29 variations found. LOC_Os04g16690 (expressed protein), ranging from 9,081,330 bp to 9,082,198 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081379 (J) | chr04 | 9081379 | C | T | 96.40% | 0.00% | C -> T | NA |
LOC_Os04g16690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.804; most accessible tissue: Zhenshan97 young leaf, score: 87.153 |
| vg0409081384 (J) | chr04 | 9081384 | A | G | 65.00% | 0.00% | G -> A | NA |
LOC_Os04g16690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.641; most accessible tissue: Zhenshan97 young leaf, score: 87.153 |
| vg0409081390 (J) | chr04 | 9081390 | G | A | 88.20% | 0.02% | G -> A |
mr1047 (Jap_All); LR P-value: 4.12E-06;
mr1121 (Jap_All); LR P-value: 4.14E-07; mr1157 (Jap_All); LR P-value: 7.62E-06; mr1271 (Jap_All); LR P-value: 4.23E-07; mr1301 (All); LR P-value: 3.49E-25; mr1301 (Jap_All); LR P-value: 7.32E-15; mr1410 (All); LR P-value: 5.31E-15; mr1425 (All); LR P-value: 8.59E-06; mr1446 (Jap_All); LR P-value: 4.35E-06; mr1449 (All); LR P-value: 7.90E-14; mr1454 (All); LR P-value: 1.61E-13; mr1471 (Jap_All); LR P-value: 2.14E-06; mr1539 (All); LR P-value: 2.66E-08; mr1580 (Jap_All); LR P-value: 5.46E-10; mr1642 (All); LR P-value: 2.48E-07; mr1699 (All); LR P-value: 3.06E-31; mr1715 (All); LR P-value: 2.13E-20; mr1732 (All); LR P-value: 9.79E-13; mr1739 (Jap_All); LR P-value: 3.81E-07; mr1864 (All); LR P-value: 6.05E-12; mr1993 (All); LR P-value: 4.26E-07; mr1993 (Jap_All); LR P-value: 3.57E-08; mr1301_2 (All); LMM P-value: 3.75E-06; LR P-value: 2.15E-26; mr1301_2 (Jap_All); LR P-value: 1.45E-17; mr1410_2 (All); LR P-value: 1.13E-15; mr1699_2 (All); LR P-value: 6.95E-29; mr1905_2 (All); LR P-value: 1.30E-08; mr1993_2 (All); LR P-value: 2.93E-12; mr1993_2 (Jap_All); LR P-value: 1.04E-12 |
LOC_Os04g16690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g16690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 69.903; most accessible tissue: Zhenshan97 young leaf, score: 87.004 |
| vg0409081428 (J) | chr04 | 9081428 | C | T | 85.30% | 0.02% | C -> T |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g16690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g16690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 70.877; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
| vg0409081464 (J) | chr04 | 9081464 | C | T | 85.30% | 0.00% | C -> T |
mr1045 (Jap_All); LR P-value: 3.31E-06;
mr1090 (Jap_All); LR P-value: 1.57E-06; mr1194 (Jap_All); LR P-value: 5.09E-08; mr1206 (All); LR P-value: 1.64E-06; mr1330 (All); LR P-value: 6.67E-13; mr1403 (Jap_All); LR P-value: 8.01E-07; mr1454 (All); LR P-value: 1.75E-13; mr1642 (All); LR P-value: 8.84E-07; mr1739 (Jap_All); LR P-value: 4.88E-07; mr1864 (All); LR P-value: 1.80E-11; mr1194_2 (Jap_All); LR P-value: 7.69E-06; mr1398_2 (All); LR P-value: 1.10E-09 |
LOC_Os04g16690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.095; most accessible tissue: Zhenshan97 young leaf, score: 85.886 |
| vg0409081465 (J) | chr04 | 9081465 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os04g16690.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.165; most accessible tissue: Zhenshan97 young leaf, score: 85.886 |
| vg0409081468 (J) | chr04 | 9081468 | C | T | 88.30% | 0.00% | C -> T |
mr1090 (Jap_All); LR P-value: 2.38E-06;
mr1121 (Jap_All); LR P-value: 5.05E-07; mr1301 (All); LMM P-value: 5.75E-06; LR P-value: 5.05E-26; mr1301 (Jap_All); LR P-value: 1.68E-15; mr1364 (Jap_All); LR P-value: 7.76E-06; mr1410 (All); LR P-value: 8.75E-16; mr1449 (All); LR P-value: 4.95E-13; mr1454 (All); LR P-value: 5.85E-13; mr1642 (All); LR P-value: 8.14E-07; mr1699 (All); LR P-value: 2.54E-30; mr1715 (All); LR P-value: 1.16E-19; mr1739 (Jap_All); LR P-value: 5.03E-07; mr1864 (All); LR P-value: 2.31E-11; mr1993 (All); LR P-value: 1.59E-07; mr1993 (Jap_All); LR P-value: 9.76E-09; mr1090_2 (Jap_All); LR P-value: 2.98E-07; mr1121_2 (Jap_All); LR P-value: 2.91E-06; mr1301_2 (All); LMM P-value: 4.43E-06; LR P-value: 1.09E-26; mr1301_2 (Jap_All); LR P-value: 1.02E-17; mr1410_2 (All); LR P-value: 2.77E-16; mr1699_2 (All); LR P-value: 6.28E-29; mr1993_2 (All); LR P-value: 1.87E-12; mr1993_2 (Jap_All); LR P-value: 7.29E-13 |
LOC_Os04g16690.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.491; most accessible tissue: Zhenshan97 young leaf, score: 86.220 |
| vg0409081469 (J) | chr04 | 9081469 | A | G | 85.30% | 0.02% | A -> G |
mr1045 (Jap_All); LR P-value: 3.31E-06;
mr1090 (Jap_All); LR P-value: 1.57E-06; mr1194 (Jap_All); LR P-value: 5.09E-08; mr1206 (All); LR P-value: 1.64E-06; mr1330 (All); LR P-value: 6.67E-13; mr1403 (Jap_All); LR P-value: 8.01E-07; mr1454 (All); LR P-value: 1.75E-13; mr1642 (All); LR P-value: 8.84E-07; mr1739 (Jap_All); LR P-value: 4.88E-07; mr1864 (All); LR P-value: 1.80E-11; mr1194_2 (Jap_All); LR P-value: 7.69E-06; mr1398_2 (All); LR P-value: 1.10E-09 |
LOC_Os04g16690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g16690.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 70.421; most accessible tissue: Zhenshan97 young leaf, score: 86.220 |
| vg0409081514 (J) | chr04 | 9081514 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os04g16690.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g16680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g16700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.005; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
| vg0409081548 (J) | chr04 | 9081548 | G | T | 85.30% | 0.00% | G -> T |
mr1045 (Jap_All); LR P-value: 1.28E-06;
mr1090 (Jap_All); LR P-value: 1.21E-06; mr1194 (Jap_All); LR P-value: 5.35E-08; mr1206 (All); LR P-value: 7.47E-07; mr1206 (Jap_All); LR P-value: 3.19E-07; mr1330 (All); LR P-value: 7.54E-13; mr1378 (Jap_All); LR P-value: 7.57E-06; mr1403 (Jap_All); LR P-value: 5.72E-07; mr1454 (All); LR P-value: 4.65E-13; mr1629 (Jap_All); LR P-value: 1.66E-06; mr1642 (All); LR P-value: 1.27E-07; mr1715 (Jap_All); LR P-value: 4.33E-07; mr1739 (Jap_All); LR P-value: 7.46E-07; mr1789 (Jap_All); LR P-value: 7.00E-14; mr1864 (All); LR P-value: 9.32E-12; mr1301_2 (Jap_All); LR P-value: 4.02E-15; mr1398_2 (All); LR P-value: 1.79E-09; mr1993_2 (Jap_All); LR P-value: 2.09E-11 |
LOC_Os04g16680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.271; most accessible tissue: Zhenshan97 young leaf, score: 84.431 |
| vg0409081582 (J) | chr04 | 9081582 | A | T | 72.60% | 0.02% | A -> T |
mr1386 (Ind_All); LR P-value: 1.76E-06;
mr1403 (All); LR P-value: 7.66E-11; mr1403 (Ind_All); LR P-value: 3.13E-08; mr1830 (Ind_All); LR P-value: 1.42E-07; mr1846 (All); LMM P-value: 4.77E-08; mr1846 (Ind_All); LMM P-value: 1.02E-07; LR P-value: 4.21E-13; mr1925 (All); LR P-value: 1.28E-06; mr1830_2 (Ind_All); LR P-value: 2.54E-11; mr1846_2 (All); LMM P-value: 1.37E-12; LR P-value: 1.82E-15; mr1846_2 (Ind_All); LMM P-value: 9.21E-11; LR P-value: 2.00E-27 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g16680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.032; most accessible tissue: Zhenshan97 young leaf, score: 82.763 |
| vg0409081591 (J) | chr04 | 9081591 | A | AT | 88.20% | 0.00% | A -> AT | NA |
LOC_Os04g16680.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.058; most accessible tissue: Minghui63 flag leaf, score: 82.750 |
| vg0409081691 (J) | chr04 | 9081691 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.730; most accessible tissue: Minghui63 flag leaf, score: 81.052 |
| vg0409081696 (J) | chr04 | 9081696 | G | A | 65.10% | 0.00% | A -> G | NA |
LOC_Os04g16680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.884; most accessible tissue: Minghui63 flag leaf, score: 80.786 |
| vg0409081698 (J) | chr04 | 9081698 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os04g16680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g16700.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g16690.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.040; most accessible tissue: Minghui63 flag leaf, score: 80.786 |
| vg0409081713 (J) | chr04 | 9081713 | T | A | 97.20% | 0.00% | T -> A | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.935; most accessible tissue: Minghui63 flag leaf, score: 79.962 |
| vg0409081763 (J) | chr04 | 9081763 | A | G | 85.30% | 0.00% | A -> G |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g16680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.546; most accessible tissue: Minghui63 flag leaf, score: 79.676 |
| vg0409081764 (J) | chr04 | 9081764 | C | CT | 99.90% | 0.00% | C -> CT | NA |
LOC_Os04g16680.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g16700.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g16690.1 Alt: CT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.546; most accessible tissue: Minghui63 flag leaf, score: 79.676 |
| vg0409081774 (J) | chr04 | 9081774 | G | C | 85.30% | 0.08% | G -> C |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g16680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.072; most accessible tissue: Minghui63 flag leaf, score: 80.516 |
| vg0409081800 (J) | chr04 | 9081800 | G | A | 79.90% | 0.00% | A -> G |
mr1045 (All); LR P-value: 7.38E-08;
mr1045 (Jap_All); LR P-value: 3.82E-06; mr1077 (All); LR P-value: 1.35E-18; mr1090 (Jap_All); LR P-value: 2.17E-06; mr1093 (All); LR P-value: 1.15E-40; mr1175 (All); LR P-value: 6.49E-10; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1241 (All); LR P-value: 3.86E-54; mr1282 (All); LR P-value: 4.25E-10; mr1310 (All); LR P-value: 3.50E-35; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1563 (All); LR P-value: 5.01E-44; mr1650 (All); LR P-value: 3.06E-12; mr1658 (All); LR P-value: 8.19E-09; mr1679 (All); LR P-value: 2.89E-20; mr1712 (All); LR P-value: 9.25E-10; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1741 (All); LR P-value: 4.39E-12; mr1746 (All); LR P-value: 4.24E-09; mr1771 (All); LR P-value: 2.82E-45; mr1789 (All); LR P-value: 1.31E-33; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1790 (All); LR P-value: 6.47E-10; mr1805 (All); LR P-value: 1.42E-23; mr1844 (All); LR P-value: 1.69E-13; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1926 (All); LR P-value: 1.92E-43; mr1959 (All); LR P-value: 3.06E-09; mr1982 (All); LR P-value: 6.51E-14; mr1093_2 (All); LR P-value: 3.90E-49; mr1282_2 (All); LR P-value: 5.74E-10; mr1310_2 (All); LR P-value: 6.53E-32; mr1334_2 (All); LR P-value: 2.11E-93; mr1399_2 (All); LR P-value: 8.43E-08; mr1520_2 (All); LR P-value: 1.02E-11; mr1789_2 (All); LR P-value: 1.80E-28; mr1959_2 (All); LR P-value: 1.81E-13 |
LOC_Os04g16680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.126; most accessible tissue: Minghui63 flag leaf, score: 82.053 |
| vg0409081804 (J) | chr04 | 9081804 | G | A | 97.20% | 0.00% | G -> A,T | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.209; most accessible tissue: Minghui63 flag leaf, score: 82.289 |
| vg0409081874 (J) | chr04 | 9081874 | C | T | 88.10% | 0.00% | C -> T |
mr1047 (Jap_All); LR P-value: 4.12E-06;
mr1121 (Jap_All); LR P-value: 4.14E-07; mr1157 (Jap_All); LR P-value: 7.62E-06; mr1271 (Jap_All); LR P-value: 4.23E-07; mr1301 (All); LR P-value: 7.99E-24; mr1301 (Jap_All); LR P-value: 7.32E-15; mr1338 (All); LR P-value: 1.42E-06; mr1410 (All); LR P-value: 3.30E-14; mr1425 (All); LR P-value: 2.75E-06; mr1446 (Jap_All); LR P-value: 4.35E-06; mr1449 (All); LR P-value: 1.42E-13; mr1454 (All); LR P-value: 8.86E-14; mr1471 (Jap_All); LR P-value: 2.14E-06; mr1539 (All); LR P-value: 1.92E-08; mr1580 (Jap_All); LR P-value: 5.46E-10; mr1642 (All); LR P-value: 6.43E-08; mr1699 (All); LR P-value: 3.70E-30; mr1715 (All); LR P-value: 4.81E-20; mr1732 (All); LR P-value: 7.17E-13; mr1739 (Jap_All); LR P-value: 3.81E-07; mr1864 (All); LR P-value: 1.58E-12; mr1990 (All); LR P-value: 3.68E-06; mr1993 (All); LR P-value: 5.95E-07; mr1993 (Jap_All); LR P-value: 3.57E-08; mr1301_2 (All); LR P-value: 1.57E-25; mr1301_2 (Jap_All); LR P-value: 1.45E-17; mr1398_2 (All); LR P-value: 1.43E-09; mr1410_2 (All); LR P-value: 5.99E-15; mr1905_2 (All); LR P-value: 5.08E-09; mr1993_2 (All); LR P-value: 4.91E-12; mr1993_2 (Jap_All); LR P-value: 1.04E-12 |
LOC_Os04g16680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.529; most accessible tissue: Minghui63 flag leaf, score: 82.521 |
| vg0409081969 (J) | chr04 | 9081969 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.334; most accessible tissue: Zhenshan97 young leaf, score: 80.056 |
| vg0409081975 (J) | chr04 | 9081975 | A | G | 65.10% | 0.00% | G -> A | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.490; most accessible tissue: Zhenshan97 young leaf, score: 80.589 |
| vg0409081987 (J) | chr04 | 9081987 | G | C | 79.90% | 0.00% | C -> G |
mr1045 (All); LR P-value: 6.66E-08;
mr1045 (Jap_All); LR P-value: 3.82E-06; mr1077 (All); LR P-value: 1.41E-18; mr1090 (Jap_All); LR P-value: 2.17E-06; mr1175 (All); LR P-value: 6.23E-10; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1241 (All); LR P-value: 6.01E-54; mr1282 (All); LR P-value: 3.58E-10; mr1310 (All); LR P-value: 4.68E-35; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1563 (All); LR P-value: 7.46E-44; mr1650 (All); LR P-value: 2.46E-12; mr1658 (All); LR P-value: 7.00E-09; mr1679 (All); LR P-value: 2.06E-20; mr1712 (All); LR P-value: 8.39E-10; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1741 (All); LR P-value: 4.00E-12; mr1746 (All); LR P-value: 4.35E-09; mr1771 (All); LR P-value: 1.71E-45; mr1789 (All); LR P-value: 1.22E-33; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1790 (All); LR P-value: 6.56E-10; mr1805 (All); LR P-value: 1.34E-23; mr1844 (All); LR P-value: 1.73E-13; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1926 (All); LR P-value: 2.09E-43; mr1959 (All); LR P-value: 3.51E-09; mr1982 (All); LR P-value: 5.88E-14; mr1093_2 (All); LR P-value: 4.38E-49; mr1282_2 (All); LR P-value: 5.17E-10; mr1310_2 (All); LR P-value: 7.52E-32; mr1399_2 (All); LR P-value: 7.12E-08; mr1520_2 (All); LR P-value: 1.24E-11; mr1778_2 (All); LR P-value: 1.09E-72; mr1789_2 (All); LR P-value: 1.52E-28 |
LOC_Os04g16680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16700.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16690.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.062; most accessible tissue: Zhenshan97 young leaf, score: 81.841 |
| vg0409082025 (J) | chr04 | 9082025 | T | A | 99.60% | 0.00% | T -> A | NA |
LOC_Os04g16680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g16700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g16690.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.124; most accessible tissue: Minghui63 flag leaf, score: 80.516 |
| vg0409082049 (J) | chr04 | 9082049 | T | G | 65.10% | 0.00% | G -> T | NA |
LOC_Os04g16690.1 Alt: T| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
The average chromatin accessibility score: 55.455; most accessible tissue: Zhenshan97 young leaf, score: 81.102 |
| vg0409082182 (J) | chr04 | 9082182 | A | T | 85.30% | 0.23% | A -> T |
mr1045 (Jap_All); LR P-value: 3.82E-06;
mr1090 (Jap_All); LR P-value: 2.17E-06; mr1194 (Jap_All); LR P-value: 9.29E-08; mr1206 (All); LR P-value: 1.11E-06; mr1330 (All); LR P-value: 1.64E-13; mr1403 (Jap_All); LR P-value: 5.73E-07; mr1454 (All); LR P-value: 4.87E-14; mr1454 (Jap_All); LR P-value: 3.88E-11; mr1642 (All); LR P-value: 2.90E-07; mr1715 (Jap_All); LR P-value: 3.67E-07; mr1739 (Jap_All); LR P-value: 3.57E-07; mr1789 (Jap_All); LR P-value: 3.46E-13; mr1864 (All); LR P-value: 4.95E-12; mr1880 (Jap_All); LR P-value: 2.12E-09; mr1398_2 (All); LR P-value: 1.21E-09; mr1454_2 (All); LR P-value: 8.97E-14 |
LOC_Os04g16690.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g16690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 56.654; most accessible tissue: Zhenshan97 young leaf, score: 81.600 |
| STR0409081592 (J) | chr04 | 9081592 | TT | TTT | 94.30% | 0.00% | TT -> TTT | NA |
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