17 variations found. LOC_Os10g40830 (metalloendoproteinase 1 precursor; putative; expressed), ranging from 21,955,039 bp to 21,957,289 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1021955049 (J) | chr10 | 21955049 | A | G | 63.40% | 0.61% | A -> G |
mr1794 (Ind_All); LR P-value: 8.62E-08;
mr1860 (All); LR P-value: 2.40E-09; mr1904 (Ind_All); LR P-value: 3.95E-06; mr1183_2 (Ind_All); LR P-value: 1.39E-07; mr1321_2 (All); LR P-value: 8.44E-07; mr1322_2 (Ind_All); LR P-value: 9.24E-07; mr1323_2 (Ind_All); LR P-value: 2.84E-06; mr1330_2 (Ind_All); LR P-value: 3.73E-11; mr1332_2 (All); LR P-value: 6.54E-06; mr1336_2 (Ind_All); LR P-value: 2.27E-07; mr1349_2 (All); LR P-value: 4.29E-11; mr1360_2 (Ind_All); LR P-value: 7.50E-06; mr1438_2 (Ind_All); LR P-value: 7.90E-06; mr1478_2 (All); LR P-value: 8.43E-09; mr1527_2 (Ind_All); LR P-value: 4.95E-07; mr1540_2 (Ind_All); LR P-value: 2.68E-06; mr1598_2 (All); LR P-value: 8.11E-36; mr1598_2 (Ind_All); LR P-value: 7.89E-10; mr1715_2 (Ind_All); LR P-value: 6.04E-12; mr1728_2 (All); LR P-value: 2.91E-11; mr1732_2 (Ind_All); LR P-value: 1.04E-06; mr1754_2 (All); LR P-value: 1.00E-06; mr1860_2 (All); LR P-value: 2.20E-09; mr1875_2 (All); LR P-value: 5.06E-06; mr1895_2 (All); LR P-value: 1.66E-07; mr1895_2 (Ind_All); LR P-value: 8.25E-07; mr1899_2 (All); LR P-value: 7.36E-06; mr1910_2 (All); LR P-value: 5.20E-06; mr1946_2 (All); LR P-value: 1.79E-10; mr1948_2 (All); LR P-value: 1.79E-10; mr1962_2 (Ind_All); LR P-value: 1.16E-08 |
LOC_Os10g40824.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40820.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955122 (J) | chr10 | 21955122 | C | T | 70.20% | 0.47% | C -> T |
LOC_Os10g40824.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40820.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg1021955133 (J) | chr10 | 21955133 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os10g40824.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os10g40830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os10g40820.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g40840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955454 (J) | chr10 | 21955454 | C | T | 63.30% | 0.61% | C -> T |
mr1717 (All); LR P-value: 1.24E-07;
mr1794 (Ind_All); LR P-value: 2.51E-08; mr1860 (All); LR P-value: 1.19E-08; mr1183_2 (Ind_All); LR P-value: 1.13E-07; mr1321_2 (All); LR P-value: 2.63E-07; mr1322_2 (Ind_All); LR P-value: 8.45E-07; mr1323_2 (Ind_All); LR P-value: 1.57E-06; mr1330_2 (Ind_All); LR P-value: 5.53E-11; mr1336_2 (Ind_All); LR P-value: 2.74E-07; mr1349_2 (All); LR P-value: 1.74E-11; mr1355_2 (All); LR P-value: 4.50E-06; mr1360_2 (Ind_All); LR P-value: 9.98E-06; mr1438_2 (Ind_All); LR P-value: 5.37E-06; mr1479_2 (All); LR P-value: 1.44E-06; mr1527_2 (Ind_All); LR P-value: 1.13E-06; mr1540_2 (Ind_All); LR P-value: 2.14E-06; mr1598_2 (All); LR P-value: 2.12E-32; mr1598_2 (Ind_All); LR P-value: 1.02E-09; mr1715_2 (Ind_All); LR P-value: 4.69E-12; mr1717_2 (All); LR P-value: 9.06E-13; mr1728_2 (All); LR P-value: 2.89E-11; mr1732_2 (Ind_All); LR P-value: 8.62E-07; mr1754_2 (All); LR P-value: 1.58E-06; mr1860_2 (All); LR P-value: 3.71E-10; mr1895_2 (All); LR P-value: 4.24E-07; mr1895_2 (Ind_All); LR P-value: 6.73E-07; mr1904_2 (Ind_All); LR P-value: 1.09E-06; mr1910_2 (All); LR P-value: 4.50E-06; mr1946_2 (All); LR P-value: 3.20E-09; mr1948_2 (All); LR P-value: 3.20E-09 |
LOC_Os10g40824.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40820.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955624 (J) | chr10 | 21955624 | CT | CTT | 98.20% | 0.00% | CT -> CTT,C | NA |
LOC_Os10g40830.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40830.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40820.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955625 (J) | chr10 | 21955625 | T | A | 98.20% | 1.14% | T -> A | NA |
LOC_Os10g40830.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955677 (J) | chr10 | 21955677 | T | C | 63.50% | 0.11% | T -> C |
Grain_width (Ind_All); LR P-value: 2.87E-10;
mr1503 (Ind_All); LR P-value: 1.13E-06; mr1717 (All); LR P-value: 2.01E-07; mr1794 (Ind_All); LR P-value: 8.82E-08; mr1860 (All); LR P-value: 3.53E-09; mr1183_2 (Ind_All); LR P-value: 7.42E-08; mr1321_2 (All); LR P-value: 3.39E-07; mr1322_2 (Ind_All); LR P-value: 4.79E-07; mr1323_2 (Ind_All); LR P-value: 1.00E-06; mr1330_2 (Ind_All); LR P-value: 2.80E-11; mr1332_2 (All); LR P-value: 6.61E-06; mr1336_2 (Ind_All); LR P-value: 1.27E-07; mr1349_2 (All); LR P-value: 1.58E-11; mr1349_2 (Ind_All); LR P-value: 5.61E-06; mr1355_2 (All); LR P-value: 5.83E-06; mr1360_2 (Ind_All); LR P-value: 2.95E-06; mr1478_2 (All); LR P-value: 6.06E-09; mr1527_2 (Ind_All); LR P-value: 1.39E-06; mr1540_2 (Ind_All); LR P-value: 1.30E-06; mr1598_2 (All); LR P-value: 1.19E-34; mr1598_2 (Ind_All); LR P-value: 4.97E-09; mr1715_2 (Ind_All); LR P-value: 9.85E-13; mr1728_2 (All); LR P-value: 2.72E-11; mr1732_2 (Ind_All); LR P-value: 3.93E-07; mr1754_2 (All); LR P-value: 3.09E-06; mr1860_2 (All); LR P-value: 1.15E-09; mr1895_2 (All); LR P-value: 8.52E-08; mr1895_2 (Ind_All); LR P-value: 3.27E-07; mr1899_2 (All); LR P-value: 6.89E-06; mr1910_2 (All); LR P-value: 3.76E-06; mr1946_2 (All); LR P-value: 3.18E-10; mr1948_2 (All); LR P-value: 3.18E-10 |
LOC_Os10g40830.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021955737 (J) | chr10 | 21955737 | C | G | 70.20% | 0.59% | C -> G |
LOC_Os10g40830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g40830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg1021955776 (J) | chr10 | 21955776 | T | A | 63.50% | 0.51% | T -> A |
Grain_length (Ind_All); LR P-value: 2.01E-13;
mr1441 (Ind_All); LR P-value: 2.14E-06; mr1503 (Ind_All); LR P-value: 6.45E-07; mr1715 (Ind_All); LR P-value: 2.67E-06; mr1717 (All); LR P-value: 9.02E-08; mr1794 (Ind_All); LR P-value: 1.22E-08; mr1860 (All); LR P-value: 6.16E-09; mr1183_2 (Ind_All); LR P-value: 5.45E-08; mr1319_2 (Ind_All); LR P-value: 4.73E-06; mr1321_2 (All); LR P-value: 7.34E-07; mr1322_2 (Ind_All); LR P-value: 5.35E-07; mr1323_2 (Ind_All); LR P-value: 1.43E-06; mr1330_2 (Ind_All); LR P-value: 4.82E-11; mr1332_2 (All); LR P-value: 5.51E-06; mr1336_2 (Ind_All); LR P-value: 3.62E-07; mr1349_2 (All); LR P-value: 2.97E-11; mr1360_2 (Ind_All); LR P-value: 9.90E-06; mr1438_2 (Ind_All); LR P-value: 3.50E-06; mr1527_2 (Ind_All); LR P-value: 1.45E-06; mr1540_2 (Ind_All); LR P-value: 1.99E-06; mr1598_2 (All); LR P-value: 1.66E-36; mr1598_2 (Ind_All); LR P-value: 3.05E-10; mr1715_2 (Ind_All); LR P-value: 5.51E-12; mr1728_2 (All); LR P-value: 4.83E-11; mr1732_2 (Ind_All); LR P-value: 1.00E-06; mr1754_2 (All); LR P-value: 9.16E-07; mr1860_2 (All); LR P-value: 6.33E-09; mr1875_2 (All); LR P-value: 4.54E-06; mr1895_2 (All); LR P-value: 7.55E-08; mr1895_2 (Ind_All); LR P-value: 6.34E-07; mr1910_2 (All); LR P-value: 2.92E-06; mr1946_2 (All); LR P-value: 2.70E-09; mr1948_2 (All); LR P-value: 2.70E-09 |
LOC_Os10g40830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g40830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021956177 (J) | chr10 | 21956177 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os10g40830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021956657 (J) | chr10 | 21956657 | G | GCCGTGC CCGTGC | 63.50% | 0.00% | G -> GCCGTGCCCG TGC | NA |
LOC_Os10g40830.1 Alt: GCCGTGCCCGTGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021956826 (J) | chr10 | 21956826 | C | T | 63.50% | 0.40% | C -> T |
mr1717 (All); LR P-value: 1.86E-07;
mr1794 (Ind_All); LR P-value: 2.51E-08; mr1860 (All); LR P-value: 1.12E-08; mr1183_2 (Ind_All); LR P-value: 1.13E-07; mr1321_2 (All); LR P-value: 6.06E-07; mr1322_2 (Ind_All); LR P-value: 8.45E-07; mr1323_2 (Ind_All); LR P-value: 1.57E-06; mr1330_2 (Ind_All); LR P-value: 5.53E-11; mr1336_2 (Ind_All); LR P-value: 2.74E-07; mr1349_2 (All); LR P-value: 3.53E-11; mr1355_2 (All); LR P-value: 9.83E-06; mr1360_2 (Ind_All); LR P-value: 9.98E-06; mr1438_2 (Ind_All); LR P-value: 5.37E-06; mr1478_2 (All); LR P-value: 1.07E-08; mr1527_2 (Ind_All); LR P-value: 1.13E-06; mr1540_2 (Ind_All); LR P-value: 2.14E-06; mr1598_2 (All); LR P-value: 6.99E-36; mr1598_2 (Ind_All); LR P-value: 1.02E-09; mr1715_2 (Ind_All); LR P-value: 4.69E-12; mr1728_2 (All); LR P-value: 2.81E-11; mr1732_2 (Ind_All); LR P-value: 8.62E-07; mr1754_2 (All); LR P-value: 4.61E-07; mr1860_2 (All); LR P-value: 2.88E-09; mr1895_2 (All); LR P-value: 1.51E-07; mr1895_2 (Ind_All); LR P-value: 6.73E-07; mr1904_2 (Ind_All); LR P-value: 1.09E-06; mr1910_2 (All); LR P-value: 3.46E-06; mr1946_2 (All); LR P-value: 6.56E-10; mr1948_2 (All); LR P-value: 6.56E-10 |
LOC_Os10g40830.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021957010 (J) | chr10 | 21957010 | T | G | 63.30% | 0.47% | T -> G |
Grain_width (Ind_All); LR P-value: 2.49E-10;
mr1503 (Ind_All); LR P-value: 8.87E-07; mr1717 (All); LR P-value: 2.17E-07; mr1794 (Ind_All); LR P-value: 1.69E-08; mr1860 (All); LR P-value: 6.14E-09; mr1183_2 (Ind_All); LR P-value: 6.18E-08; mr1321_2 (All); LR P-value: 2.19E-07; mr1322_2 (Ind_All); LR P-value: 5.60E-07; mr1323_2 (Ind_All); LR P-value: 1.20E-06; mr1330_2 (Ind_All); LR P-value: 1.38E-11; mr1332_2 (All); LR P-value: 9.97E-06; mr1336_2 (Ind_All); LR P-value: 1.65E-07; mr1349_2 (All); LR P-value: 1.13E-11; mr1349_2 (Ind_All); LR P-value: 6.05E-06; mr1355_2 (All); LR P-value: 3.70E-06; mr1360_2 (Ind_All); LR P-value: 4.14E-06; mr1438_2 (Ind_All); LR P-value: 4.78E-06; mr1478_2 (All); LR P-value: 1.75E-08; mr1479_2 (All); LR P-value: 1.54E-06; mr1527_2 (Ind_All); LR P-value: 4.80E-07; mr1540_2 (Ind_All); LR P-value: 1.07E-06; mr1598_2 (All); LR P-value: 1.33E-31; mr1598_2 (Ind_All); LR P-value: 2.13E-09; mr1715_2 (Ind_All); LR P-value: 2.38E-12; mr1717_2 (All); LR P-value: 9.89E-13; mr1728_2 (All); LR P-value: 4.53E-11; mr1732_2 (Ind_All); LR P-value: 4.36E-07; mr1754_2 (All); LR P-value: 2.31E-06; mr1860_2 (All); LR P-value: 3.22E-10; mr1895_2 (All); LR P-value: 3.58E-07; mr1895_2 (Ind_All); LR P-value: 4.13E-07; mr1899_2 (All); LR P-value: 7.32E-06; mr1910_2 (All); LR P-value: 4.60E-06; mr1946_2 (All); LR P-value: 1.69E-09; mr1948_2 (All); LR P-value: 1.69E-09 |
LOC_Os10g40830.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021957237 (J) | chr10 | 21957237 | G | T | 93.40% | 0.00% | G -> T |
mr1692 (Ind_All); LR P-value: 7.35E-06;
mr1045_2 (All); LR P-value: 5.42E-07; mr1045_2 (Ind_All); LR P-value: 6.86E-06; mr1053_2 (All); LR P-value: 6.75E-07; mr1115_2 (Ind_All); LR P-value: 3.91E-07; mr1236_2 (Ind_All); LR P-value: 6.25E-07; mr1306_2 (Ind_All); LR P-value: 7.89E-06; mr1517_2 (Ind_All); LR P-value: 1.16E-06; mr1611_2 (Ind_All); LR P-value: 6.93E-07; mr1641_2 (Ind_All); LR P-value: 1.78E-06; mr1696_2 (Ind_All); LR P-value: 8.31E-07; mr1735_2 (Ind_All); LR P-value: 4.99E-06; mr1758_2 (Ind_All); LR P-value: 2.17E-08; mr1763_2 (All); LR P-value: 2.17E-06; mr1820_2 (Ind_All); LR P-value: 9.35E-06; mr1838_2 (Ind_All); LR P-value: 8.15E-08; mr1876_2 (All); LR P-value: 3.60E-06; mr1901_2 (All); LR P-value: 2.05E-06; mr1906_2 (Ind_All); LR P-value: 5.91E-06; mr1909_2 (Ind_All); LR P-value: 3.00E-06; mr1959_2 (Ind_All); LR P-value: 4.50E-07; mr1960_2 (Ind_All); LR P-value: 4.79E-06 |
LOC_Os10g40830.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021957258 (J) | chr10 | 21957258 | G | A | 63.20% | 0.47% | G -> A |
Grain_width (Ind_All); LR P-value: 2.49E-10;
mr1503 (Ind_All); LR P-value: 8.87E-07; mr1717 (All); LR P-value: 2.14E-07; mr1794 (Ind_All); LR P-value: 1.69E-08; mr1860 (All); LR P-value: 4.80E-09; mr1183_2 (Ind_All); LR P-value: 6.18E-08; mr1321_2 (All); LR P-value: 2.15E-07; mr1322_2 (Ind_All); LR P-value: 5.60E-07; mr1323_2 (Ind_All); LR P-value: 1.20E-06; mr1330_2 (Ind_All); LR P-value: 1.38E-11; mr1332_2 (All); LR P-value: 6.64E-06; mr1336_2 (Ind_All); LR P-value: 1.65E-07; mr1349_2 (All); LR P-value: 5.36E-12; mr1349_2 (Ind_All); LR P-value: 6.05E-06; mr1355_2 (All); LR P-value: 2.85E-06; mr1360_2 (Ind_All); LR P-value: 4.14E-06; mr1438_2 (Ind_All); LR P-value: 4.78E-06; mr1462_2 (All); LR P-value: 7.71E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1527_2 (Ind_All); LR P-value: 4.80E-07; mr1540_2 (Ind_All); LR P-value: 1.07E-06; mr1598_2 (All); LR P-value: 9.62E-32; mr1598_2 (Ind_All); LR P-value: 2.13E-09; mr1715_2 (Ind_All); LR P-value: 2.38E-12; mr1717_2 (All); LR P-value: 5.29E-13; mr1728_2 (All); LR P-value: 2.37E-11; mr1732_2 (Ind_All); LR P-value: 4.36E-07; mr1754_2 (All); LR P-value: 2.02E-06; mr1860_2 (All); LR P-value: 2.56E-10; mr1895_2 (All); LR P-value: 2.08E-07; mr1895_2 (Ind_All); LR P-value: 4.13E-07; mr1899_2 (All); LR P-value: 7.47E-06; mr1910_2 (All); LR P-value: 3.51E-06; mr1946_2 (All); LR P-value: 2.45E-09; mr1948_2 (All); LR P-value: 2.45E-09 |
LOC_Os10g40830.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g40820.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g40824.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021957284 (J) | chr10 | 21957284 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os10g40830.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os10g40820.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g40840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g40824.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| STR1021956658 (J) | chr10 | 21956658 | CCGTGCC CGTGC | CCGTGCC CGTGCCC GTGCCCG TGC | 68.10% | 0.00% | CCGTGCCCGT GC -> CCGTGCCCGT GCCCGTGCCC GTGC | NA |
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