24 variations found. LOC_Os03g37120 (retrotransposon protein; putative; unclassified; expressed), ranging from 20,569,312 bp to 20,572,626 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320569347 (J) | chr03 | 20569347 | A | G | 67.50% | 0.44% | G -> A |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 1.42E-10; mr1215 (All); LR P-value: 7.00E-06; mr1217 (All); LR P-value: 1.18E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 1.51E-07; mr1304 (All); LR P-value: 8.15E-18; mr1386 (All); LR P-value: 8.00E-12; mr1750 (All); LMM P-value: 1.95E-08; LR P-value: 3.65E-116; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 1.04E-19; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1077_2 (All); LR P-value: 1.90E-23; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 1.64E-11; mr1718_2 (All); LMM P-value: 9.84E-06; LR P-value: 3.46E-110; mr1750_2 (All); LMM P-value: 4.96E-10 |
LOC_Os03g37120.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 78.880; most accessible tissue: Zhenshan97 panicle, score: 91.845 |
| vg0320569546 (J) | chr03 | 20569546 | T | C | 67.50% | 0.44% | C -> T |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 9.95E-12; mr1215 (All); LR P-value: 3.94E-06; mr1217 (All); LR P-value: 1.53E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1218 (All); LR P-value: 9.21E-14; mr1227 (All); LR P-value: 1.14E-07; mr1304 (All); LR P-value: 3.38E-18; mr1386 (All); LR P-value: 6.17E-12; mr1622 (All); LR P-value: 2.95E-06; mr1680 (All); LR P-value: 3.90E-07; mr1750 (All); LMM P-value: 6.85E-08; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 1.37E-19; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 2.21E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 2.93E-12; mr1718_2 (All); LMM P-value: 7.64E-07; LR P-value: 8.93E-113; mr1750_2 (All); LMM P-value: 9.70E-10; mr1827_2 (All); LR P-value: 8.01E-14; mr1893_2 (All); LR P-value: 1.64E-10; mr1933_2 (All); LR P-value: 4.19E-22 |
LOC_Os03g37120.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 84.908; most accessible tissue: Zhenshan97 young leaf, score: 92.818 |
| vg0320569863 (J) | chr03 | 20569863 | C | T | 67.70% | 0.30% | T -> C |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 1.49E-10; mr1215 (All); LR P-value: 5.56E-06; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 2.48E-07; mr1304 (All); LR P-value: 1.25E-17; mr1750 (All); LMM P-value: 1.05E-08; LR P-value: 3.18E-113; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 3.89E-19; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 6.51E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 4.70E-11; mr1750_2 (All); LMM P-value: 3.83E-10; mr1827_2 (All); LR P-value: 1.29E-13 |
LOC_Os03g37120.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.135; most accessible tissue: Zhenshan97 young leaf, score: 90.270 |
| vg0320569880 (J) | chr03 | 20569880 | A | G | 67.50% | 0.42% | G -> A |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 3.44E-11; mr1215 (All); LR P-value: 4.13E-06; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 5.32E-07; mr1304 (All); LR P-value: 1.83E-17; mr1750 (All); LMM P-value: 8.57E-08; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 3.37E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 9.90E-12; mr1718_2 (All); LMM P-value: 1.82E-06; LR P-value: 3.24E-109; mr1750_2 (All); LMM P-value: 1.62E-09; mr1827_2 (All); LR P-value: 3.56E-14; mr1933_2 (All); LR P-value: 5.96E-22 |
LOC_Os03g37120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.291; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |
| vg0320569919 (J) | chr03 | 20569919 | T | A | 99.50% | 0.00% | T -> A | NA |
LOC_Os03g37120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g37110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g37100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g37130.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.747; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
| vg0320569997 (J) | chr03 | 20569997 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os03g37120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g37110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g37100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g37130.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.529; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
| vg0320570050 (J) | chr03 | 20570050 | AGTCGTC GTC | A | 66.30% | 0.47% | A -> AGTCGTCGTC ,AGTCGTC,A GTCGTCGTCG TC | NA |
LOC_Os03g37120.1 Alt: AGTCGTC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g37120.1 Alt: AGTCGTCGTCGTC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g37120.1 Alt: AGTCGTCGTC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 77.894; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
| vg0320570289 (J) | chr03 | 20570289 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os03g37120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.904; most accessible tissue: Zhenshan97 panicle, score: 89.623 |
| vg0320570767 (J) | chr03 | 20570767 | G | A | 96.40% | 0.00% | G -> A | NA |
LOC_Os03g37120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 84.729; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0320570772 (J) | chr03 | 20570772 | C | T | 67.70% | 0.42% | T -> C |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 4.74E-11; mr1215 (All); LR P-value: 5.92E-06; mr1217 (All); LR P-value: 9.43E-22; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1218 (All); LR P-value: 5.54E-14; mr1227 (All); LR P-value: 6.95E-08; mr1304 (All); LR P-value: 3.29E-18; mr1386 (All); LR P-value: 6.39E-12; mr1750 (All); LMM P-value: 2.76E-09; LR P-value: 5.22E-116; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 7.85E-20; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 5.00E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 1.34E-11; mr1718_2 (All); LR P-value: 1.88E-108; mr1750_2 (All); LMM P-value: 4.58E-11; mr1933_2 (All); LR P-value: 4.69E-22 |
LOC_Os03g37120.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.931; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0320571133 (J) | chr03 | 20571133 | C | A | 52.00% | 0.72% | A -> C |
mr1439 (All); LMM P-value: 8.40E-06;
mr1439 (Ind_All); LMM P-value: 4.06E-06; LR P-value: 1.83E-06; mr1750 (All); LMM P-value: 4.75E-06; mr1750 (Ind_All); LR P-value: 2.58E-06; mr1645_2 (All); LR P-value: 6.74E-08; mr1750_2 (All); LMM P-value: 3.90E-09; mr1835_2 (All); LR P-value: 3.43E-09; mr1893_2 (All); LR P-value: 2.85E-12 |
LOC_Os03g37110.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.425; most accessible tissue: Zhenshan97 root, score: 86.362 |
| vg0320571321 (J) | chr03 | 20571321 | CAAAA | CA | 55.60% | 0.36% | CAAAA -> CAA,CA,C,C AAA | NA |
LOC_Os03g37110.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37110.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g37110.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37110.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.579; most accessible tissue: Callus, score: 85.877 |
| vg0320571598 (J) | chr03 | 20571598 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g37120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g37110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g37130.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.900; most accessible tissue: Zhenshan97 young leaf, score: 80.325 |
| vg0320571876 (J) | chr03 | 20571876 | T | G | 67.50% | 0.44% | G -> T |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 1.34E-11; mr1215 (All); LR P-value: 5.81E-06; mr1217 (All); LR P-value: 5.58E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 3.09E-07; mr1304 (All); LR P-value: 1.29E-17; mr1750 (All); LMM P-value: 9.54E-09; LR P-value: 8.10E-113; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 4.27E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 2.66E-12; mr1718_2 (All); LMM P-value: 8.27E-07; LR P-value: 5.25E-112; mr1750_2 (All); LMM P-value: 6.35E-11; mr1827_2 (All); LR P-value: 3.60E-14; mr1893_2 (All); LR P-value: 1.39E-10; mr1933_2 (All); LR P-value: 2.31E-22 |
LOC_Os03g37120.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.506; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0320571981 (J) | chr03 | 20571981 | G | C | 67.50% | 0.42% | C -> G |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 6.00E-11; mr1215 (All); LR P-value: 7.80E-06; mr1217 (All); LR P-value: 2.49E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 1.42E-07; mr1304 (All); LR P-value: 8.73E-18; mr1750 (All); LMM P-value: 8.96E-10; LR P-value: 7.64E-116; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 2.07E-19; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 8.22E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 1.32E-11; mr1718_2 (All); LR P-value: 1.24E-107; mr1750_2 (All); LMM P-value: 1.12E-11; mr1827_2 (All); LR P-value: 1.30E-13; mr1933_2 (All); LR P-value: 3.48E-22 |
LOC_Os03g37120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g37120.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 74.964; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0320572067 (J) | chr03 | 20572067 | T | C | 92.40% | 0.00% | T -> C | NA |
LOC_Os03g37110.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.490; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0320572071 (J) | chr03 | 20572071 | T | C | 67.50% | 0.44% | C -> T |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 1.54E-11; mr1215 (All); LR P-value: 8.28E-06; mr1217 (All); LR P-value: 3.19E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 1.24E-07; mr1304 (All); LR P-value: 2.76E-18; mr1386 (All); LR P-value: 7.69E-12; mr1622 (All); LR P-value: 1.99E-06; mr1718 (All); LR P-value: 5.23E-78; mr1750 (All); LMM P-value: 8.66E-09; LR P-value: 5.75E-114; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (All); LR P-value: 3.19E-19; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 6.45E-16; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 6.25E-12; mr1718_2 (All); LMM P-value: 2.24E-07; LR P-value: 1.25E-114; mr1750_2 (All); LMM P-value: 2.74E-10; mr1893_2 (All); LR P-value: 2.05E-10; mr1933_2 (All); LR P-value: 4.71E-22; mr1987_2 (All); LMM P-value: 8.49E-06 |
LOC_Os03g37110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 72.110; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
| vg0320572124 (J) | chr03 | 20572124 | A | T | 98.30% | 0.00% | A -> T | NA |
LOC_Os03g37110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.792; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
| vg0320572180 (J) | chr03 | 20572180 | T | C | 67.50% | 0.44% | C -> T |
mr1136 (Jap_All); LR P-value: 3.38E-07;
mr1188 (All); LR P-value: 1.34E-11; mr1215 (All); LR P-value: 5.81E-06; mr1217 (All); LR P-value: 5.58E-21; mr1217 (Jap_All); LR P-value: 1.48E-07; mr1227 (All); LR P-value: 3.09E-07; mr1304 (All); LR P-value: 1.29E-17; mr1750 (All); LMM P-value: 9.54E-09; LR P-value: 8.10E-113; mr1830 (Jap_All); LR P-value: 2.41E-06; mr1845 (Jap_All); LR P-value: 4.09E-07; mr1852 (Jap_All); LR P-value: 7.10E-08; mr1933 (All); LR P-value: 4.27E-15; mr1136_2 (Jap_All); LR P-value: 1.76E-08; mr1188_2 (All); LR P-value: 2.66E-12; mr1718_2 (All); LMM P-value: 8.27E-07; LR P-value: 5.25E-112; mr1750_2 (All); LMM P-value: 6.35E-11; mr1827_2 (All); LR P-value: 3.60E-14; mr1893_2 (All); LR P-value: 1.39E-10; mr1933_2 (All); LR P-value: 2.31E-22 |
LOC_Os03g37110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.686; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg0320572223 (J) | chr03 | 20572223 | T | TA | 67.70% | 0.44% | TA -> T | NA |
LOC_Os03g37110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37130.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 76.440; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0320572269 (J) | chr03 | 20572269 | T | A | 99.60% | 0.00% | T -> A | NA |
LOC_Os03g37120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 79.325; most accessible tissue: Minghui63 panicle, score: 86.442 |
| vg0320572436 (J) | chr03 | 20572436 | C | CCGCG | 85.00% | 0.00% | C -> CCGCG | NA |
LOC_Os03g37120.1 Alt: CCGCG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.116; most accessible tissue: Callus, score: 90.133 |
| vg0320572496 (J) | chr03 | 20572496 | G | A | 59.30% | 0.53% | G -> A |
LOC_Os03g37120.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g37110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g37130.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.256; most accessible tissue: Callus, score: 90.133 |
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| STR0320572495 (J) | chr03 | 20572495 | TG | TA | 54.90% | 0.00% | TG -> TA | NA |
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