9 variations found. LOC_Os03g44130 (expressed protein), ranging from 24,792,644 bp to 24,794,517 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0324792824 (J) | chr03 | 24792824 | G | A | 61.30% | 30.55% | G -> A | NA |
LOC_Os03g44130.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g44140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.913; most accessible tissue: Zhenshan97 panicle, score: 24.575 |
| vg0324793542 (J) | chr03 | 24793542 | T | TA | 52.70% | 34.21% | T -> TA | NA |
LOC_Os03g44140.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g44130.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0324793943 (J) | chr03 | 24793943 | G | A | 56.00% | 33.33% | G -> A | NA |
LOC_Os03g44130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g44130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.887; most accessible tissue: Zhenshan97 flower, score: 22.370 |
| vg0324794159 (J) | chr03 | 24794159 | C | T | 61.40% | 13.44% | C -> T | NA |
LOC_Os03g44130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g44130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.549; most accessible tissue: Zhenshan97 flower, score: 32.793 |
| vg0324794178 (J) | chr03 | 24794178 | G | A | 65.00% | 25.88% | G -> A | NA |
LOC_Os03g44130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g44130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.907; most accessible tissue: Zhenshan97 flower, score: 32.793 |
| vg0324794198 (J) | chr03 | 24794198 | CA | C | 66.80% | 26.68% | CA -> C | NA |
LOC_Os03g44140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g44130.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 11.241; most accessible tissue: Zhenshan97 flower, score: 32.793 |
| vg0324794399 (J) | chr03 | 24794399 | C | A | 44.70% | 33.94% | C -> A | NA |
LOC_Os03g44130.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g44130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g44140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 19.855; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 |
| vg0324794420 (J) | chr03 | 24794420 | G | T | 57.20% | 30.43% | G -> T | NA |
LOC_Os03g44130.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g44140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 21.443; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 |
| vg0324794507 (J) | chr03 | 24794507 | G | A | 62.40% | 29.09% | G -> A | NA |
LOC_Os03g44130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g44140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 22.568; most accessible tissue: Zhenshan97 flag leaf, score: 57.420 |