46 variations found. LOC_Os03g39930 (retrotransposon protein; putative; unclassified; expressed), ranging from 22,193,675 bp to 22,195,637 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193675 (J) | chr03 | 22193675 | C | T | 62.30% | 35.10% | C -> T | NA |
LOC_Os03g39920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920-LOC_Os03g39930 Alt: T| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193676 (J) | chr03 | 22193676 | T | G | 62.30% | 36.16% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: G| splice_region_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g39930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193677 (J) | chr03 | 22193677 | G | A | 62.10% | 36.14% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193680 (J) | chr03 | 22193680 | G | A | 57.40% | 36.16% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193685 (J) | chr03 | 22193685 | A | G | 62.40% | 36.16% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 12.508; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193701 (J) | chr03 | 22193701 | G | A | 62.50% | 36.12% | G -> A,GATTACAG ATTTA | NA |
LOC_Os03g39930.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g39930.1 Alt: GATTACAGATTTA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g39920.1 Alt: GATTACAGATTTA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g39940.1 Alt: GATTACAGATTTA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 12.429; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193714 (J) | chr03 | 22193714 | A | G | 62.40% | 36.10% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193716 (J) | chr03 | 22193716 | C | T | 62.30% | 36.16% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.265; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0322193886 (J) | chr03 | 22193886 | C | T | 9.70% | 57.64% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.623; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg0322193997 (J) | chr03 | 22193997 | G | A | 38.80% | 58.80% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.179; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0322194006 (J) | chr03 | 22194006 | A | G | 39.90% | 58.38% | A -> G | NA |
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g39930.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194009 (J) | chr03 | 22194009 | G | A | 40.00% | 58.84% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194015 (J) | chr03 | 22194015 | G | T | 39.80% | 59.04% | G -> A,T | NA |
LOC_Os03g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194016 (J) | chr03 | 22194016 | G | A | 39.80% | 59.04% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194024 (J) | chr03 | 22194024 | G | A | 39.70% | 59.06% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194029 (J) | chr03 | 22194029 | C | A | 39.60% | 59.04% | C -> A | NA |
LOC_Os03g39930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194032 (J) | chr03 | 22194032 | G | A | 40.10% | 59.04% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194034 (J) | chr03 | 22194034 | A | G | 40.00% | 59.06% | A -> G | NA |
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g39930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194036 (J) | chr03 | 22194036 | G | A | 39.80% | 59.04% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194042 (J) | chr03 | 22194042 | C | T | 39.90% | 59.04% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194047 (J) | chr03 | 22194047 | C | T | 40.00% | 59.04% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.348; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0322194048 (J) | chr03 | 22194048 | C | T | 39.60% | 59.06% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194053 (J) | chr03 | 22194053 | G | A | 39.10% | 59.08% | G -> A,T | NA |
LOC_Os03g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194054 (J) | chr03 | 22194054 | G | A | 40.00% | 59.08% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194058 (J) | chr03 | 22194058 | A | C | 40.00% | 59.06% | A -> C | NA |
LOC_Os03g39930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194065 (J) | chr03 | 22194065 | T | A | 39.90% | 59.08% | T -> A | NA |
LOC_Os03g39930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194069 (J) | chr03 | 22194069 | G | A | 39.70% | 59.12% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194071 (J) | chr03 | 22194071 | AT | A | 39.80% | 59.16% | AT -> A | NA |
LOC_Os03g39930.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194072 (J) | chr03 | 22194072 | T | C | 39.70% | 59.18% | T -> C | NA |
LOC_Os03g39930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194073 (J) | chr03 | 22194073 | GAC | G | 39.90% | 59.18% | GAC -> G | NA |
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g39930.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194078 (J) | chr03 | 22194078 | G | A | 39.70% | 59.20% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194093 (J) | chr03 | 22194093 | C | G | 39.70% | 59.54% | C -> G | NA |
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g39930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194096 (J) | chr03 | 22194096 | C | A | 35.00% | 60.16% | C -> A | NA |
LOC_Os03g39930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194098 (J) | chr03 | 22194098 | C | T | 33.50% | 61.17% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194102 (J) | chr03 | 22194102 | G | A | 31.20% | 62.97% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194110 (J) | chr03 | 22194110 | G | C | 20.70% | 68.15% | G -> C,T | NA |
LOC_Os03g39930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g39930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194116 (J) | chr03 | 22194116 | C | T | 10.10% | 77.42% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194119 (J) | chr03 | 22194119 | C | T | 24.60% | 69.78% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194129 (J) | chr03 | 22194129 | T | C | 8.50% | 87.60% | T -> C | NA |
LOC_Os03g39930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg0322194333 (J) | chr03 | 22194333 | G | A | 7.20% | 72.39% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g39930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.955; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0322195173 (J) | chr03 | 22195173 | C | T | 6.00% | 67.92% | T -> C | NA |
LOC_Os03g39930.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.149; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0322195244 (J) | chr03 | 22195244 | C | T | 12.80% | 65.38% | C -> T | NA |
LOC_Os03g39930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.319; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg0322195295 (J) | chr03 | 22195295 | C | T | 8.80% | 71.54% | C -> T,G | NA |
LOC_Os03g39930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g39930.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.019; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0322195519 (J) | chr03 | 22195519 | G | A | 11.30% | 69.02% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g39930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 23.952; most accessible tissue: Minghui63 panicle, score: 42.799 |
| vg0322195583 (J) | chr03 | 22195583 | G | A | 4.50% | 70.78% | G -> A | NA |
LOC_Os03g39930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 20.770; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0322195585 (J) | chr03 | 22195585 | CGG | C | 2.20% | 73.83% | CGG -> C | NA |
LOC_Os03g39930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g39920.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g39940.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 20.770; most accessible tissue: Minghui63 panicle, score: 34.226 |