25 variations found. LOC_Os05g43140 (expressed protein), ranging from 25,044,638 bp to 25,045,646 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0525044639 (J) | chr05 | 25044639 | T | A | 62.60% | 0.00% | A -> T |
mr1032 (All); LR P-value: 8.88E-15;
mr1066 (All); LR P-value: 7.07E-06; mr1105 (All); LR P-value: 1.73E-38; mr1165 (All); LR P-value: 3.62E-16; mr1478 (All); LR P-value: 4.22E-15; mr1842 (All); LR P-value: 2.07E-16; mr1889 (All); LR P-value: 4.20E-62; mr1889 (Ind_All); LR P-value: 3.14E-10; mr1896 (All); LMM P-value: 2.00E-06; LR P-value: 2.65E-82; mr1896 (Ind_All); LMM P-value: 2.06E-06; LR P-value: 1.20E-12; mr1902 (All); LR P-value: 2.96E-12; mr1903 (All); LMM P-value: 6.42E-08; LR P-value: 2.74E-34; mr1903 (Ind_All); LMM P-value: 1.07E-06; LR P-value: 3.03E-12; mr1907 (All); LMM P-value: 2.05E-08; LR P-value: 2.38E-95; mr1907 (Ind_All); LMM P-value: 8.30E-07; LR P-value: 1.15E-15; mr1934 (All); LMM P-value: 1.93E-11; LR P-value: 2.36E-92; mr1934 (Ind_All); LMM P-value: 9.63E-10; LR P-value: 9.33E-16; mr1935 (All); LMM P-value: 6.47E-10; LR P-value: 3.60E-67; mr1935 (Ind_All); LMM P-value: 1.61E-08; LR P-value: 1.13E-14; mr1162_2 (All); LR P-value: 4.15E-16; mr1175_2 (All); LR P-value: 1.75E-23; mr1195_2 (All); LR P-value: 1.35E-22; mr1195_2 (Ind_All); LR P-value: 1.18E-09; mr1253_2 (Ind_All); LR P-value: 7.94E-06; mr1281_2 (All); LR P-value: 1.52E-17; mr1299_2 (All); LR P-value: 4.35E-08; mr1478_2 (All); LR P-value: 1.15E-08; mr1546_2 (All); LR P-value: 8.36E-46; mr1588_2 (All); LR P-value: 1.52E-24; mr1645_2 (All); LR P-value: 8.96E-08; mr1756_2 (All); LR P-value: 1.35E-10; mr1790_2 (All); LR P-value: 8.41E-15; mr1828_2 (All); LMM P-value: 2.97E-06; LR P-value: 2.86E-71; mr1828_2 (Ind_All); LMM P-value: 7.32E-10; LR P-value: 6.44E-16; mr1842_2 (All); LR P-value: 7.38E-17; mr1889_2 (All); LR P-value: 1.97E-72; mr1889_2 (Ind_All); LR P-value: 6.22E-12; mr1896_2 (All); LR P-value: 6.30E-72; mr1896_2 (Ind_All); LR P-value: 7.25E-11; mr1907_2 (All); LMM P-value: 1.54E-06; LR P-value: 7.08E-105; mr1907_2 (Ind_All); LMM P-value: 7.07E-08; LR P-value: 4.55E-19; mr1933_2 (All); LR P-value: 2.19E-22; mr1934_2 (All); LMM P-value: 2.68E-07; LR P-value: 9.28E-92; mr1934_2 (Ind_All); LMM P-value: 1.68E-07; LR P-value: 4.41E-17; mr1938_2 (All); LR P-value: 4.41E-14; mr1938_2 (Ind_All); LR P-value: 5.52E-06; mr1947_2 (All); LR P-value: 8.69E-09 |
LOC_Os05g43140.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.710; most accessible tissue: Zhenshan97 panicle, score: 94.594 |
| vg0525044699 (J) | chr05 | 25044699 | C | CA | 37.30% | 21.24% | C -> CA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g43140.1 Alt: CA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.654; most accessible tissue: Minghui63 panicle, score: 94.218 |
| vg0525044703 (J) | chr05 | 25044703 | A | AAGCTCG | 51.80% | 0.00% | A -> AAGCTCG | NA |
LOC_Os05g43140.1 Alt: AAGCTCG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: AAGCTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: AAGCTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.500; most accessible tissue: Minghui63 panicle, score: 94.218 |
| vg0525044720 (J) | chr05 | 25044720 | G | GCT | 37.30% | 21.29% | G -> GCT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g43140.1 Alt: GCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: GCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: GCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.126; most accessible tissue: Minghui63 panicle, score: 93.936 |
| vg0525044723 (J) | chr05 | 25044723 | T | C | 37.70% | 20.55% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g43140.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.948; most accessible tissue: Minghui63 panicle, score: 93.936 |
| vg0525044725 (J) | chr05 | 25044725 | C | G | 37.70% | 21.14% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g43140.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.896; most accessible tissue: Minghui63 panicle, score: 93.936 |
| vg0525044726 (J) | chr05 | 25044726 | T | C | 37.70% | 11.70% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g43140.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os05g43140.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.678; most accessible tissue: Callus, score: 93.754 |
| vg0525044741 (J) | chr05 | 25044741 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os05g43140.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os05g43130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g43150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.995; most accessible tissue: Callus, score: 93.754 |
| vg0525044750 (J) | chr05 | 25044750 | G | A | 62.50% | 0.00% | A -> G |
mr1032 (All); LR P-value: 1.81E-14;
mr1066 (All); LR P-value: 8.99E-06; mr1105 (All); LR P-value: 4.73E-38; mr1165 (All); LR P-value: 3.46E-16; mr1478 (All); LR P-value: 8.37E-15; mr1842 (All); LR P-value: 9.43E-16; mr1889 (All); LR P-value: 1.31E-60; mr1889 (Ind_All); LR P-value: 2.72E-10; mr1896 (All); LMM P-value: 9.34E-08; LR P-value: 4.85E-83; mr1896 (Ind_All); LMM P-value: 5.04E-06; LR P-value: 4.57E-12; mr1902 (All); LR P-value: 2.96E-11; mr1903 (All); LMM P-value: 1.37E-08; LR P-value: 1.60E-34; mr1903 (Ind_All); LMM P-value: 1.09E-06; LR P-value: 4.24E-12; mr1907 (All); LMM P-value: 6.58E-08; LR P-value: 1.48E-93; mr1907 (Ind_All); LMM P-value: 3.29E-06; LR P-value: 4.86E-15; mr1934 (All); LMM P-value: 8.94E-10; LR P-value: 8.67E-89; mr1934 (Ind_All); LMM P-value: 2.01E-09; LR P-value: 3.64E-15; mr1935 (All); LMM P-value: 9.51E-09; LR P-value: 5.40E-65; mr1935 (Ind_All); LMM P-value: 1.22E-07; LR P-value: 1.18E-13; mr1162_2 (All); LR P-value: 1.57E-15; mr1175_2 (All); LR P-value: 5.03E-23; mr1195_2 (All); LR P-value: 1.04E-22; mr1195_2 (Ind_All); LR P-value: 2.68E-09; mr1281_2 (All); LR P-value: 5.63E-18; mr1520_2 (All); LR P-value: 2.96E-11; mr1546_2 (All); LR P-value: 9.12E-46; mr1713_2 (All); LR P-value: 2.44E-12; mr1756_2 (All); LR P-value: 3.30E-10; mr1790_2 (All); LR P-value: 1.17E-14; mr1828_2 (All); LMM P-value: 1.39E-06; LR P-value: 2.57E-72; mr1828_2 (Ind_All); LMM P-value: 6.47E-08; LR P-value: 2.94E-14; mr1842_2 (All); LR P-value: 8.82E-16; mr1889_2 (All); LR P-value: 1.80E-70; mr1889_2 (Ind_All); LR P-value: 4.15E-11; mr1896_2 (All); LR P-value: 1.01E-70; mr1896_2 (Ind_All); LR P-value: 1.52E-10; mr1907_2 (All); LMM P-value: 8.39E-06; LR P-value: 1.77E-103; mr1907_2 (Ind_All); LMM P-value: 2.31E-07; LR P-value: 1.92E-18; mr1934_2 (All); LR P-value: 4.16E-89; mr1934_2 (Ind_All); LMM P-value: 6.03E-07; LR P-value: 1.88E-16; mr1938_2 (All); LR P-value: 6.32E-14 |
LOC_Os05g43140.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.487; most accessible tissue: Callus, score: 93.754 |
| vg0525044791 (J) | chr05 | 25044791 | G | T | 92.70% | 0.00% | G -> T | NA |
LOC_Os05g43140.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.608; most accessible tissue: Callus, score: 93.754 |
| vg0525044796 (J) | chr05 | 25044796 | C | G | 62.70% | 0.00% | G -> C |
mr1032 (All); LR P-value: 1.62E-14;
mr1105 (All); LR P-value: 2.46E-38; mr1165 (All); LR P-value: 4.63E-16; mr1478 (All); LR P-value: 7.92E-15; mr1842 (All); LR P-value: 7.68E-16; mr1889 (All); LR P-value: 5.77E-62; mr1889 (Ind_All); LR P-value: 2.72E-10; mr1896 (All); LMM P-value: 4.02E-07; LR P-value: 6.53E-83; mr1896 (Ind_All); LMM P-value: 5.04E-06; LR P-value: 4.57E-12; mr1902 (All); LR P-value: 1.79E-11; mr1903 (All); LMM P-value: 4.86E-09; LR P-value: 2.91E-35; mr1903 (Ind_All); LMM P-value: 1.09E-06; LR P-value: 4.24E-12; mr1907 (All); LMM P-value: 1.23E-07; LR P-value: 1.03E-93; mr1907 (Ind_All); LMM P-value: 3.29E-06; LR P-value: 4.86E-15; mr1934 (All); LMM P-value: 1.71E-10; LR P-value: 6.53E-91; mr1934 (Ind_All); LMM P-value: 2.01E-09; LR P-value: 3.64E-15; mr1935 (All); LMM P-value: 3.77E-09; LR P-value: 2.35E-66; mr1935 (Ind_All); LMM P-value: 1.22E-07; LR P-value: 1.18E-13; mr1162_2 (All); LR P-value: 3.68E-16; mr1175_2 (All); LR P-value: 2.08E-22; mr1195_2 (All); LR P-value: 1.03E-22; mr1195_2 (Ind_All); LR P-value: 2.68E-09; mr1281_2 (All); LR P-value: 2.88E-18; mr1546_2 (All); LR P-value: 2.27E-46; mr1756_2 (All); LR P-value: 6.35E-10; mr1790_2 (All); LR P-value: 9.23E-15; mr1828_2 (All); LMM P-value: 3.19E-06; LR P-value: 4.45E-72; mr1828_2 (Ind_All); LMM P-value: 6.47E-08; LR P-value: 2.94E-14; mr1842_2 (All); LR P-value: 4.09E-16; mr1889_2 (All); LR P-value: 2.13E-71; mr1889_2 (Ind_All); LR P-value: 4.15E-11; mr1896_2 (All); LR P-value: 9.76E-72; mr1896_2 (Ind_All); LR P-value: 1.52E-10; mr1907_2 (All); LMM P-value: 1.20E-06; LR P-value: 8.24E-105; mr1907_2 (Ind_All); LMM P-value: 2.31E-07; LR P-value: 1.92E-18; mr1934_2 (All); LMM P-value: 2.03E-06; LR P-value: 8.81E-91; mr1934_2 (Ind_All); LMM P-value: 6.03E-07; LR P-value: 1.88E-16 |
LOC_Os05g43140.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.578; most accessible tissue: Callus, score: 93.754 |
| vg0525044917 (J) | chr05 | 25044917 | A | G | 62.50% | 0.02% | G -> A |
mr1032 (All); LR P-value: 1.85E-14;
mr1105 (All); LR P-value: 5.75E-38; mr1165 (All); LR P-value: 4.46E-16; mr1478 (All); LR P-value: 8.64E-15; mr1842 (All); LR P-value: 1.05E-15; mr1889 (All); LR P-value: 1.39E-63; mr1889 (Ind_All); LR P-value: 2.72E-10; mr1896 (All); LMM P-value: 1.83E-07; LR P-value: 6.69E-84; mr1896 (Ind_All); LMM P-value: 5.04E-06; LR P-value: 4.57E-12; mr1902 (All); LR P-value: 2.33E-11; mr1903 (All); LMM P-value: 1.03E-08; LR P-value: 3.53E-35; mr1903 (Ind_All); LMM P-value: 1.09E-06; LR P-value: 4.24E-12; mr1907 (All); LMM P-value: 1.26E-07; LR P-value: 5.51E-94; mr1907 (Ind_All); LMM P-value: 3.29E-06; LR P-value: 4.86E-15; mr1934 (All); LMM P-value: 9.35E-10; LR P-value: 2.38E-90; mr1934 (Ind_All); LMM P-value: 2.01E-09; LR P-value: 3.64E-15; mr1935 (All); LMM P-value: 5.78E-09; LR P-value: 2.64E-66; mr1935 (Ind_All); LMM P-value: 1.22E-07; LR P-value: 1.18E-13; mr1162_2 (All); LR P-value: 4.09E-16; mr1175_2 (All); LR P-value: 6.71E-22; mr1195_2 (All); LR P-value: 1.07E-22; mr1195_2 (Ind_All); LR P-value: 2.68E-09; mr1281_2 (All); LR P-value: 1.79E-18; mr1546_2 (All); LR P-value: 2.74E-46; mr1713_2 (All); LR P-value: 2.72E-12; mr1790_2 (All); LR P-value: 6.85E-15; mr1828_2 (All); LMM P-value: 1.86E-06; LR P-value: 1.02E-72; mr1828_2 (Ind_All); LMM P-value: 6.47E-08; LR P-value: 2.94E-14; mr1842_2 (All); LR P-value: 5.80E-16; mr1889_2 (All); LR P-value: 2.32E-72; mr1889_2 (Ind_All); LR P-value: 4.15E-11; mr1896_2 (All); LR P-value: 2.89E-72; mr1896_2 (Ind_All); LR P-value: 1.52E-10; mr1907_2 (All); LMM P-value: 7.36E-07; LR P-value: 1.20E-105; mr1907_2 (Ind_All); LMM P-value: 2.31E-07; LR P-value: 1.92E-18; mr1934_2 (All); LMM P-value: 3.83E-06; LR P-value: 1.32E-90; mr1934_2 (Ind_All); LMM P-value: 6.03E-07; LR P-value: 1.88E-16; mr1938_2 (All); LR P-value: 5.16E-14 |
LOC_Os05g43140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g43140.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 83.764; most accessible tissue: Minghui63 panicle, score: 92.928 |
| vg0525044919 (J) | chr05 | 25044919 | C | CCCCG | 62.30% | 0.00% | CCCCG -> C | NA |
LOC_Os05g43140.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.779; most accessible tissue: Minghui63 panicle, score: 92.928 |
| vg0525044925 (J) | chr05 | 25044925 | C | CGGCGGC GGTG | 61.80% | 0.02% | CGGCGGCGGT G -> C | NA |
LOC_Os05g43140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g43140.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 86.761; most accessible tissue: Minghui63 panicle, score: 93.053 |
| vg0525044940 (J) | chr05 | 25044940 | G | GCACA | 60.50% | 0.13% | GCACA -> G | NA |
LOC_Os05g43140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g43140.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 86.436; most accessible tissue: Minghui63 panicle, score: 93.053 |
| vg0525044944 (J) | chr05 | 25044944 | A | G | 38.60% | 59.35% | A -> G | NA |
LOC_Os05g43140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g43140.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.310; most accessible tissue: Minghui63 panicle, score: 93.053 |
| vg0525044988 (J) | chr05 | 25044988 | C | T | 62.50% | 0.23% | T -> C |
mr1032 (All); LR P-value: 2.09E-14;
mr1059 (All); LR P-value: 1.73E-14; mr1066 (All); LR P-value: 5.36E-06; mr1105 (All); LR P-value: 8.67E-38; mr1165 (All); LR P-value: 6.43E-16; mr1478 (All); LR P-value: 1.02E-14; mr1495 (All); LR P-value: 1.02E-22; mr1889 (All); LR P-value: 5.34E-64; mr1889 (Ind_All); LR P-value: 2.72E-10; mr1896 (All); LMM P-value: 4.68E-07; LR P-value: 7.52E-84; mr1896 (Ind_All); LMM P-value: 5.04E-06; LR P-value: 4.57E-12; mr1902 (All); LR P-value: 1.82E-11; mr1903 (All); LMM P-value: 7.74E-09; LR P-value: 1.86E-35; mr1903 (Ind_All); LMM P-value: 1.09E-06; LR P-value: 4.24E-12; mr1907 (All); LMM P-value: 1.15E-07; LR P-value: 2.27E-94; mr1907 (Ind_All); LMM P-value: 3.29E-06; LR P-value: 4.86E-15; mr1934 (All); LMM P-value: 1.10E-10; LR P-value: 7.34E-92; mr1934 (Ind_All); LMM P-value: 2.01E-09; LR P-value: 3.64E-15; mr1935 (All); LMM P-value: 3.41E-09; LR P-value: 6.34E-67; mr1935 (Ind_All); LMM P-value: 1.22E-07; LR P-value: 1.18E-13; mr1162_2 (All); LR P-value: 1.17E-16; mr1175_2 (All); LR P-value: 6.95E-23; mr1195_2 (All); LR P-value: 2.61E-22; mr1195_2 (Ind_All); LR P-value: 2.68E-09; mr1281_2 (All); LR P-value: 1.60E-18; mr1478_2 (All); LR P-value: 1.38E-08; mr1546_2 (All); LR P-value: 8.17E-46; mr1588_2 (All); LR P-value: 9.14E-25; mr1645_2 (All); LR P-value: 1.03E-07; mr1756_2 (All); LR P-value: 5.14E-10; mr1828_2 (All); LR P-value: 1.28E-70; mr1828_2 (Ind_All); LMM P-value: 6.47E-08; LR P-value: 2.94E-14; mr1842_2 (All); LR P-value: 6.28E-16; mr1889_2 (All); LR P-value: 2.69E-73; mr1889_2 (Ind_All); LR P-value: 4.15E-11; mr1896_2 (All); LR P-value: 9.36E-73; mr1896_2 (Ind_All); LR P-value: 1.52E-10; mr1907_2 (All); LMM P-value: 2.30E-06; LR P-value: 1.20E-104; mr1907_2 (Ind_All); LMM P-value: 2.31E-07; LR P-value: 1.92E-18; mr1934_2 (All); LMM P-value: 8.41E-07; LR P-value: 7.50E-92; mr1934_2 (Ind_All); LMM P-value: 6.03E-07; LR P-value: 1.88E-16 |
LOC_Os05g43140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g43140.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.863; most accessible tissue: Minghui63 panicle, score: 92.380 |
| vg0525045102 (J) | chr05 | 25045102 | T | C | 62.60% | 0.00% | C -> T |
mr1032 (All); LR P-value: 7.87E-15;
mr1105 (All); LR P-value: 4.50E-38; mr1165 (All); LR P-value: 3.30E-16; mr1478 (All); LR P-value: 4.00E-15; mr1842 (All); LR P-value: 2.80E-16; mr1889 (All); LR P-value: 5.40E-61; mr1889 (Ind_All); LR P-value: 3.14E-10; mr1896 (All); LMM P-value: 3.71E-07; LR P-value: 4.94E-83; mr1896 (Ind_All); LMM P-value: 2.06E-06; LR P-value: 1.20E-12; mr1902 (All); LR P-value: 5.68E-12; mr1903 (All); LMM P-value: 4.90E-09; LR P-value: 3.60E-35; mr1903 (Ind_All); LMM P-value: 1.07E-06; LR P-value: 3.03E-12; mr1907 (All); LMM P-value: 5.80E-08; LR P-value: 3.05E-94; mr1907 (Ind_All); LMM P-value: 8.30E-07; LR P-value: 1.15E-15; mr1934 (All); LMM P-value: 4.55E-11; LR P-value: 9.91E-92; mr1934 (Ind_All); LMM P-value: 9.63E-10; LR P-value: 9.33E-16; mr1935 (All); LMM P-value: 6.16E-10; LR P-value: 4.66E-67; mr1935 (Ind_All); LMM P-value: 1.61E-08; LR P-value: 1.13E-14; mr1162_2 (All); LR P-value: 8.07E-16; mr1175_2 (All); LR P-value: 8.69E-23; mr1195_2 (All); LR P-value: 8.25E-23; mr1195_2 (Ind_All); LR P-value: 1.18E-09; mr1253_2 (Ind_All); LR P-value: 7.94E-06; mr1281_2 (All); LR P-value: 7.73E-18; mr1299_2 (All); LR P-value: 3.89E-08; mr1478_2 (All); LR P-value: 1.51E-08; mr1546_2 (All); LR P-value: 4.87E-46; mr1588_2 (All); LR P-value: 2.83E-24; mr1592_2 (All); LR P-value: 1.59E-16; mr1645_2 (All); LR P-value: 1.05E-07; mr1713_2 (All); LR P-value: 1.46E-12; mr1756_2 (All); LR P-value: 2.24E-10; mr1790_2 (All); LR P-value: 6.51E-15; mr1828_2 (All); LMM P-value: 3.28E-07; LR P-value: 3.37E-73; mr1828_2 (Ind_All); LMM P-value: 7.32E-10; LR P-value: 6.44E-16; mr1842_2 (All); LR P-value: 1.18E-16; mr1889_2 (All); LR P-value: 8.90E-72; mr1889_2 (Ind_All); LR P-value: 6.22E-12; mr1896_2 (All); LR P-value: 7.62E-72; mr1896_2 (Ind_All); LR P-value: 7.25E-11; mr1907_2 (All); LMM P-value: 9.26E-07; LR P-value: 4.92E-105; mr1907_2 (Ind_All); LMM P-value: 7.07E-08; LR P-value: 4.55E-19; mr1933_2 (All); LR P-value: 5.42E-22; mr1934_2 (All); LMM P-value: 6.83E-07; LR P-value: 2.22E-91; mr1934_2 (Ind_All); LMM P-value: 1.68E-07; LR P-value: 4.41E-17; mr1938_2 (All); LR P-value: 3.63E-14; mr1938_2 (Ind_All); LR P-value: 5.52E-06 |
LOC_Os05g43140.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.373; most accessible tissue: Minghui63 panicle, score: 91.034 |
| vg0525045129 (J) | chr05 | 25045129 | G | T | 62.70% | 0.00% | T -> G |
mr1032 (All); LR P-value: 1.12E-14;
mr1066 (All); LR P-value: 5.42E-06; mr1105 (All); LR P-value: 1.33E-37; mr1165 (All); LR P-value: 5.04E-16; mr1478 (All); LR P-value: 5.56E-15; mr1495 (All); LR P-value: 9.57E-23; mr1842 (All); LR P-value: 5.94E-16; mr1889 (All); LR P-value: 2.79E-63; mr1889 (Ind_All); LR P-value: 3.14E-10; mr1896 (All); LMM P-value: 9.17E-07; LR P-value: 1.69E-83; mr1896 (Ind_All); LMM P-value: 2.06E-06; LR P-value: 1.20E-12; mr1902 (All); LR P-value: 4.74E-12; mr1903 (All); LMM P-value: 2.42E-08; LR P-value: 5.72E-35; mr1903 (Ind_All); LMM P-value: 1.07E-06; LR P-value: 3.03E-12; mr1907 (All); LMM P-value: 4.27E-08; LR P-value: 4.63E-95; mr1907 (Ind_All); LMM P-value: 8.30E-07; LR P-value: 1.15E-15; mr1934 (All); LMM P-value: 2.62E-11; LR P-value: 1.12E-92; mr1934 (Ind_All); LMM P-value: 9.63E-10; LR P-value: 9.33E-16; mr1935 (All); LMM P-value: 6.80E-10; LR P-value: 1.61E-67; mr1935 (Ind_All); LMM P-value: 1.61E-08; LR P-value: 1.13E-14; mr1162_2 (All); LR P-value: 2.17E-16; mr1175_2 (All); LR P-value: 1.75E-23; mr1193_2 (All); LR P-value: 2.66E-10; mr1195_2 (All); LR P-value: 2.75E-22; mr1195_2 (Ind_All); LR P-value: 1.18E-09; mr1253_2 (Ind_All); LR P-value: 7.94E-06; mr1281_2 (All); LR P-value: 5.97E-18; mr1478_2 (All); LR P-value: 9.57E-09; mr1546_2 (All); LR P-value: 2.63E-45; mr1588_2 (All); LR P-value: 3.55E-25; mr1645_2 (All); LR P-value: 6.08E-08; mr1756_2 (All); LR P-value: 1.55E-10; mr1790_2 (All); LR P-value: 4.47E-14; mr1828_2 (All); LMM P-value: 4.81E-06; LR P-value: 7.49E-71; mr1828_2 (Ind_All); LMM P-value: 7.32E-10; LR P-value: 6.44E-16; mr1842_2 (All); LR P-value: 1.64E-16; mr1889_2 (All); LR P-value: 9.15E-74; mr1889_2 (Ind_All); LR P-value: 6.22E-12; mr1896_2 (All); LR P-value: 1.00E-72; mr1896_2 (Ind_All); LR P-value: 7.25E-11; mr1907_2 (All); LMM P-value: 2.41E-06; LR P-value: 1.59E-104; mr1907_2 (Ind_All); LMM P-value: 7.07E-08; LR P-value: 4.55E-19; mr1933_2 (All); LR P-value: 3.43E-22; mr1934_2 (All); LMM P-value: 2.15E-07; LR P-value: 2.34E-92; mr1934_2 (Ind_All); LMM P-value: 1.68E-07; LR P-value: 4.41E-17; mr1938_2 (All); LR P-value: 3.34E-14; mr1938_2 (Ind_All); LR P-value: 5.52E-06 |
LOC_Os05g43140.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.242; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0525045350 (J) | chr05 | 25045350 | AT | A | 92.60% | 0.00% | AT -> A,ATT | NA |
LOC_Os05g43140.1 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43140.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43130.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.348; most accessible tissue: Minghui63 panicle, score: 81.412 |
| vg0525045368 (J) | chr05 | 25045368 | C | G | 92.70% | 0.00% | C -> G | NA |
LOC_Os05g43140.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.461; most accessible tissue: Minghui63 panicle, score: 77.956 |
| vg0525045469 (J) | chr05 | 25045469 | A | T | 92.70% | 0.00% | A -> T | NA |
LOC_Os05g43140.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.342; most accessible tissue: Callus, score: 89.172 |
| vg0525045476 (J) | chr05 | 25045476 | T | C | 92.70% | 0.00% | T -> C | NA |
LOC_Os05g43140.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g43130.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g43150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.685; most accessible tissue: Callus, score: 89.172 |
| vg0525045619 (J) | chr05 | 25045619 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os05g43140.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g43130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g43150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.048; most accessible tissue: Callus, score: 78.141 |
| STR0525044787 (J) | chr05 | 25044787 | CGCCGCC TCG | CGCCTCC TCC | 88.50% | 0.00% | CGCCGCCTCG -> CGCCTCCTCC ,CGCCGCCTC C | NA |
|