19 variations found. LOC_Os04g41740 (expressed protein), ranging from 24,740,702 bp to 24,742,677 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424740725 (J) | chr04 | 24740725 | A | G | 59.80% | 0.63% | G -> A |
mr1379 (All); LR P-value: 1.03E-09;
mr1509 (All); LR P-value: 5.15E-41; mr1571 (All); LR P-value: 2.88E-24; mr1580 (All); LR P-value: 4.02E-22; mr1825 (All); LR P-value: 5.65E-19; mr1335_2 (All); LR P-value: 1.24E-07; mr1524_2 (All); LR P-value: 5.73E-06; mr1559_2 (All); LR P-value: 1.86E-06; mr1578_2 (All); LR P-value: 3.98E-15; mr1579_2 (All); LR P-value: 2.30E-14; mr1580_2 (All); LR P-value: 1.02E-30; mr1666_2 (All); LR P-value: 9.07E-12; mr1698_2 (All); LR P-value: 2.81E-21; mr1825_2 (All); LR P-value: 1.64E-29; mr1924_2 (All); LR P-value: 1.11E-20 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41740.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.175; most accessible tissue: Minghui63 root, score: 96.290 |
| vg0424741072 (J) | chr04 | 24741072 | C | T | 59.90% | 0.66% | T -> C |
mr1379 (All); LR P-value: 1.38E-09;
mr1509 (All); LR P-value: 6.58E-42; mr1571 (All); LR P-value: 7.02E-24; mr1580 (All); LR P-value: 9.52E-22; mr1731 (All); LR P-value: 1.20E-24; mr1825 (All); LR P-value: 5.54E-19; mr1524_2 (All); LR P-value: 5.87E-06; mr1559_2 (All); LR P-value: 3.03E-06; mr1578_2 (All); LR P-value: 2.97E-15; mr1580_2 (All); LR P-value: 3.32E-30; mr1666_2 (All); LR P-value: 4.41E-12; mr1698_2 (All); LR P-value: 2.34E-21; mr1731_2 (All); LR P-value: 2.69E-19; mr1825_2 (All); LR P-value: 4.35E-29 |
LOC_Os04g41740.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g41740.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.964; most accessible tissue: Callus, score: 92.469 |
| vg0424741090 (J) | chr04 | 24741090 | G | A | 52.40% | 0.63% | A -> G |
mr1026 (All); LR P-value: 5.91E-33;
mr1063 (All); LR P-value: 1.67E-52; mr1125 (All); LR P-value: 2.23E-48; mr1161 (All); LR P-value: 2.29E-33; mr1221 (All); LR P-value: 6.18E-28; mr1260 (All); LR P-value: 8.69E-09; mr1261 (All); LR P-value: 5.92E-16; mr1531 (All); LR P-value: 5.97E-13; mr1745 (All); LR P-value: 4.35E-31; mr1914 (All); LR P-value: 5.67E-12; mr1037_2 (All); LR P-value: 1.08E-30; mr1094_2 (All); LR P-value: 3.92E-44; mr1096_2 (All); LR P-value: 1.09E-59; mr1109_2 (All); LR P-value: 1.72E-55; mr1111_2 (All); LR P-value: 9.17E-51; mr1121_2 (All); LR P-value: 7.53E-53; mr1125_2 (All); LR P-value: 3.99E-65; mr1129_2 (All); LR P-value: 3.31E-36; mr1144_2 (All); LR P-value: 1.26E-53; mr1208_2 (All); LR P-value: 1.80E-36; mr1244_2 (All); LR P-value: 7.20E-25; mr1255_2 (All); LR P-value: 1.79E-20; mr1270_2 (All); LR P-value: 8.47E-27; mr1457_2 (All); LR P-value: 6.96E-17; mr1514_2 (All); LR P-value: 8.44E-13; mr1551_2 (All); LR P-value: 3.60E-22; mr1578_2 (All); LR P-value: 5.16E-15; mr1690_2 (All); LR P-value: 7.29E-08; mr1744_2 (All); LR P-value: 4.68E-16; mr1745_2 (All); LR P-value: 5.55E-41; mr1798_2 (All); LR P-value: 1.83E-73; mr1913_2 (All); LR P-value: 2.88E-32; mr1932_2 (All); LR P-value: 6.60E-30 |
LOC_Os04g41740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 77.868; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg0424741232 (J) | chr04 | 24741232 | G | A | 59.90% | 0.61% | A -> G |
mr1379 (All); LR P-value: 1.38E-09;
mr1509 (All); LR P-value: 6.58E-42; mr1571 (All); LR P-value: 7.02E-24; mr1580 (All); LR P-value: 9.52E-22; mr1731 (All); LR P-value: 1.20E-24; mr1825 (All); LR P-value: 5.54E-19; mr1524_2 (All); LR P-value: 5.87E-06; mr1559_2 (All); LR P-value: 3.03E-06; mr1578_2 (All); LR P-value: 2.97E-15; mr1580_2 (All); LR P-value: 3.32E-30; mr1666_2 (All); LR P-value: 4.41E-12; mr1698_2 (All); LR P-value: 2.34E-21; mr1731_2 (All); LR P-value: 2.69E-19; mr1825_2 (All); LR P-value: 4.35E-29 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.922; most accessible tissue: Zhenshan97 flower, score: 84.217 |
| vg0424741326 (J) | chr04 | 24741326 | T | C | 58.40% | 0.59% | C -> T |
mr1509 (All); LR P-value: 6.43E-43;
mr1558 (All); LR P-value: 3.67E-46; mr1571 (All); LR P-value: 6.99E-24; mr1580 (All); LR P-value: 8.70E-21; mr1731 (All); LR P-value: 2.43E-24; mr1825 (All); LR P-value: 5.55E-18; mr1524_2 (All); LR P-value: 9.36E-06; mr1559_2 (All); LR P-value: 3.37E-06; mr1578_2 (All); LR P-value: 6.02E-15 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.355; most accessible tissue: Zhenshan97 panicle, score: 88.888 |
| vg0424741333 (J) | chr04 | 24741333 | C | T | 94.10% | 0.00% | C -> T | NA |
LOC_Os04g41730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.410; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
| vg0424741426 (J) | chr04 | 24741426 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os04g41740.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g41730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.649; most accessible tissue: Zhenshan97 panicle, score: 94.026 |
| vg0424741940 (J) | chr04 | 24741940 | G | A | 52.40% | 0.61% | A -> G |
mr1026 (All); LR P-value: 2.46E-33;
mr1063 (All); LR P-value: 3.95E-54; mr1125 (All); LR P-value: 1.86E-48; mr1161 (All); LR P-value: 1.39E-33; mr1164 (All); LR P-value: 9.52E-15; mr1221 (All); LR P-value: 2.56E-28; mr1260 (All); LR P-value: 4.20E-09; mr1261 (All); LR P-value: 1.52E-16; mr1531 (All); LR P-value: 1.05E-13; mr1571 (All); LR P-value: 3.52E-23; mr1914 (All); LR P-value: 5.67E-12; mr1037_2 (All); LR P-value: 8.52E-31; mr1094_2 (All); LR P-value: 3.20E-44; mr1096_2 (All); LR P-value: 1.07E-59; mr1109_2 (All); LR P-value: 1.71E-55; mr1111_2 (All); LR P-value: 6.22E-51; mr1121_2 (All); LR P-value: 3.42E-52; mr1125_2 (All); LR P-value: 5.52E-66; mr1129_2 (All); LR P-value: 7.75E-36; mr1144_2 (All); LR P-value: 6.14E-54; mr1244_2 (All); LR P-value: 5.48E-25; mr1255_2 (All); LR P-value: 7.88E-21; mr1457_2 (All); LR P-value: 1.16E-16; mr1514_2 (All); LR P-value: 3.86E-13; mr1551_2 (All); LR P-value: 1.18E-22; mr1690_2 (All); LR P-value: 7.37E-08; mr1744_2 (All); LR P-value: 5.12E-16; mr1745_2 (All); LR P-value: 5.05E-41; mr1793_2 (All); LR P-value: 5.58E-45; mr1798_2 (All); LR P-value: 1.69E-73; mr1913_2 (All); LR P-value: 8.55E-32; mr1932_2 (All); LR P-value: 1.18E-29 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.961; most accessible tissue: Zhenshan97 panicle, score: 97.940 |
| vg0424742100 (J) | chr04 | 24742100 | G | A | 95.50% | 0.00% | G -> A,T | NA |
LOC_Os04g41740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g41740.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.178; most accessible tissue: Zhenshan97 panicle, score: 98.935 |
| vg0424742142 (J) | chr04 | 24742142 | T | G | 55.50% | 33.01% | T -> G | NA |
LOC_Os04g41740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41740.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.121; most accessible tissue: Zhenshan97 panicle, score: 99.146 |
| vg0424742197 (J) | chr04 | 24742197 | C | Unkown | 93.60% | 2.24% | C -> G | NA |
LOC_Os04g41740.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os04g41730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41759.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.000; most accessible tissue: Zhenshan97 panicle, score: 99.254 |
| vg0424742305 (J) | chr04 | 24742305 | T | C | 52.40% | 0.59% | C -> T |
mr1026 (All); LR P-value: 2.19E-32;
mr1063 (All); LR P-value: 9.19E-53; mr1125 (All); LR P-value: 1.37E-48; mr1161 (All); LR P-value: 1.39E-32; mr1221 (All); LR P-value: 4.76E-28; mr1260 (All); LR P-value: 4.46E-09; mr1261 (All); LR P-value: 2.10E-16; mr1531 (All); LR P-value: 1.26E-13; mr1571 (All); LR P-value: 3.88E-23; mr1914 (All); LR P-value: 2.93E-12; mr1096_2 (All); LR P-value: 2.23E-58; mr1109_2 (All); LR P-value: 9.24E-55; mr1111_2 (All); LR P-value: 8.74E-50; mr1121_2 (All); LR P-value: 6.28E-51; mr1125_2 (All); LR P-value: 4.02E-65; mr1144_2 (All); LR P-value: 6.13E-53; mr1244_2 (All); LR P-value: 7.36E-25; mr1255_2 (All); LR P-value: 1.81E-20; mr1457_2 (All); LR P-value: 3.57E-16; mr1514_2 (All); LR P-value: 8.15E-13; mr1551_2 (All); LR P-value: 6.08E-23; mr1690_2 (All); LR P-value: 4.75E-08; mr1744_2 (All); LR P-value: 3.69E-16; mr1745_2 (All); LR P-value: 1.86E-40; mr1798_2 (All); LR P-value: 1.66E-72; mr1913_2 (All); LR P-value: 1.66E-31; mr1932_2 (All); LR P-value: 1.27E-29 |
LOC_Os04g41740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 94.449; most accessible tissue: Zhenshan97 panicle, score: 99.254 |
| vg0424742486 (J) | chr04 | 24742486 | G | A | 59.90% | 0.66% | A -> G |
mr1379 (All); LR P-value: 1.77E-09;
mr1509 (All); LR P-value: 8.09E-41; mr1571 (All); LR P-value: 1.12E-23; mr1580 (All); LR P-value: 6.32E-22; mr1731 (All); LR P-value: 2.91E-24; mr1825 (All); LR P-value: 4.96E-19; mr1524_2 (All); LR P-value: 6.05E-06; mr1559_2 (All); LR P-value: 2.89E-06; mr1578_2 (All); LR P-value: 3.42E-15; mr1580_2 (All); LR P-value: 2.96E-29; mr1666_2 (All); LR P-value: 2.63E-12; mr1698_2 (All); LR P-value: 9.69E-22 |
LOC_Os04g41740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.596; most accessible tissue: Zhenshan97 panicle, score: 98.230 |
| vg0424742515 (J) | chr04 | 24742515 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os04g41740.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g41730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41750.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41759.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.641; most accessible tissue: Zhenshan97 panicle, score: 97.798 |
| vg0424742530 (J) | chr04 | 24742530 | C | A | 52.40% | 0.61% | A -> C |
mr1063 (All); LR P-value: 5.28E-51;
mr1260 (All); LR P-value: 1.49E-08; mr1261 (All); LR P-value: 1.62E-15; mr1744 (All); LR P-value: 5.64E-12; mr1745 (All); LR P-value: 8.92E-31; mr1913 (All); LR P-value: 4.70E-17; mr1914 (All); LR P-value: 1.10E-11; mr1094_2 (All); LR P-value: 5.17E-45; mr1096_2 (All); LR P-value: 1.31E-60; mr1111_2 (All); LR P-value: 1.15E-50; mr1121_2 (All); LR P-value: 2.50E-53; mr1125_2 (All); LR P-value: 2.01E-63; mr1129_2 (All); LR P-value: 1.69E-35; mr1144_2 (All); LR P-value: 2.12E-53; mr1244_2 (All); LR P-value: 2.85E-25; mr1255_2 (All); LR P-value: 1.99E-20; mr1270_2 (All); LR P-value: 2.32E-27; mr1457_2 (All); LR P-value: 2.66E-16; mr1551_2 (All); LR P-value: 3.31E-22; mr1690_2 (All); LR P-value: 6.23E-08; mr1744_2 (All); LR P-value: 3.41E-16; mr1745_2 (All); LR P-value: 4.77E-41; mr1798_2 (All); LR P-value: 8.39E-72; mr1913_2 (All); LR P-value: 2.92E-32; mr1932_2 (All); LR P-value: 8.92E-30 |
LOC_Os04g41740.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.463; most accessible tissue: Zhenshan97 panicle, score: 97.556 |
| vg0424742629 (J) | chr04 | 24742629 | TTA | T | 94.00% | 0.04% | TTA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41740.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.860; most accessible tissue: Zhenshan97 root, score: 94.300 |
| vg0424742630 (J) | chr04 | 24742630 | T | TA | 53.50% | 0.57% | TA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41740.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.742; most accessible tissue: Zhenshan97 root, score: 94.256 |
| vg0424742654 (J) | chr04 | 24742654 | T | TCTATC | 98.20% | 0.00% | T -> TCTATTA,TC TATC,TCTAT CTATTATATA ATTAAAGGAA ,TCTATCTAT TA,TCTATTA TATAATTAAA GGAA,TCTAT CTATTATA | NA |
LOC_Os04g41740.1 Alt: TCTATCTATTATATAATTAAAGGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41730.1 Alt: TCTATCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: TCTATCTATTATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: TCTATCTATTATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATCTATTATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATCTATTATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: TCTATC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: TCTATC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: TCTATCTATTA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: TCTATCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: TCTATTA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: TCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41740.1 Alt: TCTATTATATAATTAAAGGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41730.1 Alt: TCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: TCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: TCTATTATATAATTAAAGGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.121; most accessible tissue: Minghui63 root, score: 92.448 |
| STR0424742623 (J) | chr04 | 24742623 | TTT | TT | 59.00% | 0.00% | TTTT -> TT,TTT | NA |
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