21 variations found. LOC_Os10g01740 (hypothetical protein), ranging from 477,514 bp to 477,832 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477520 (J) | chr10 | 477520 | T | C | 55.00% | 6.52% | C -> T |
Grain_length (All); LR P-value: 4.78E-14;
mr1011 (Jap_All); LMM P-value: 9.09E-06; LR P-value: 9.09E-06; mr1156 (Jap_All); LR P-value: 2.26E-08; mr1157 (All); LR P-value: 2.03E-07; mr1163 (Jap_All); LR P-value: 3.71E-07; mr1179 (Jap_All); LR P-value: 5.05E-07; mr1192 (Jap_All); LR P-value: 3.76E-07; mr1251 (Jap_All); LR P-value: 4.87E-10; mr1252 (Jap_All); LR P-value: 4.55E-07; mr1300 (Jap_All); LR P-value: 4.10E-09; mr1310 (Jap_All); LR P-value: 2.96E-11; mr1328 (All); LR P-value: 3.01E-08; mr1378 (All); LR P-value: 1.23E-06; mr1446 (All); LR P-value: 4.26E-09; mr1486 (Jap_All); LR P-value: 6.16E-11; mr1495 (Jap_All); LR P-value: 3.14E-06; mr1520 (All); LR P-value: 8.31E-07; mr1531 (Jap_All); LR P-value: 6.32E-06; mr1539 (All); LR P-value: 6.26E-12; mr1539 (Jap_All); LR P-value: 1.72E-10; mr1540 (All); LR P-value: 1.13E-18; mr1548 (Jap_All); LR P-value: 9.67E-07; mr1549 (Jap_All); LR P-value: 1.67E-11; mr1550 (Jap_All); LR P-value: 9.83E-06; mr1570 (Jap_All); LR P-value: 5.15E-07; mr1580 (Jap_All); LR P-value: 4.31E-11; mr1588 (Jap_All); LR P-value: 6.45E-06; mr1614 (All); LR P-value: 2.39E-06; mr1621 (All); LR P-value: 4.52E-06; mr1624 (Jap_All); LR P-value: 8.35E-09; mr1715 (Jap_All); LR P-value: 1.98E-07; mr1732 (All); LR P-value: 3.90E-19; mr1733 (Jap_All); LR P-value: 2.19E-07; mr1736 (Jap_All); LMM P-value: 2.92E-06; LR P-value: 1.81E-09; mr1757 (Jap_All); LR P-value: 1.14E-10; mr1780 (Jap_All); LR P-value: 3.66E-06; mr1825 (Jap_All); LR P-value: 1.72E-10; mr1870 (Jap_All); LR P-value: 7.45E-07; mr1912 (Jap_All); LR P-value: 9.28E-07; mr1926 (All); LMM P-value: 9.68E-06; mr1926 (Jap_All); LR P-value: 5.91E-12; mr1959 (Jap_All); LR P-value: 3.13E-06; mr1126_2 (All); LR P-value: 7.59E-10; mr1310_2 (Jap_All); LMM P-value: 2.53E-06; LR P-value: 1.89E-13; mr1486_2 (Jap_All); LR P-value: 5.14E-10; mr1959_2 (Jap_All); LR P-value: 1.40E-08 |
LOC_Os10g01740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.595; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1000477536 (J) | chr10 | 477536 | C | G | 92.50% | 6.39% | C -> G | NA |
LOC_Os10g01740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.624; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1000477554 (J) | chr10 | 477554 | C | T | 54.10% | 6.79% | C -> T |
mr1156 (Jap_All); LR P-value: 1.10E-07;
mr1163 (Jap_All); LR P-value: 1.29E-06; mr1179 (Jap_All); LR P-value: 1.31E-06; mr1192 (All); LR P-value: 5.00E-06; mr1192 (Jap_All); LR P-value: 3.28E-06; mr1229 (All); LR P-value: 1.44E-06; mr1300 (Jap_All); LR P-value: 1.95E-08; mr1310 (Jap_All); LR P-value: 5.57E-11; mr1486 (Jap_All); LR P-value: 3.78E-10; mr1539 (All); LR P-value: 4.51E-10; mr1540 (All); LR P-value: 5.71E-13; mr1548 (Jap_All); LR P-value: 1.34E-06; mr1549 (Jap_All); LR P-value: 3.52E-10; mr1580 (Jap_All); LR P-value: 2.76E-11; mr1588 (Jap_All); LR P-value: 2.28E-06; mr1679 (Jap_All); LR P-value: 5.13E-09; mr1732 (All); LR P-value: 5.32E-13; mr1736 (Jap_All); LR P-value: 1.35E-08; mr1757 (Jap_All); LR P-value: 2.49E-09; mr1769 (All); LR P-value: 3.02E-10; mr1780 (Jap_All); LR P-value: 5.75E-06; mr1825 (Jap_All); LR P-value: 2.87E-10; mr1880 (All); LR P-value: 3.50E-07; mr1912 (Jap_All); LR P-value: 1.68E-06; mr1926 (Jap_All); LR P-value: 5.20E-11; mr1951 (All); LR P-value: 5.65E-08; mr1959 (Jap_All); LR P-value: 6.15E-06; mr1310_2 (Jap_All); LMM P-value: 7.67E-06; LR P-value: 1.53E-12; mr1486_2 (Jap_All); LR P-value: 2.52E-09; mr1959_2 (Jap_All); LR P-value: 4.47E-08 |
LOC_Os10g01740.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.645; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1000477555 (J) | chr10 | 477555 | A | G | 55.00% | 6.64% | G -> A |
mr1156 (Jap_All); LR P-value: 4.56E-08;
mr1157 (All); LR P-value: 2.28E-07; mr1163 (Jap_All); LR P-value: 5.63E-07; mr1179 (Jap_All); LR P-value: 7.88E-07; mr1192 (Jap_All); LR P-value: 5.33E-07; mr1251 (Jap_All); LR P-value: 1.42E-09; mr1252 (Jap_All); LR P-value: 8.40E-07; mr1300 (Jap_All); LR P-value: 3.05E-09; mr1310 (Jap_All); LMM P-value: 9.20E-06; LR P-value: 2.16E-11; mr1328 (All); LR P-value: 4.00E-08; mr1378 (All); LR P-value: 7.75E-07; mr1446 (All); LR P-value: 1.96E-08; mr1486 (Jap_All); LR P-value: 2.09E-10; mr1495 (Jap_All); LR P-value: 3.53E-06; mr1520 (All); LR P-value: 6.23E-07; mr1531 (Jap_All); LR P-value: 9.11E-06; mr1539 (All); LR P-value: 2.58E-11; mr1539 (Jap_All); LR P-value: 3.75E-10; mr1540 (All); LR P-value: 1.10E-17; mr1548 (Jap_All); LR P-value: 2.36E-06; mr1549 (Jap_All); LR P-value: 4.03E-11; mr1570 (Jap_All); LR P-value: 6.84E-07; mr1580 (Jap_All); LR P-value: 2.58E-11; mr1614 (All); LR P-value: 2.64E-06; mr1621 (All); LR P-value: 7.00E-06; mr1624 (Jap_All); LR P-value: 2.18E-08; mr1715 (Jap_All); LR P-value: 2.08E-07; mr1732 (All); LR P-value: 3.24E-18; mr1733 (Jap_All); LR P-value: 3.89E-07; mr1736 (All); LMM P-value: 1.14E-06; LR P-value: 1.13E-06; mr1736 (Jap_All); LMM P-value: 6.86E-06; LR P-value: 3.10E-09; mr1757 (Jap_All); LR P-value: 2.69E-10; mr1780 (Jap_All); LR P-value: 3.28E-06; mr1825 (Jap_All); LR P-value: 1.41E-10; mr1870 (Jap_All); LR P-value: 7.44E-07; mr1912 (Jap_All); LR P-value: 1.83E-06; mr1926 (All); LMM P-value: 6.87E-06; mr1926 (Jap_All); LR P-value: 3.98E-12; mr1959 (Jap_All); LR P-value: 4.10E-06; mr1126_2 (All); LR P-value: 4.29E-09; mr1310_2 (Jap_All); LMM P-value: 1.21E-06; LR P-value: 1.13E-13; mr1486_2 (Jap_All); LR P-value: 1.38E-09; mr1959_2 (Jap_All); LR P-value: 1.38E-08 |
LOC_Os10g01740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g01740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.645; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1000477580 (J) | chr10 | 477580 | G | A | 76.10% | 7.19% | G -> A |
LOC_Os10g01740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.201; most accessible tissue: Minghui63 panicle, score: 25.313 |
|
| vg1000477607 (J) | chr10 | 477607 | A | G | 55.10% | 7.60% | G -> A |
Grain_length (All); LR P-value: 2.13E-13;
mr1011 (Jap_All); LMM P-value: 6.52E-06; LR P-value: 6.51E-06; mr1156 (Jap_All); LR P-value: 1.07E-08; mr1157 (All); LR P-value: 2.45E-07; mr1163 (Jap_All); LR P-value: 2.58E-07; mr1179 (Jap_All); LR P-value: 3.34E-07; mr1192 (Jap_All); LR P-value: 2.92E-07; mr1251 (Jap_All); LR P-value: 1.39E-10; mr1252 (Jap_All); LR P-value: 2.30E-07; mr1300 (Jap_All); LR P-value: 9.33E-09; mr1310 (Jap_All); LR P-value: 7.88E-11; mr1328 (All); LR P-value: 5.44E-08; mr1378 (All); LR P-value: 9.20E-07; mr1446 (All); LR P-value: 1.70E-08; mr1486 (Jap_All); LR P-value: 1.45E-11; mr1495 (Jap_All); LR P-value: 3.33E-06; mr1520 (All); LR P-value: 1.50E-06; mr1531 (Jap_All); LR P-value: 4.48E-06; mr1539 (All); LR P-value: 4.07E-10; mr1539 (Jap_All); LR P-value: 8.08E-11; mr1540 (All); LR P-value: 1.27E-16; mr1548 (Jap_All); LR P-value: 3.03E-07; mr1549 (Jap_All); LR P-value: 7.16E-12; mr1550 (Jap_All); LR P-value: 9.07E-06; mr1570 (Jap_All); LR P-value: 4.39E-07; mr1580 (Jap_All); LR P-value: 1.51E-10; mr1588 (Jap_All); LR P-value: 3.01E-06; mr1614 (All); LR P-value: 2.13E-06; mr1621 (All); LR P-value: 4.96E-06; mr1624 (Jap_All); LR P-value: 2.65E-09; mr1715 (Jap_All); LR P-value: 2.48E-07; mr1729 (Jap_All); LR P-value: 4.87E-06; mr1732 (All); LR P-value: 5.97E-17; mr1733 (Jap_All); LR P-value: 1.20E-07; mr1736 (All); LMM P-value: 2.23E-06; LR P-value: 2.22E-06; mr1736 (Jap_All); LMM P-value: 1.37E-06; LR P-value: 1.19E-09; mr1757 (Jap_All); LR P-value: 4.79E-11; mr1780 (Jap_All); LR P-value: 5.45E-06; mr1825 (Jap_All); LR P-value: 3.66E-10; mr1870 (Jap_All); LR P-value: 9.74E-07; mr1912 (Jap_All); LR P-value: 4.13E-07; mr1926 (Jap_All); LR P-value: 1.83E-11; mr1959 (Jap_All); LR P-value: 2.61E-06; mr1126_2 (All); LR P-value: 5.48E-09; mr1136_2 (Ind_All); LR P-value: 5.12E-06; mr1156_2 (Jap_All); LR P-value: 1.51E-07; mr1310_2 (Jap_All); LR P-value: 7.61E-13; mr1486_2 (Jap_All); LR P-value: 1.68E-10; mr1733_2 (Jap_All); LR P-value: 4.47E-07; mr1959_2 (Jap_All); LR P-value: 2.05E-08 |
LOC_Os10g01740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.595; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg1000477617 (J) | chr10 | 477617 | A | C | 74.90% | 7.83% | C -> A |
mr1300 (All); LMM P-value: 2.88E-25; LR P-value: 9.27E-47;
mr1300 (Jap_All); LMM P-value: 8.22E-12; LR P-value: 1.36E-16; mr1310 (All); LMM P-value: 6.98E-27; LR P-value: 4.87E-66; mr1310 (Jap_All); LMM P-value: 1.53E-12; LR P-value: 9.11E-20; mr1498 (All); LMM P-value: 1.19E-06; LR P-value: 1.44E-06; mr1926 (All); LMM P-value: 1.40E-34; LR P-value: 2.70E-80; mr1926 (Jap_All); LMM P-value: 2.95E-14; LR P-value: 1.89E-23; mr1959 (All); LMM P-value: 4.37E-13; LR P-value: 2.49E-19; mr1959 (Jap_All); LMM P-value: 3.24E-09; LR P-value: 1.57E-11; mr1310_2 (All); LMM P-value: 9.32E-44; LR P-value: 4.32E-79; mr1310_2 (Jap_All); LMM P-value: 1.17E-21; LR P-value: 8.88E-34; mr1959_2 (All); LMM P-value: 2.38E-20; LR P-value: 6.58E-32; mr1959_2 (Jap_All); LMM P-value: 3.13E-12; LR P-value: 1.81E-19 |
LOC_Os10g01740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.211; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1000477621 (J) | chr10 | 477621 | C | T | 76.00% | 7.62% | C -> T |
LOC_Os10g01740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.991; most accessible tissue: Minghui63 panicle, score: 29.741 |
|
| vg1000477626 (J) | chr10 | 477626 | G | A | 77.10% | 7.32% | G -> A | NA |
LOC_Os10g01740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g01740.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.913; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1000477627 (J) | chr10 | 477627 | G | A | 74.40% | 7.32% | G -> A,GTGTCTAT CC | NA |
LOC_Os10g01740.1 Alt: GTGTCTATCC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os10g01740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.947; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1000477640 (J) | chr10 | 477640 | C | T | 77.10% | 7.15% | C -> T | NA |
LOC_Os10g01740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g01740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.597; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1000477670 (J) | chr10 | 477670 | G | A | 77.20% | 6.62% | G -> A |
LOC_Os10g01740.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 19.712; most accessible tissue: Minghui63 panicle, score: 25.313 |
|
| vg1000477675 (J) | chr10 | 477675 | G | A | 73.00% | 6.50% | A -> G |
mr1011 (Jap_All); LMM P-value: 8.41E-07; LR P-value: 8.40E-07;
mr1156 (Jap_All); LR P-value: 1.88E-07; mr1163 (Jap_All); LR P-value: 1.29E-08; mr1179 (Jap_All); LR P-value: 3.33E-06; mr1192 (Jap_All); LR P-value: 1.53E-06; mr1300 (All); LMM P-value: 6.82E-07; LR P-value: 3.60E-22; mr1300 (Jap_All); LR P-value: 1.86E-09; mr1310 (All); LMM P-value: 1.17E-08; LR P-value: 3.14E-35; mr1310 (Jap_All); LMM P-value: 2.23E-06; LR P-value: 3.45E-12; mr1486 (Jap_All); LR P-value: 6.78E-12; mr1502 (Jap_All); LR P-value: 3.41E-06; mr1539 (Jap_All); LR P-value: 1.30E-10; mr1548 (Jap_All); LR P-value: 1.84E-08; mr1549 (Jap_All); LR P-value: 3.95E-09; mr1570 (Jap_All); LR P-value: 4.74E-07; mr1588 (Jap_All); LR P-value: 5.18E-07; mr1624 (Jap_All); LR P-value: 4.28E-08; mr1729 (Jap_All); LR P-value: 3.32E-06; mr1736 (Jap_All); LR P-value: 8.74E-07; mr1757 (Jap_All); LR P-value: 1.57E-08; mr1780 (Jap_All); LR P-value: 1.73E-06; mr1825 (Jap_All); LR P-value: 1.38E-08; mr1912 (Jap_All); LR P-value: 3.19E-06; mr1926 (All); LMM P-value: 2.69E-07; mr1926 (Jap_All); LMM P-value: 2.52E-06; LR P-value: 4.30E-13; mr1959 (All); LMM P-value: 3.81E-06; LR P-value: 1.54E-11; mr1959 (Jap_All); LR P-value: 1.78E-07; mr1310_2 (All); LMM P-value: 2.18E-07; mr1310_2 (Jap_All); LMM P-value: 3.44E-06; LR P-value: 4.07E-14; mr1486_2 (Jap_All); LR P-value: 4.34E-11; mr1588_2 (Jap_All); LR P-value: 9.21E-06; mr1959_2 (All); LR P-value: 2.59E-15; mr1959_2 (Jap_All); LR P-value: 2.08E-09 |
LOC_Os10g01740.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.020; most accessible tissue: Callus, score: 37.292 |
| vg1000477694 (J) | chr10 | 477694 | G | A | 92.60% | 5.27% | G -> A | NA |
LOC_Os10g01730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01740.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.141; most accessible tissue: Callus, score: 37.292 |
| vg1000477701 (J) | chr10 | 477701 | G | A | 54.30% | 6.09% | G -> A |
mr1011 (Jap_All); LMM P-value: 6.52E-06; LR P-value: 6.51E-06;
mr1156 (Jap_All); LR P-value: 1.07E-08; mr1163 (Jap_All); LR P-value: 2.58E-07; mr1179 (Jap_All); LR P-value: 3.34E-07; mr1192 (All); LR P-value: 1.50E-06; mr1192 (Jap_All); LR P-value: 2.92E-07; mr1251 (Jap_All); LR P-value: 1.39E-10; mr1252 (Jap_All); LR P-value: 2.30E-07; mr1300 (Jap_All); LR P-value: 9.33E-09; mr1310 (Jap_All); LR P-value: 7.88E-11; mr1486 (Jap_All); LR P-value: 1.45E-11; mr1495 (Jap_All); LR P-value: 3.33E-06; mr1531 (Jap_All); LR P-value: 4.48E-06; mr1539 (All); LR P-value: 4.64E-10; mr1539 (Jap_All); LR P-value: 8.08E-11; mr1540 (All); LR P-value: 2.45E-12; mr1548 (Jap_All); LR P-value: 3.03E-07; mr1549 (Jap_All); LR P-value: 7.16E-12; mr1550 (Jap_All); LR P-value: 9.07E-06; mr1570 (Jap_All); LR P-value: 4.39E-07; mr1580 (Jap_All); LR P-value: 1.51E-10; mr1588 (Jap_All); LR P-value: 3.01E-06; mr1624 (Jap_All); LR P-value: 2.65E-09; mr1715 (Jap_All); LR P-value: 2.48E-07; mr1729 (Jap_All); LR P-value: 4.87E-06; mr1733 (Jap_All); LR P-value: 1.20E-07; mr1736 (Jap_All); LMM P-value: 1.37E-06; LR P-value: 1.19E-09; mr1757 (Jap_All); LR P-value: 4.79E-11; mr1769 (All); LR P-value: 8.99E-10; mr1780 (Jap_All); LR P-value: 5.45E-06; mr1825 (Jap_All); LR P-value: 3.66E-10; mr1870 (Jap_All); LR P-value: 9.74E-07; mr1880 (All); LR P-value: 4.47E-07; mr1912 (Jap_All); LR P-value: 4.13E-07; mr1926 (Jap_All); LR P-value: 1.83E-11; mr1951 (All); LR P-value: 3.03E-07; mr1959 (Jap_All); LR P-value: 2.61E-06; mr1156_2 (Jap_All); LR P-value: 1.51E-07; mr1310_2 (Jap_All); LR P-value: 7.61E-13; mr1486_2 (Jap_All); LR P-value: 1.68E-10; mr1733_2 (Jap_All); LR P-value: 4.47E-07; mr1959_2 (Jap_All); LR P-value: 2.05E-08 |
LOC_Os10g01730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01740.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.216; most accessible tissue: Callus, score: 37.292 |
| vg1000477711 (J) | chr10 | 477711 | G | A | 77.30% | 5.95% | G -> A | NA |
LOC_Os10g01730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01740.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.831; most accessible tissue: Callus, score: 37.292 |
| vg1000477770 (J) | chr10 | 477770 | G | A | 58.20% | 6.52% | A -> G |
Grain_length (All); LR P-value: 1.62E-14;
mr1011 (Jap_All); LMM P-value: 1.99E-06; LR P-value: 1.99E-06; mr1156 (Jap_All); LR P-value: 1.19E-07; mr1163 (Jap_All); LR P-value: 1.67E-08; mr1179 (Jap_All); LR P-value: 2.07E-06; mr1192 (Jap_All); LR P-value: 5.07E-07; mr1251 (Jap_All); LR P-value: 1.84E-09; mr1300 (All); LMM P-value: 1.25E-06; mr1300 (Jap_All); LMM P-value: 5.23E-06; LR P-value: 5.05E-10; mr1310 (All); LMM P-value: 7.35E-07; mr1310 (Jap_All); LMM P-value: 9.07E-06; LR P-value: 9.12E-12; mr1328 (All); LR P-value: 6.02E-07; mr1378 (All); LR P-value: 7.25E-06; mr1486 (Jap_All); LR P-value: 2.00E-12; mr1520 (All); LR P-value: 4.02E-06; mr1539 (All); LR P-value: 1.27E-09; mr1539 (Jap_All); LR P-value: 2.77E-11; mr1540 (All); LR P-value: 1.63E-13; mr1548 (Jap_All); LR P-value: 2.02E-08; mr1549 (Jap_All); LR P-value: 5.82E-10; mr1563 (Jap_All); LR P-value: 5.75E-09; mr1570 (Jap_All); LR P-value: 3.23E-07; mr1580 (Jap_All); LR P-value: 1.37E-10; mr1588 (Jap_All); LR P-value: 1.12E-06; mr1624 (Jap_All); LR P-value: 1.79E-08; mr1732 (All); LR P-value: 1.04E-13; mr1736 (Jap_All); LR P-value: 5.16E-07; mr1757 (Jap_All); LR P-value: 1.06E-08; mr1780 (Jap_All); LR P-value: 2.31E-06; mr1825 (Jap_All); LR P-value: 2.68E-10; mr1870 (Jap_All); LR P-value: 5.00E-08; mr1912 (Jap_All); LR P-value: 1.84E-06; mr1926 (All); LMM P-value: 4.19E-07; mr1926 (Jap_All); LMM P-value: 6.64E-06; LR P-value: 9.84E-13; mr1959 (Jap_All); LR P-value: 8.46E-07; mr1126_2 (All); LR P-value: 3.63E-07; mr1156_2 (Jap_All); LR P-value: 1.38E-07; mr1310_2 (Jap_All); LMM P-value: 1.38E-06; LR P-value: 1.60E-14; mr1354_2 (Jap_All); LR P-value: 8.89E-06; mr1486_2 (Jap_All); LR P-value: 6.11E-12; mr1563_2 (Jap_All); LR P-value: 3.89E-08; mr1588_2 (Jap_All); LR P-value: 5.68E-06; mr1959_2 (Jap_All); LR P-value: 1.13E-09 |
LOC_Os10g01740.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.000; most accessible tissue: Callus, score: 37.292 |
| vg1000477780 (J) | chr10 | 477780 | G | A | 73.90% | 6.83% | A -> G |
mr1011 (Jap_All); LMM P-value: 1.40E-06; LR P-value: 1.40E-06;
mr1156 (All); LR P-value: 1.05E-16; mr1156 (Jap_All); LR P-value: 4.81E-08; mr1163 (Jap_All); LR P-value: 1.80E-08; mr1179 (Jap_All); LR P-value: 9.39E-07; mr1192 (Jap_All); LR P-value: 1.31E-06; mr1252 (Jap_All); LR P-value: 1.45E-06; mr1300 (All); LMM P-value: 3.73E-12; LR P-value: 5.11E-33; mr1300 (Jap_All); LMM P-value: 2.54E-06; LR P-value: 3.81E-10; mr1310 (All); LMM P-value: 1.20E-14; LR P-value: 2.33E-53; mr1310 (Jap_All); LMM P-value: 2.73E-06; LR P-value: 3.53E-12; mr1486 (All); LR P-value: 2.12E-36; mr1486 (Jap_All); LR P-value: 4.93E-12; mr1539 (All); LR P-value: 7.02E-09; mr1539 (Jap_All); LR P-value: 6.05E-11; mr1548 (Jap_All); LR P-value: 1.93E-08; mr1549 (Jap_All); LR P-value: 3.20E-10; mr1570 (Jap_All); LR P-value: 1.30E-07; mr1580 (Jap_All); LR P-value: 8.62E-10; mr1588 (Jap_All); LR P-value: 5.08E-07; mr1624 (All); LR P-value: 1.21E-10; mr1624 (Jap_All); LR P-value: 9.04E-09; mr1723 (Jap_All); LR P-value: 3.00E-07; mr1729 (Jap_All); LR P-value: 5.17E-07; mr1736 (All); LMM P-value: 8.12E-06; LR P-value: 8.12E-06; mr1736 (Jap_All); LR P-value: 3.22E-07; mr1740 (Jap_All); LR P-value: 7.66E-06; mr1757 (Jap_All); LR P-value: 4.92E-09; mr1780 (Jap_All); LR P-value: 7.90E-07; mr1825 (Jap_All); LR P-value: 7.76E-10; mr1870 (Jap_All); LR P-value: 9.59E-07; mr1912 (Jap_All); LR P-value: 4.06E-06; mr1926 (All); LMM P-value: 1.33E-15; LR P-value: 2.26E-59; mr1926 (Jap_All); LMM P-value: 1.04E-06; LR P-value: 1.40E-13; mr1959 (All); LMM P-value: 2.57E-08; LR P-value: 2.33E-14; mr1959 (Jap_All); LR P-value: 3.39E-07; mr1156_2 (All); LR P-value: 9.44E-20; mr1310_2 (All); LMM P-value: 2.51E-15; LR P-value: 2.46E-49; mr1310_2 (Jap_All); LMM P-value: 3.11E-07; LR P-value: 4.77E-15; mr1486_2 (Jap_All); LR P-value: 1.71E-11; mr1563_2 (Jap_All); LR P-value: 1.81E-07; mr1588_2 (Jap_All); LR P-value: 6.04E-06; mr1624_2 (All); LR P-value: 1.75E-09; mr1959_2 (All); LMM P-value: 3.36E-09; LR P-value: 6.07E-21; mr1959_2 (Jap_All); LR P-value: 6.62E-10 |
LOC_Os10g01740.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.706; most accessible tissue: Callus, score: 37.292 |
| vg1000477806 (J) | chr10 | 477806 | G | A | 74.10% | 6.90% | A -> G |
mr1011 (Jap_All); LMM P-value: 1.40E-06; LR P-value: 1.40E-06;
mr1156 (All); LR P-value: 9.36E-16; mr1156 (Jap_All); LR P-value: 4.81E-08; mr1163 (Jap_All); LR P-value: 1.80E-08; mr1179 (Jap_All); LR P-value: 9.39E-07; mr1192 (Jap_All); LR P-value: 1.31E-06; mr1252 (Jap_All); LR P-value: 1.45E-06; mr1300 (All); LMM P-value: 1.26E-13; LR P-value: 7.24E-35; mr1300 (Jap_All); LMM P-value: 2.54E-06; LR P-value: 3.81E-10; mr1310 (All); LMM P-value: 1.59E-15; LR P-value: 6.83E-55; mr1310 (Jap_All); LMM P-value: 2.73E-06; LR P-value: 3.53E-12; mr1486 (All); LR P-value: 9.41E-37; mr1486 (Jap_All); LR P-value: 4.93E-12; mr1539 (Jap_All); LR P-value: 6.05E-11; mr1548 (Jap_All); LR P-value: 1.93E-08; mr1549 (Jap_All); LR P-value: 3.20E-10; mr1570 (Jap_All); LR P-value: 1.30E-07; mr1580 (Jap_All); LR P-value: 8.62E-10; mr1588 (Jap_All); LR P-value: 5.08E-07; mr1624 (All); LR P-value: 8.21E-10; mr1624 (Jap_All); LR P-value: 9.04E-09; mr1723 (Jap_All); LR P-value: 3.00E-07; mr1729 (Jap_All); LR P-value: 5.17E-07; mr1736 (Jap_All); LR P-value: 3.22E-07; mr1740 (Jap_All); LR P-value: 7.66E-06; mr1757 (Jap_All); LR P-value: 4.92E-09; mr1780 (Jap_All); LR P-value: 7.90E-07; mr1825 (Jap_All); LR P-value: 7.76E-10; mr1870 (Jap_All); LR P-value: 9.59E-07; mr1912 (Jap_All); LR P-value: 4.06E-06; mr1926 (All); LMM P-value: 2.89E-17; LR P-value: 4.98E-62; mr1926 (Jap_All); LMM P-value: 1.04E-06; LR P-value: 1.40E-13; mr1959 (All); LMM P-value: 7.85E-09; LR P-value: 8.64E-15; mr1959 (Jap_All); LR P-value: 3.39E-07; mr1156_2 (All); LR P-value: 4.62E-20; mr1310_2 (All); LMM P-value: 2.91E-17; LR P-value: 3.53E-52; mr1310_2 (Jap_All); LMM P-value: 3.11E-07; LR P-value: 4.77E-15; mr1486_2 (All); LR P-value: 8.19E-45; mr1486_2 (Jap_All); LR P-value: 1.71E-11; mr1563_2 (Jap_All); LR P-value: 1.81E-07; mr1588_2 (Jap_All); LR P-value: 6.04E-06; mr1624_2 (All); LR P-value: 2.27E-09; mr1959_2 (All); LMM P-value: 1.89E-09; LR P-value: 4.96E-21; mr1959_2 (Jap_All); LR P-value: 6.62E-10 |
LOC_Os10g01740.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.471; most accessible tissue: Callus, score: 37.292 |
| vg1000477812 (J) | chr10 | 477812 | G | A | 89.80% | 6.37% | G -> A | NA |
LOC_Os10g01740.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g01730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g01750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.471; most accessible tissue: Callus, score: 37.292 |
| STR1000477779 (J) | chr10 | 477779 | GG | GA | 69.40% | 0.00% | GA -> GG | NA |
|