7 variations found. LOC_Os03g38400 (GDSL-motif lipase%2Fhydrolase family protein; putative; expressed), ranging from 21,315,329 bp to 21,315,763 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0321315383 (J) | chr03 | 21315383 | TC | T | 98.50% | 0.00% | TC -> T | NA |
LOC_Os03g38400.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 64.905; most accessible tissue: Minghui63 root, score: 75.155 |
| vg0321315420 (J) | chr03 | 21315420 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os03g38390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g38400.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.443; most accessible tissue: Minghui63 root, score: 76.119 |
| vg0321315548 (J) | chr03 | 21315548 | G | A | 98.50% | 0.00% | G -> A | NA |
LOC_Os03g38400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.738; most accessible tissue: Minghui63 root, score: 82.349 |
| vg0321315554 (J) | chr03 | 21315554 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os03g38400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.984; most accessible tissue: Minghui63 root, score: 82.511 |
| vg0321315578 (J) | chr03 | 21315578 | T | C | 50.50% | 0.00% | C -> T |
LOC_Os03g38400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.199; most accessible tissue: Minghui63 root, score: 84.447 |
|
| vg0321315611 (J) | chr03 | 21315611 | C | T | 90.90% | 0.00% | C -> T |
Spikelet_length (Ind_All); LR P-value: 2.45E-06;
mr1215 (All); LR P-value: 2.30E-06; mr1389 (All); LR P-value: 1.17E-06 |
LOC_Os03g38400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.980; most accessible tissue: Minghui63 root, score: 85.968 |
| vg0321315684 (J) | chr03 | 21315684 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os03g38400.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os03g38390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.560; most accessible tissue: Callus, score: 90.271 |