33 variations found. Os03g0836400/LOC_Os03g62020 (harpin-induced protein 1 domain containing protein; expressed), ranging from 35,145,633 bp to 35,146,690 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g62020 | harpin-induced protein 1 domain containing protein, expressed; RAP ID: Os03g0836400; MSU ID: LOC_Os03g62020 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335145641 (J) | chr03 | 35145641 | CTACGTA TCAACGA GGTGAAA GCA | C | 99.20% | 0.00% | CTACGTATCA ACGAGGTGAA AGCA -> C | NA |
LOC_Os03g62020.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.534; most accessible tissue: Zhenshan97 root, score: 83.590 |
| vg0335145688 (J) | chr03 | 35145688 | C | CT | 98.50% | 0.00% | C -> CT | NA |
LOC_Os03g62020.1 Alt: CT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62040.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62010.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.285; most accessible tissue: Callus, score: 91.643 |
| vg0335145712 (J) | chr03 | 35145712 | A | T | 98.50% | 0.00% | A -> T | NA |
LOC_Os03g62020.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g62020.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.453; most accessible tissue: Callus, score: 91.643 |
| vg0335145732 (J) | chr03 | 35145732 | C | A | 98.50% | 0.00% | C -> A | NA |
LOC_Os03g62020.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g62020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.429; most accessible tissue: Callus, score: 91.643 |
| vg0335145735 (J) | chr03 | 35145735 | A | G | 94.80% | 0.00% | A -> G |
LOC_Os03g62020.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.376; most accessible tissue: Callus, score: 91.643 |
|
| vg0335145925 (J) | chr03 | 35145925 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os03g62020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.713; most accessible tissue: Minghui63 flower, score: 87.888 |
| vg0335145943 (J) | chr03 | 35145943 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os03g62020.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g62040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.600; most accessible tissue: Minghui63 flower, score: 88.293 |
| vg0335145952 (J) | chr03 | 35145952 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os03g62020.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g62040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.686; most accessible tissue: Zhenshan97 flag leaf, score: 88.196 |
| vg0335145995 (J) | chr03 | 35145995 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os03g62020.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.360; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 |
| vg0335146010 (J) | chr03 | 35146010 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g62020.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.892; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 |
| vg0335146049 (J) | chr03 | 35146049 | G | T | 67.30% | 0.40% | G -> T,GCTGA | NA |
LOC_Os03g62020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g62020.1 Alt: GCTGA| frameshift_variant HIGH(snpEff) LOC_Os03g62040.1 Alt: GCTGA| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: GCTGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62020.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.393; most accessible tissue: Minghui63 young leaf, score: 87.677 |
| vg0335146191 (J) | chr03 | 35146191 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os03g62020.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.089; most accessible tissue: Minghui63 flower, score: 89.589 |
| vg0335146207 (J) | chr03 | 35146207 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os03g62020.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.925; most accessible tissue: Minghui63 flower, score: 89.427 |
| vg0335146216 (J) | chr03 | 35146216 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os03g62020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.104; most accessible tissue: Minghui63 flower, score: 89.589 |
| vg0335146226 (J) | chr03 | 35146226 | C | G | 99.50% | 0.00% | C -> G | NA |
LOC_Os03g62020.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.860; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |
| vg0335146243 (J) | chr03 | 35146243 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os03g62020.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os03g62040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.336; most accessible tissue: Minghui63 flower, score: 89.091 |
| vg0335146245 (J) | chr03 | 35146245 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g62020.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.302; most accessible tissue: Minghui63 flower, score: 89.091 |
| vg0335146264 (J) | chr03 | 35146264 | G | A | 67.40% | 0.17% | G -> A | NA |
LOC_Os03g62020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g62020.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.007; most accessible tissue: Minghui63 flower, score: 89.852 |
| vg0335146385 (J) | chr03 | 35146385 | G | C | 65.80% | 0.00% | G -> C | NA |
LOC_Os03g62020.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.403; most accessible tissue: Minghui63 flower, score: 88.853 |
| vg0335146396 (J) | chr03 | 35146396 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os03g62020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.946; most accessible tissue: Minghui63 flower, score: 88.853 |
| vg0335146450 (J) | chr03 | 35146450 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g62020.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.217; most accessible tissue: Minghui63 flower, score: 89.033 |
| vg0335146484 (J) | chr03 | 35146484 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os03g62020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.518; most accessible tissue: Callus, score: 88.843 |
| vg0335146490 (J) | chr03 | 35146490 | TCTA | T | 99.90% | 0.00% | TCTA -> T | NA |
LOC_Os03g62020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.613; most accessible tissue: Callus, score: 88.843 |
| vg0335146504 (J) | chr03 | 35146504 | T | G | 67.20% | 0.44% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g62020.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.123; most accessible tissue: Callus, score: 88.843 |
| vg0335146524 (J) | chr03 | 35146524 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g62020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.350; most accessible tissue: Callus, score: 88.843 |
| vg0335146542 (J) | chr03 | 35146542 | T | C | 83.30% | 0.32% | T -> C |
mr1098 (Ind_All); LR P-value: 3.10E-06;
mr1180 (All); LR P-value: 4.16E-11; mr1180 (Ind_All); LR P-value: 8.02E-07; mr1503 (All); LR P-value: 2.76E-13; mr1918 (Ind_All); LR P-value: 2.00E-07; mr1929 (All); LR P-value: 6.81E-09; mr1095_2 (Ind_All); LR P-value: 2.97E-06; mr1098_2 (Ind_All); LR P-value: 6.67E-06; mr1099_2 (Ind_All); LR P-value: 4.17E-06; mr1428_2 (All); LR P-value: 6.74E-06 |
LOC_Os03g62020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.647; most accessible tissue: Callus, score: 88.843 |
| vg0335146548 (J) | chr03 | 35146548 | AT | A | 99.20% | 0.00% | AT -> ATT,A | NA |
LOC_Os03g62020.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62020.1 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62040.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.198; most accessible tissue: Callus, score: 88.843 |
| vg0335146568 (J) | chr03 | 35146568 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os03g62020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.464; most accessible tissue: Zhenshan97 root, score: 89.337 |
| vg0335146574 (J) | chr03 | 35146574 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os03g62020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.473; most accessible tissue: Zhenshan97 root, score: 89.337 |
| vg0335146580 (J) | chr03 | 35146580 | A | ATACTAT | 99.90% | 0.00% | A -> ATACTAT | NA |
LOC_Os03g62020.1 Alt: ATACTAT| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: ATACTAT| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: ATACTAT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.017; most accessible tissue: Zhenshan97 root, score: 89.403 |
| vg0335146589 (J) | chr03 | 35146589 | T | TTCATGA A | 99.90% | 0.00% | T -> TTCATGAA | NA |
LOC_Os03g62020.1 Alt: TTCATGAA| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: TTCATGAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: TTCATGAA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.767; most accessible tissue: Zhenshan97 root, score: 89.203 |
| vg0335146609 (J) | chr03 | 35146609 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g62020.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g62030.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.005; most accessible tissue: Zhenshan97 root, score: 88.924 |
| vg0335146664 (J) | chr03 | 35146664 | TTTTATA A | T | 83.30% | 0.34% | TTTTATAA -> T | NA |
LOC_Os03g62020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62030.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.513; most accessible tissue: Zhenshan97 root, score: 89.064 |