4 variations found. LOC_Os07g48730 (tyrosine protein kinase domain containing protein; putative; expressed), ranging from 29,179,660 bp to 29,181,610 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0729180318 (J) | chr07 | 29180318 | G | A | 63.50% | 0.00% | A -> G |
mr1342 (All); LR P-value: 9.10E-09;
mr1592 (All); LR P-value: 6.22E-15; mr1795 (All); LR P-value: 1.35E-51; mr1837 (All); LR P-value: 5.51E-06; mr1915 (All); LR P-value: 5.00E-07; mr1592_2 (All); LR P-value: 2.28E-16; mr1700_2 (All); LR P-value: 2.15E-08; mr1713_2 (All); LR P-value: 1.41E-12; mr1727_2 (All); LR P-value: 5.03E-07; mr1756_2 (All); LR P-value: 3.68E-10; mr1785_2 (All); LR P-value: 5.21E-06; mr1837_2 (All); LR P-value: 1.77E-08; mr1915_2 (All); LR P-value: 8.67E-07; mr1938_2 (All); LR P-value: 5.37E-14 |
LOC_Os07g48750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.192; most accessible tissue: Zhenshan97 root, score: 95.193 |
| vg0729181278 (J) | chr07 | 29181278 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os07g48730.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g48750.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g48720.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g48720.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g48720.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.477; most accessible tissue: Callus, score: 97.666 |
| vg0729181313 (J) | chr07 | 29181313 | T | C | 92.60% | 0.00% | C -> T | NA |
LOC_Os07g48730.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48750.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.378; most accessible tissue: Callus, score: 97.666 |
| vg0729181328 (J) | chr07 | 29181328 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os07g48730.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g48750.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g48720.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.518; most accessible tissue: Callus, score: 94.374 |