8 variations found. LOC_Os01g71410 (glycosyl hydrolases family 17; putative; expressed), ranging from 41,375,171 bp to 41,376,297 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0141375211 (J) | chr01 | 41375211 | T | A | 66.70% | 0.42% | T -> A |
Grain_length (All); LR P-value: 3.44E-16;
Grain_length (Ind_All); LR P-value: 1.75E-16; Grain_thickness (Ind_All); LR P-value: 5.59E-08; Grain_width (Ind_All); LR P-value: 3.63E-14; mr1399 (Ind_All); LR P-value: 2.30E-06; mr1458 (Ind_All); LR P-value: 5.25E-07; mr1974 (Ind_All); LR P-value: 1.22E-06; mr1319_2 (All); LR P-value: 2.20E-10; mr1322_2 (All); LR P-value: 3.03E-09; mr1323_2 (Ind_All); LR P-value: 7.10E-06; mr1330_2 (All); LR P-value: 4.96E-15; mr1438_2 (All); LR P-value: 5.22E-06; mr1458_2 (Ind_All); LR P-value: 1.44E-07; mr1527_2 (All); LR P-value: 1.31E-07 |
LOC_Os01g71410.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g71410.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.305; most accessible tissue: Callus, score: 88.048 |
| vg0141375257 (J) | chr01 | 41375257 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g71400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71410.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.064; most accessible tissue: Callus, score: 88.048 |
| vg0141375315 (J) | chr01 | 41375315 | CT | C | 99.80% | 0.00% | CT -> C | NA |
LOC_Os01g71410.1 Alt: C| frameshift_variant HIGH(snpEff)
The average chromatin accessibility score: 70.066; most accessible tissue: Callus, score: 88.048 |
| vg0141375724 (J) | chr01 | 41375724 | C | T | 67.20% | 0.40% | C -> T |
Grain_length (All); LR P-value: 3.04E-16;
Grain_length (Ind_All); LR P-value: 2.57E-16; Grain_thickness (Ind_All); LR P-value: 7.10E-08; Grain_width (Ind_All); LR P-value: 8.73E-14; mr1399 (Ind_All); LR P-value: 2.91E-06; mr1458 (Ind_All); LR P-value: 3.12E-07; mr1974 (All); LR P-value: 6.27E-06; mr1974 (Ind_All); LR P-value: 6.58E-07; mr1319_2 (All); LR P-value: 1.78E-09; mr1322_2 (All); LR P-value: 6.02E-09; mr1330_2 (All); LR P-value: 1.40E-13; mr1458_2 (Ind_All); LR P-value: 1.12E-07; mr1527_2 (All); LR P-value: 2.23E-07 |
LOC_Os01g71410.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g71410.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 70.818; most accessible tissue: Zhenshan97 flower, score: 73.946 |
| vg0141375811 (J) | chr01 | 41375811 | C | T | 94.40% | 0.00% | C -> T | NA |
LOC_Os01g71410.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.566; most accessible tissue: Minghui63 panicle, score: 77.956 |
| vg0141376024 (J) | chr01 | 41376024 | G | A | 96.20% | 0.00% | G -> A | NA |
LOC_Os01g71410.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.678; most accessible tissue: Zhenshan97 young leaf, score: 78.044 |
| vg0141376032 (J) | chr01 | 41376032 | C | A | 67.20% | 0.36% | C -> A |
Grain_length (All); LR P-value: 4.24E-16;
Grain_length (Ind_All); LR P-value: 2.10E-16; Grain_thickness (Ind_All); LR P-value: 7.49E-08; Grain_width (Ind_All); LR P-value: 5.19E-14; mr1458 (Ind_All); LR P-value: 4.29E-07; mr1974 (All); LR P-value: 6.84E-06; mr1974 (Ind_All); LR P-value: 7.87E-07; mr1319_2 (All); LR P-value: 1.84E-09; mr1322_2 (All); LR P-value: 5.84E-09; mr1330_2 (All); LR P-value: 1.28E-13; mr1458_2 (Ind_All); LR P-value: 1.39E-07; mr1527_2 (All); LR P-value: 2.01E-07 |
LOC_Os01g71410.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71410.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 71.765; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
| vg0141376224 (J) | chr01 | 41376224 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os01g71410.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g71400.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.207; most accessible tissue: Callus, score: 75.453 |