11 variations found. LOC_Os01g49320 (glycosyl hydrolase; putative; expressed), ranging from 28,354,770 bp to 28,356,109 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128354789 (J) | chr01 | 28354789 | C | T | 69.50% | 0.00% | T -> C |
Grain_weight (All); LR P-value: 2.39E-11;
mr1334 (All); LR P-value: 3.71E-86; mr1350 (All); LR P-value: 1.00E-35; mr1423 (All); LR P-value: 1.18E-26; mr1653 (All); LR P-value: 1.26E-13; mr1805 (All); LR P-value: 6.81E-25; mr1089_2 (All); LR P-value: 6.76E-52; mr1093_2 (All); LR P-value: 1.63E-50; mr1235_2 (All); LR P-value: 2.02E-56; mr1243_2 (All); LR P-value: 2.80E-42; mr1248_2 (All); LR P-value: 1.70E-12; mr1251_2 (All); LR P-value: 1.78E-37; mr1277_2 (All); LR P-value: 1.28E-14; mr1334_2 (All); LR P-value: 3.11E-95; mr1403_2 (All); LR P-value: 1.84E-26; mr1423_2 (All); LR P-value: 8.24E-32; mr1435_2 (All); LR P-value: 1.40E-37; mr1486_2 (All); LR P-value: 3.46E-46; mr1599_2 (All); LR P-value: 2.55E-62; mr1790_2 (All); LR P-value: 2.78E-14; mr1805_2 (All); LR P-value: 2.13E-44; mr1844_2 (All); LR P-value: 9.98E-11; mr1893_2 (All); LR P-value: 3.04E-11; mr1991_2 (All); LR P-value: 3.55E-56 |
LOC_Os01g49320.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g49310.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g49310.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.633; most accessible tissue: Callus, score: 90.261 |
| vg0128354954 (J) | chr01 | 28354954 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g49320.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g49310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g49310.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.894; most accessible tissue: Callus, score: 94.082 |
| vg0128355003 (J) | chr01 | 28355003 | G | A | 77.30% | 0.00% | G -> A |
Plant_height (All); LR P-value: 2.30E-22;
Plant_height (Ind_All); LR P-value: 1.32E-18; mr1186 (Ind_All); LR P-value: 6.55E-08; mr1249 (All); LR P-value: 5.98E-08; mr1616 (Ind_All); LR P-value: 1.27E-06; mr1639 (Ind_All); LR P-value: 2.27E-06; mr1648 (Ind_All); LR P-value: 3.66E-06; mr1706 (Ind_All); LR P-value: 1.72E-07; mr1717 (All); LR P-value: 7.03E-07; mr1906 (Ind_All); LR P-value: 6.99E-06; mr1960 (Ind_All); LR P-value: 2.00E-07; mr1115_2 (Ind_All); LR P-value: 2.08E-06; mr1180_2 (All); LR P-value: 1.35E-17; mr1180_2 (Ind_All); LR P-value: 1.70E-07; mr1183_2 (All); LR P-value: 2.99E-20; mr1215_2 (All); LR P-value: 4.56E-08; mr1220_2 (All); LR P-value: 1.75E-10; mr1220_2 (Ind_All); LR P-value: 9.58E-06; mr1236_2 (All); LR P-value: 1.38E-06; mr1236_2 (Ind_All); LR P-value: 3.95E-07; mr1302_2 (All); LR P-value: 3.64E-07; mr1319_2 (All); LR P-value: 2.18E-09; mr1320_2 (All); LR P-value: 1.56E-06; mr1320_2 (Ind_All); LR P-value: 2.35E-06; mr1330_2 (All); LR P-value: 3.83E-12; mr1352_2 (All); LR P-value: 3.01E-18; mr1359_2 (Ind_All); LR P-value: 4.91E-07; mr1376_2 (All); LR P-value: 1.15E-08; mr1376_2 (Ind_All); LR P-value: 3.59E-06; mr1428_2 (All); LR P-value: 1.23E-06; mr1428_2 (Ind_All); LR P-value: 9.02E-06; mr1431_2 (All); LR P-value: 2.80E-09; mr1431_2 (Ind_All); LR P-value: 2.35E-06; mr1478_2 (Ind_All); LR P-value: 1.63E-06; mr1517_2 (Ind_All); LR P-value: 8.59E-07; mr1545_2 (Ind_All); LR P-value: 5.02E-06; mr1550_2 (Ind_All); LR P-value: 7.95E-08; mr1653_2 (Ind_All); LR P-value: 8.88E-08; mr1654_2 (Ind_All); LR P-value: 1.65E-06; mr1735_2 (Ind_All); LR P-value: 4.74E-06; mr1850_2 (All); LR P-value: 5.23E-12; mr1968_2 (Ind_All); LR P-value: 5.11E-06; mr1971_2 (Ind_All); LR P-value: 4.12E-07 |
LOC_Os01g49320.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g49310.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g49310.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.436; most accessible tissue: Callus, score: 94.082 |
| vg0128355011 (J) | chr01 | 28355011 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os01g49320.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g49310.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g49310.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.505; most accessible tissue: Callus, score: 94.082 |
| vg0128355240 (J) | chr01 | 28355240 | G | A | 98.40% | 0.00% | G -> A | NA |
LOC_Os01g49320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.078; most accessible tissue: Callus, score: 89.629 |
| vg0128355340 (J) | chr01 | 28355340 | C | A | 72.00% | 0.00% | C -> A | NA |
LOC_Os01g49320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.171; most accessible tissue: Zhenshan97 flag leaf, score: 90.894 |
| vg0128355694 (J) | chr01 | 28355694 | CGGA | C | 97.20% | 0.00% | CGGA -> C | NA |
LOC_Os01g49320.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 88.109; most accessible tissue: Zhenshan97 flag leaf, score: 93.925 |
| vg0128355872 (J) | chr01 | 28355872 | G | A | 77.20% | 0.00% | G -> A |
Plant_height (All); LR P-value: 2.82E-22;
Plant_height (Ind_All); LR P-value: 3.86E-18; mr1186 (Ind_All); LR P-value: 7.05E-08; mr1249 (All); LR P-value: 5.66E-08; mr1616 (Ind_All); LR P-value: 7.77E-07; mr1639 (Ind_All); LR P-value: 2.30E-06; mr1648 (Ind_All); LR P-value: 4.71E-06; mr1706 (Ind_All); LR P-value: 1.74E-07; mr1717 (All); LR P-value: 7.95E-07; mr1906 (Ind_All); LR P-value: 6.40E-06; mr1960 (Ind_All); LR P-value: 2.22E-07; mr1115_2 (Ind_All); LR P-value: 2.11E-06; mr1172_2 (All); LR P-value: 1.33E-08; mr1180_2 (All); LR P-value: 4.71E-18; mr1180_2 (Ind_All); LR P-value: 1.95E-07; mr1183_2 (All); LR P-value: 6.95E-21; mr1215_2 (All); LR P-value: 2.15E-08; mr1220_2 (All); LR P-value: 1.20E-10; mr1236_2 (All); LR P-value: 8.86E-07; mr1236_2 (Ind_All); LR P-value: 4.52E-07; mr1302_2 (All); LR P-value: 1.64E-07; mr1319_2 (All); LR P-value: 1.63E-09; mr1320_2 (All); LR P-value: 1.41E-06; mr1320_2 (Ind_All); LR P-value: 3.11E-06; mr1352_2 (All); LR P-value: 1.42E-18; mr1359_2 (Ind_All); LR P-value: 7.53E-07; mr1376_2 (All); LR P-value: 4.33E-09; mr1376_2 (Ind_All); LR P-value: 2.56E-06; mr1428_2 (All); LR P-value: 8.79E-07; mr1431_2 (All); LR P-value: 9.93E-10; mr1431_2 (Ind_All); LR P-value: 1.63E-06; mr1478_2 (Ind_All); LR P-value: 3.09E-06; mr1517_2 (Ind_All); LR P-value: 9.14E-07; mr1545_2 (Ind_All); LR P-value: 3.80E-06; mr1550_2 (Ind_All); LR P-value: 5.23E-08; mr1582_2 (Ind_All); LR P-value: 9.10E-06; mr1653_2 (Ind_All); LR P-value: 1.20E-07; mr1654_2 (Ind_All); LR P-value: 2.25E-06; mr1735_2 (Ind_All); LR P-value: 3.89E-06; mr1850_2 (All); LR P-value: 2.30E-12; mr1968_2 (Ind_All); LR P-value: 4.19E-06; mr1971_2 (Ind_All); LR P-value: 8.71E-07 |
LOC_Os01g49320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.298; most accessible tissue: Zhenshan97 young leaf, score: 95.157 |
| vg0128355966 (J) | chr01 | 28355966 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g49320.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g49310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g49310.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.525; most accessible tissue: Zhenshan97 young leaf, score: 95.576 |
| vg0128355978 (J) | chr01 | 28355978 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os01g49320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.005; most accessible tissue: Zhenshan97 young leaf, score: 95.297 |
| STR0128355695 (J) | chr01 | 28355695 | GGAG | G | 96.40% | 0.00% | GGAG -> G | NA |
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