40% | 0.08% | C -> CT,CTT | NA |
LOC_Os01g65190.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65190.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.218; most accessible tissue: Minghui63 flower, score: 90.298 |
| vg0137837460 (J) | chr01 | 37837460 | G | A | 58.30% | 0.00% | G -> A |
mr1375 (All); LMM P-value: 1.30E-07; LR P-value: 2.59E-25;
mr1375 (Ind_All); LMM P-value: 6.58E-06; LR P-value: 1.58E-08; mr1517 (All); LMM P-value: 2.96E-20; mr1517 (Ind_All); LMM P-value: 2.88E-17; LR P-value: 1.45E-20; mr1538 (All); LMM P-value: 4.22E-18; LR P-value: 3.48E-73; mr1538 (Ind_All); LMM P-value: 6.65E-12; LR P-value: 6.14E-15; mr1517_2 (All); LMM P-value: 1.88E-22; mr1517_2 (Ind_All); LMM P-value: 2.87E-19; LR P-value: 5.09E-21; mr1538_2 (All); LMM P-value: 3.69E-18; mr1538_2 (Ind_All); LMM P-value: 1.31E-12; LR P-value: 1.36E-19 |
LOC_Os01g65210.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.042; most accessible tissue: Minghui63 flower, score: 91.306 |
| vg0137837741 (J) | chr01 | 37837741 | A | AACTTTA AATTTAG AGTTG | 61.00% | 0.00% | AACTTTAAAT TTAGAGTTG -> A | NA |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.696; most accessible tissue: Minghui63 flower, score: 86.932 |
| vg0137837783 (J) | chr01 | 37837783 | G | A | 94.70% | 0.00% | G -> A |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.728; most accessible tissue: Minghui63 flower, score: 88.293 |
|
| vg0137837796 (J) | chr01 | 37837796 | C | T | 81.00% | 0.57% | C -> T |
mr1375 (Ind_All); LR P-value: 6.35E-07;
mr1517 (All); LMM P-value: 3.11E-09; mr1517 (Ind_All); LMM P-value: 4.34E-13; LR P-value: 1.94E-15; mr1538 (All); LMM P-value: 3.22E-08; mr1538 (Ind_All); LMM P-value: 2.50E-10; LR P-value: 1.15E-12; mr1517_2 (All); LMM P-value: 3.53E-10; mr1517_2 (Ind_All); LMM P-value: 9.85E-17; LR P-value: 9.75E-17; mr1538_2 (All); LMM P-value: 2.54E-08; mr1538_2 (Ind_All); LMM P-value: 3.38E-12; LR P-value: 3.81E-17 |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 64.100; most accessible tissue: Minghui63 flower, score: 87.534 |
| vg0137837804 (J) | chr01 | 37837804 | GT | GTT | 54.50% | 38.98% | GT -> GTT,G | NA |
LOC_Os01g65200.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.750; most accessible tissue: Minghui63 flower, score: 87.386 |
| vg0137837808 (J) | chr01 | 37837808 | T | TC | 58.40% | 0.00% | T -> TC | NA |
LOC_Os01g65200.3 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.645; most accessible tissue: Minghui63 flower, score: 87.386 |
| vg0137837843 (J) | chr01 | 37837843 | G | T | 58.60% | 0.00% | G -> T |
mr1170 (All); LR P-value: 4.69E-12;
mr1375 (All); LMM P-value: 2.21E-08; LR P-value: 3.98E-26; mr1375 (Ind_All); LMM P-value: 8.40E-06; LR P-value: 2.31E-08; mr1517 (All); LMM P-value: 2.90E-21; mr1517 (Ind_All); LMM P-value: 5.70E-18; LR P-value: 3.98E-21; mr1538 (All); LMM P-value: 5.52E-19; LR P-value: 2.19E-75; mr1538 (Ind_All); LMM P-value: 1.46E-12; LR P-value: 1.71E-15; mr1517_2 (All); LMM P-value: 3.37E-24; mr1517_2 (Ind_All); LMM P-value: 4.06E-19; LR P-value: 6.89E-21; mr1538_2 (All); LMM P-value: 7.72E-20; mr1538_2 (Ind_All); LMM P-value: 3.66E-13; LR P-value: 5.46E-20 |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.934; most accessible tissue: Minghui63 flower, score: 85.848 |
| vg0137837888 (J) | chr01 | 37837888 | G | A | 82.30% | 0.13% | G -> A,C |
mr1375 (Ind_All); LR P-value: 1.66E-07;
mr1517 (All); LMM P-value: 7.49E-10; mr1517 (Ind_All); LMM P-value: 4.03E-14; LR P-value: 2.10E-16; mr1538 (All); LMM P-value: 2.65E-08; mr1538 (Ind_All); LMM P-value: 1.22E-10; LR P-value: 4.51E-13; mr1517_2 (All); LMM P-value: 2.81E-10; mr1517_2 (Ind_All); LMM P-value: 2.48E-17; LR P-value: 3.82E-17; mr1538_2 (All); LMM P-value: 3.77E-08; mr1538_2 (Ind_All); LMM P-value: 2.33E-12; LR P-value: 8.42E-18 |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.331; most accessible tissue: Minghui63 flower, score: 82.244 |
| vg0137837903 (J) | chr01 | 37837903 | C | T | 58.20% | 0.13% | C -> T |
mr1375 (All); LMM P-value: 6.06E-08; LR P-value: 1.51E-25;
mr1375 (Ind_All); LMM P-value: 3.25E-06; LR P-value: 1.26E-08; mr1517 (All); LMM P-value: 1.62E-18; mr1517 (Ind_All); LMM P-value: 4.74E-16; LR P-value: 1.23E-19; mr1538 (All); LMM P-value: 3.79E-17; LR P-value: 3.55E-71; mr1538 (Ind_All); LMM P-value: 2.03E-11; LR P-value: 1.35E-14; mr1517_2 (All); LMM P-value: 1.89E-22; mr1517_2 (Ind_All); LMM P-value: 1.29E-18; LR P-value: 4.93E-21; mr1538_2 (All); LMM P-value: 3.13E-18; mr1538_2 (Ind_All); LMM P-value: 2.47E-13; LR P-value: 3.17E-20 |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 36.640; most accessible tissue: Minghui63 flower, score: 83.015 |
| vg0137837925 (J) | chr01 | 37837925 | T | C | 52.80% | 0.00% | T -> C |
mr1170 (All); LR P-value: 2.19E-13;
mr1375 (All); LMM P-value: 1.40E-09; LR P-value: 2.48E-36; mr1375 (Ind_All); LMM P-value: 2.40E-06; LR P-value: 9.71E-09; mr1510 (All); LR P-value: 2.05E-06; mr1517 (All); LMM P-value: 1.85E-21; LR P-value: 2.49E-87; mr1517 (Ind_All); LMM P-value: 2.52E-16; LR P-value: 1.00E-19; mr1538 (All); LMM P-value: 5.80E-18; LR P-value: 6.94E-71; mr1538 (Ind_All); LMM P-value: 5.62E-11; LR P-value: 1.71E-14; mr1517_2 (All); LMM P-value: 1.77E-24; mr1517_2 (Ind_All); LMM P-value: 8.44E-19; LR P-value: 3.87E-20; mr1538_2 (All); LMM P-value: 1.35E-20; mr1538_2 (Ind_All); LMM P-value: 1.69E-13; LR P-value: 4.09E-20 |
LOC_Os01g65200.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.774; most accessible tissue: Minghui63 flower, score: 82.376 |
| vg0137837927 (J) | chr01 | 37837927 | T | C | 52.80% | 0.00% | T -> C,G |
mr1170 (All); LR P-value: 3.70E-13;
mr1375 (All); LMM P-value: 8.08E-09; LR P-value: 2.71E-35; mr1375 (Ind_All); LMM P-value: 2.37E-06; LR P-value: 9.52E-09; mr1510 (All); LR P-value: 1.30E-06; mr1517 (All); LMM P-value: 3.76E-21; LR P-value: 4.50E-87; mr1517 (Ind_All); LMM P-value: 3.18E-16; LR P-value: 1.22E-19; mr1538 (All); LMM P-value: 3.91E-17; LR P-value: 2.23E-69; mr1538 (Ind_All); LMM P-value: 8.92E-11; LR P-value: 5.96E-14; mr1517_2 (All); LMM P-value: 1.93E-23; mr1517_2 (Ind_All); LMM P-value: 1.36E-18; LR P-value: 1.63E-20; mr1538_2 (All); LMM P-value: 2.07E-18; mr1538_2 (Ind_All); LMM P-value: 9.25E-13; LR P-value: 2.16E-19 |
LOC_Os01g65200.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.774; most accessible tissue: Minghui63 flower, score: 82.376 |
| vg0137837960 (J) | chr01 | 37837960 | A | G | 64.70% | 0.00% | G -> A |
mr1008 (All); LR P-value: 6.89E-111;
mr1009 (All); LR P-value: 7.31E-109; mr1014 (All); LR P-value: 1.71E-74; mr1015 (All); LR P-value: 2.28E-81; mr1024 (All); LR P-value: 6.45E-29; mr1027 (All); LR P-value: 3.47E-66; mr1070 (All); LR P-value: 9.23E-11; mr1074 (All); LR P-value: 5.81E-32; mr1092 (All); LR P-value: 7.08E-45; mr1097 (All); LR P-value: 5.01E-10; mr1128 (All); LR P-value: 6.65E-11; mr1130 (All); LR P-value: 6.70E-26; mr1134 (All); LMM P-value: 4.90E-10; LR P-value: 3.92E-104; mr1134 (Jap_All); LMM P-value: 7.23E-07; LR P-value: 2.77E-11; mr1135 (All); LMM P-value: 8.17E-15; LR P-value: 3.94E-104; mr1135 (Jap_All); LMM P-value: 1.82E-07; LR P-value: 4.73E-11; mr1152 (All); LR P-value: 1.44E-46; mr1154 (All); LR P-value: 9.27E-52; mr1194 (All); LR P-value: 3.19E-43; mr1223 (All); LR P-value: 3.20E-26; mr1256 (All); LR P-value: 5.06E-30; mr1375 (All); LMM P-value: 7.98E-09; LR P-value: 3.86E-33; mr1375 (Jap_All); LMM P-value: 3.13E-08; LR P-value: 3.13E-08; mr1504 (All); LMM P-value: 1.68E-10; LR P-value: 1.77E-114; mr1504 (Jap_All); LMM P-value: 4.64E-06; LR P-value: 9.71E-11; mr1517 (All); LMM P-value: 4.17E-12; LR P-value: 1.26E-113; mr1517 (Jap_All); LR P-value: 4.86E-06; mr1538 (All); LMM P-value: 4.92E-11; LR P-value: 1.77E-87; mr1538 (Jap_All); LMM P-value: 1.04E-06; LR P-value: 1.18E-11; mr1647 (All); LR P-value: 3.77E-31; mr1670 (All); LMM P-value: 1.12E-07; LR P-value: 4.32E-44; mr1672 (All); LMM P-value: 1.22E-10; LR P-value: 8.88E-105; mr1682 (All); LR P-value: 5.06E-35; mr1686 (All); LR P-value: 1.04E-25; mr1758 (All); LR P-value: 3.25E-88; mr1891 (All); LR P-value: 2.86E-39; mr1987 (All); LR P-value: 2.03E-99; mr1004_2 (All); LR P-value: 7.03E-08; mr1008_2 (All); LR P-value: 1.92E-113; mr1015_2 (All); LR P-value: 1.83E-90; mr1024_2 (All); LR P-value: 4.63E-26; mr1027_2 (All); LR P-value: 2.50E-81; mr1074_2 (All); LR P-value: 2.06E-27; mr1081_2 (All); LR P-value: 2.26E-32; mr1092_2 (All); LR P-value: 7.85E-41; mr1128_2 (All); LR P-value: 7.70E-14; mr1134_2 (All); LMM P-value: 6.67E-10; LR P-value: 1.99E-116; mr1134_2 (Jap_All); LMM P-value: 1.20E-09; LR P-value: 1.02E-20; mr1152_2 (All); LR P-value: 5.55E-42; mr1154_2 (All); LR P-value: 2.73E-51; mr1198_2 (All); LR P-value: 8.68E-09; mr1217_2 (All); LR P-value: 4.46E-13; mr1239_2 (All); LR P-value: 2.18E-18; mr1256_2 (All); LR P-value: 1.26E-33; mr1504_2 (All); LMM P-value: 5.50E-11; LR P-value: 8.96E-108; mr1504_2 (Jap_All); LMM P-value: 1.58E-10; LR P-value: 1.28E-21; mr1517_2 (All); LMM P-value: 1.26E-18; LR P-value: 4.68E-177; mr1517_2 (Jap_All); LMM P-value: 5.61E-08; LR P-value: 2.27E-12; mr1538_2 (All); LMM P-value: 8.99E-15; LR P-value: 5.63E-134; mr1538_2 (Jap_All); LMM P-value: 2.63E-08; LR P-value: 1.45E-15; mr1541_2 (All); LR P-value: 2.31E-41; mr1670_2 (All); LMM P-value: 6.03E-13; LR P-value: 2.44E-61; mr1670_2 (Jap_All); LMM P-value: 2.21E-07; LR P-value: 2.21E-07; mr1672_2 (All); LMM P-value: 2.18E-10; LR P-value: 1.03E-140; mr1672_2 (Jap_All); LR P-value: 2.89E-08 |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.792; most accessible tissue: Minghui63 flower, score: 85.386 |
| vg0137837973 (J) | chr01 | 37837973 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.173; most accessible tissue: Minghui63 flower, score: 89.206 |
| vg0137837995 (J) | chr01 | 37837995 | TA | TAA | 65.10% | 0.00% | TAA -> TA,T | NA |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os01g65200.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.408; most accessible tissue: Minghui63 flower, score: 91.463 |
| vg0137837996 (J) | chr01 | 37837996 | A | AC | 36.00% | 62.89% | A -> AC | NA |
LOC_Os01g65200.3 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: AC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.408; most accessible tissue: Minghui63 flower, score: 91.463 |
| vg0137838023 (J) | chr01 | 37838023 | C | T | 65.00% | 0.00% | T -> C |
mr1008 (All); LR P-value: 3.54E-108;
mr1009 (All); LR P-value: 6.32E-106; mr1014 (All); LR P-value: 6.79E-71; mr1015 (All); LR P-value: 1.77E-76; mr1024 (All); LR P-value: 7.80E-27; mr1027 (All); LR P-value: 3.63E-67; mr1074 (All); LR P-value: 8.15E-32; mr1092 (All); LR P-value: 6.53E-45; mr1128 (All); LR P-value: 4.93E-10; mr1130 (All); LR P-value: 5.26E-26; mr1134 (All); LMM P-value: 4.17E-11; LR P-value: 9.80E-104; mr1134 (Jap_All); LMM P-value: 2.06E-06; LR P-value: 3.47E-10; mr1135 (All); LMM P-value: 2.93E-12; LR P-value: 2.88E-101; mr1135 (Jap_All); LMM P-value: 8.78E-06; LR P-value: 6.02E-09; mr1152 (All); LR P-value: 1.29E-45; mr1154 (All); LR P-value: 4.56E-50; mr1194 (All); LR P-value: 3.68E-43; mr1256 (All); LR P-value: 1.53E-29; mr1375 (All); LMM P-value: 2.32E-08; LR P-value: 2.25E-32; mr1375 (Jap_All); LMM P-value: 2.36E-07; LR P-value: 2.36E-07; mr1504 (All); LMM P-value: 7.02E-10; LR P-value: 4.83E-113; mr1504 (Jap_All); LR P-value: 2.99E-09; mr1514 (All); LR P-value: 7.01E-08; mr1517 (All); LMM P-value: 2.22E-13; LR P-value: 1.67E-113; mr1517 (Jap_All); LMM P-value: 8.08E-06; LR P-value: 1.13E-07; mr1538 (All); LMM P-value: 1.19E-11; LR P-value: 1.59E-85; mr1538 (Jap_All); LMM P-value: 1.50E-07; LR P-value: 9.07E-12; mr1541 (All); LR P-value: 9.94E-20; mr1647 (All); LR P-value: 1.50E-31; mr1670 (All); LMM P-value: 1.28E-06; LR P-value: 1.60E-42; mr1672 (All); LMM P-value: 5.90E-10; LR P-value: 1.71E-104; mr1682 (All); LR P-value: 5.78E-36; mr1686 (All); LR P-value: 1.44E-25; mr1737 (All); LR P-value: 7.00E-30; mr1754 (All); LR P-value: 5.71E-19; mr1758 (All); LR P-value: 1.68E-89; mr1987 (All); LR P-value: 4.69E-99; mr1074_2 (All); LR P-value: 4.66E-26; mr1128_2 (All); LR P-value: 2.83E-12; mr1134_2 (All); LMM P-value: 1.16E-10; LR P-value: 8.00E-115; mr1134_2 (Jap_All); LMM P-value: 1.29E-09; LR P-value: 1.03E-18; mr1152_2 (All); LR P-value: 3.72E-39; mr1504_2 (All); LMM P-value: 2.03E-10; LR P-value: 2.52E-106; mr1504_2 (Jap_All); LMM P-value: 6.12E-10; LR P-value: 3.97E-19; mr1517_2 (All); LMM P-value: 3.23E-18; LR P-value: 3.96E-174; mr1517_2 (Jap_All); LMM P-value: 1.72E-09; LR P-value: 3.12E-14; mr1538_2 (All); LMM P-value: 8.62E-18; LR P-value: 1.58E-134; mr1538_2 (Jap_All); LMM P-value: 4.06E-11; LR P-value: 2.90E-18; mr1541_2 (All); LMM P-value: 8.58E-08; LR P-value: 7.00E-45; mr1541_2 (Jap_All); LMM P-value: 7.76E-07; LR P-value: 7.76E-07; mr1563_2 (All); LR P-value: 7.95E-79; mr1670_2 (All); LMM P-value: 3.69E-08; LR P-value: 1.63E-56; mr1672_2 (All); LMM P-value: 5.97E-12; LR P-value: 3.77E-144; mr1672_2 (Jap_All); LR P-value: 3.20E-09; mr1891_2 (All); LR P-value: 1.85E-30 |
LOC_Os01g65200.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.467; most accessible tissue: Minghui63 flower, score: 91.576 |
| vg0137838042 (J) | chr01 | 37838042 | A | G | 64.70% | 0.00% | G -> A | NA |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.127; most accessible tissue: Minghui63 flower, score: 91.539 |
| vg0137838069 (J) | chr01 | 37838069 | C | T | 82.40% | 0.00% | C -> T |
mr1375 (Ind_All); LR P-value: 1.01E-06;
mr1517 (All); LMM P-value: 2.83E-08; mr1517 (Ind_All); LMM P-value: 2.55E-12; LR P-value: 7.92E-15; mr1538 (All); LMM P-value: 7.68E-08; mr1538 (Ind_All); LMM P-value: 5.64E-10; LR P-value: 3.15E-12; mr1517_2 (All); LMM P-value: 1.39E-09; mr1517_2 (Ind_All); LMM P-value: 7.53E-16; LR P-value: 8.07E-16; mr1538_2 (All); LMM P-value: 2.46E-08; mr1538_2 (Ind_All); LMM P-value: 1.96E-11; LR P-value: 5.57E-16 |
LOC_Os01g65200.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.249; most accessible tissue: Minghui63 flower, score: 92.509 |
| vg0137838089 (J) | chr01 | 37838089 | A | C | 82.40% | 0.00% | A -> C |
mr1375 (Ind_All); LR P-value: 8.49E-07;
mr1517 (All); LMM P-value: 2.33E-09; mr1517 (Ind_All); LMM P-value: 1.75E-13; LR P-value: 6.84E-16; mr1538 (All); LMM P-value: 3.64E-08; mr1538 (Ind_All); LMM P-value: 1.54E-10; LR P-value: 9.84E-13; mr1517_2 (All); LMM P-value: 5.72E-10; mr1517_2 (Ind_All); LMM P-value: 1.65E-16; LR P-value: 7.56E-17; mr1538_2 (All); LMM P-value: 4.87E-08; mr1538_2 (Ind_All); LMM P-value: 6.89E-12; LR P-value: 5.82E-17 |
LOC_Os01g65200.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.892; most accessible tissue: Minghui63 flower, score: 93.100 |
| vg0137838108 (J) | chr01 | 37838108 | G | A | 77.10% | 0.00% | G -> A | NA |
LOC_Os01g65200.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.698; most accessible tissue: Minghui63 flower, score: 93.497 |
| vg0137838109 (J) | chr01 | 37838109 | G | A | 64.70% | 0.00% | A -> G | NA |
LOC_Os01g65200.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65200.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.698; most accessible tissue: Minghui63 flower, score: 93.497 |
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