16 variations found. LOC_Os03g39240 (expressed protein), ranging from 21,792,859 bp to 21,793,857 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0321792895 (J) | chr03 | 21792895 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g39240.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g39230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.272; most accessible tissue: Zhenshan97 young leaf, score: 93.276 |
| vg0321792912 (J) | chr03 | 21792912 | C | A | 97.70% | 0.00% | C -> A | NA |
LOC_Os03g39240.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.129; most accessible tissue: Zhenshan97 young leaf, score: 93.227 |
| vg0321792919 (J) | chr03 | 21792919 | C | G | 97.70% | 0.40% | C -> G | NA |
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g39240.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.513; most accessible tissue: Zhenshan97 young leaf, score: 91.760 |
| vg0321792934 (J) | chr03 | 21792934 | G | T | 78.90% | 2.71% | G -> T |
mr1029 (All); LR P-value: 5.95E-06;
mr1074 (Ind_All); LR P-value: 2.46E-07; mr1081 (Ind_All); LR P-value: 7.93E-07; mr1130 (Ind_All); LR P-value: 1.20E-09; mr1148 (Ind_All); LR P-value: 9.64E-10; mr1254 (Ind_All); LR P-value: 8.22E-08; mr1531 (All); LR P-value: 9.36E-13; mr1565 (Ind_All); LR P-value: 1.78E-08; mr1734 (All); LR P-value: 9.84E-06; mr1857 (All); LR P-value: 1.22E-07; mr1857 (Ind_All); LR P-value: 6.75E-09; mr1928 (Ind_All); LR P-value: 6.65E-06; mr1974 (Ind_All); LR P-value: 8.78E-06; mr1272_2 (All); LR P-value: 1.80E-06; mr1565_2 (Ind_All); LR P-value: 2.01E-10 |
LOC_Os03g39240.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.582; most accessible tissue: Zhenshan97 young leaf, score: 90.363 |
| vg0321792949 (J) | chr03 | 21792949 | C | A | 52.30% | 2.41% | C -> A |
mr1074 (Ind_All); LR P-value: 2.26E-06;
mr1081 (Ind_All); LR P-value: 1.70E-06; mr1130 (Ind_All); LR P-value: 1.19E-08; mr1148 (Ind_All); LR P-value: 6.52E-08; mr1193 (All); LR P-value: 1.11E-08; mr1221 (Ind_All); LR P-value: 2.83E-08; mr1254 (Ind_All); LR P-value: 2.28E-07; mr1857 (Ind_All); LR P-value: 9.45E-08; mr1928 (Ind_All); LR P-value: 2.09E-06 |
LOC_Os03g39240.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.107; most accessible tissue: Minghui63 panicle, score: 89.175 |
| vg0321793041 (J) | chr03 | 21793041 | A | G | 97.70% | 0.00% | A -> G | NA |
LOC_Os03g39240.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 76.700; most accessible tissue: Minghui63 panicle, score: 84.005 |
| vg0321793042 (J) | chr03 | 21793042 | C | A | 97.70% | 0.00% | C -> A | NA |
LOC_Os03g39240.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 76.507; most accessible tissue: Minghui63 panicle, score: 84.005 |
| vg0321793066 (J) | chr03 | 21793066 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os03g39240.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.582; most accessible tissue: Minghui63 panicle, score: 82.797 |
| vg0321793105 (J) | chr03 | 21793105 | G | C | 79.20% | 0.53% | G -> C |
mr1029 (All); LR P-value: 2.08E-06;
mr1074 (Ind_All); LR P-value: 4.82E-07; mr1081 (Ind_All); LR P-value: 7.78E-07; mr1130 (Ind_All); LR P-value: 5.93E-09; mr1148 (Ind_All); LR P-value: 1.29E-09; mr1254 (Ind_All); LR P-value: 6.95E-07; mr1272 (Ind_All); LR P-value: 1.63E-06; mr1531 (Ind_All); LR P-value: 9.11E-06; mr1680 (All); LR P-value: 4.38E-07; mr1734 (All); LR P-value: 2.36E-06; mr1857 (All); LR P-value: 3.82E-07; mr1857 (Ind_All); LR P-value: 3.52E-09; mr1928 (Ind_All); LR P-value: 3.11E-06; mr1974 (All); LR P-value: 8.43E-06; mr1558_2 (Ind_All); LR P-value: 3.05E-06; mr1565_2 (Ind_All); LR P-value: 4.94E-10 |
LOC_Os03g39240.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 67.254; most accessible tissue: Zhenshan97 flower, score: 78.132 |
| vg0321793118 (J) | chr03 | 21793118 | GGC | G | 99.20% | 0.00% | GGC -> G | NA |
LOC_Os03g39240.1 Alt: G| frameshift_variant HIGH(snpEff)
The average chromatin accessibility score: 66.763; most accessible tissue: Zhenshan97 flower, score: 78.317 |
| vg0321793119 (J) | chr03 | 21793119 | G | C | 80.30% | 5.40% | G -> C | NA |
LOC_Os03g39240.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.780; most accessible tissue: Zhenshan97 flower, score: 78.500 |
| vg0321793120 (J) | chr03 | 21793120 | C | T | 80.30% | 5.21% | C -> T | NA |
LOC_Os03g39240.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.032; most accessible tissue: Zhenshan97 flower, score: 78.317 |
| vg0321793551 (J) | chr03 | 21793551 | C | T | 96.70% | 1.42% | C -> T | NA |
LOC_Os03g39240.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39240.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 38.668; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 |
| vg0321793624 (J) | chr03 | 21793624 | G | A | 68.90% | 0.00% | A -> G |
mr1548 (All); LR P-value: 1.42E-22;
mr1689 (All); LR P-value: 2.93E-21; mr1718 (Ind_All); LR P-value: 1.27E-07; mr1750 (All); LMM P-value: 4.95E-08; LR P-value: 3.80E-115; mr1750 (Ind_All); LR P-value: 4.72E-11; mr1750 (Jap_All); LMM P-value: 4.59E-06; LR P-value: 4.59E-06; mr1828 (All); LR P-value: 3.86E-37; mr1874 (All); LR P-value: 1.38E-14; mr1932 (All); LR P-value: 1.35E-33; mr1312_2 (Jap_All); LMM P-value: 7.67E-06; LR P-value: 7.67E-06; mr1750_2 (Ind_All); LR P-value: 4.88E-19; mr1987_2 (Ind_All); LR P-value: 1.17E-07 |
LOC_Os03g39240.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 38.704; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 |
| vg0321793674 (J) | chr03 | 21793674 | G | T | 98.70% | 0.00% | G -> T | NA |
LOC_Os03g39240.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 38.309; most accessible tissue: Zhenshan97 flag leaf, score: 57.420 |
| vg0321793766 (J) | chr03 | 21793766 | CT | C | 97.40% | 0.00% | CT -> C,CTT | NA |
LOC_Os03g39240.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39230.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39240.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g39230.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 44.519; most accessible tissue: Zhenshan97 flag leaf, score: 65.820 |