49 variations found. Os03g0839800/LOC_Os03g62330 (expressed protein), ranging from 35,309,855 bp to 35,310,752 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g62330 | expressed protein; RAP ID: Os03g0839800; MSU ID: LOC_Os03g62330 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335309891 (J) | chr03 | 35309891 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.100; most accessible tissue: Minghui63 root, score: 82.967 |
| vg0335309927 (J) | chr03 | 35309927 | CCTCAGT G | C | 99.40% | 0.00% | CCTCAGTG -> C | NA |
LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.892; most accessible tissue: Minghui63 root, score: 82.349 |
| vg0335309939 (J) | chr03 | 35309939 | G | A | 75.80% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.344; most accessible tissue: Minghui63 root, score: 82.185 |
| vg0335310007 (J) | chr03 | 35310007 | C | T | 96.70% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.805; most accessible tissue: Minghui63 root, score: 80.951 |
| vg0335310014 (J) | chr03 | 35310014 | C | T | 59.40% | 0.00% | C -> T |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.157; most accessible tissue: Minghui63 root, score: 80.163 |
|
| vg0335310023 (J) | chr03 | 35310023 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.381; most accessible tissue: Minghui63 root, score: 79.298 |
| vg0335310039 (J) | chr03 | 35310039 | T | G | 75.70% | 0.00% | T -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.480; most accessible tissue: Minghui63 root, score: 79.068 |
| vg0335310058 (J) | chr03 | 35310058 | A | T | 70.60% | 0.00% | A -> T |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.753; most accessible tissue: Minghui63 root, score: 78.091 |
|
| vg0335310060 (J) | chr03 | 35310060 | A | T | 70.60% | 0.00% | A -> T |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.753; most accessible tissue: Minghui63 root, score: 78.091 |
|
| vg0335310070 (J) | chr03 | 35310070 | C | T | 58.00% | 0.00% | A -> T,C | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.559; most accessible tissue: Minghui63 root, score: 78.091 |
| vg0335310075 (J) | chr03 | 35310075 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.307; most accessible tissue: Minghui63 root, score: 77.832 |
| vg0335310082 (J) | chr03 | 35310082 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.024; most accessible tissue: Minghui63 root, score: 78.091 |
| vg0335310090 (J) | chr03 | 35310090 | C | T | 96.60% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.976; most accessible tissue: Minghui63 root, score: 77.832 |
| vg0335310091 (J) | chr03 | 35310091 | C | T | 82.50% | 0.00% | T -> C |
mr1137 (All); LR P-value: 1.44E-30;
mr1606 (All); LR P-value: 1.62E-07; mr1866 (All); LR P-value: 1.09E-09; mr1115_2 (All); LR P-value: 1.21E-26; mr1137_2 (All); LR P-value: 1.04E-37; mr1180_2 (Jap_All); LR P-value: 5.38E-07; mr1183_2 (Jap_All); LR P-value: 7.66E-07; mr1554_2 (Jap_All); LR P-value: 9.52E-07; mr1611_2 (All); LR P-value: 2.33E-22; mr1617_2 (All); LR P-value: 5.85E-27; mr1730_2 (Jap_All); LR P-value: 2.77E-06; mr1794_2 (Jap_All); LR P-value: 2.69E-08 |
LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.867; most accessible tissue: Minghui63 root, score: 78.091 |
| vg0335310101 (J) | chr03 | 35310101 | T | C | 59.30% | 0.00% | T -> C |
LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.333; most accessible tissue: Minghui63 root, score: 78.833 |
|
| vg0335310114 (J) | chr03 | 35310114 | G | A | 82.50% | 0.00% | A -> G |
mr1137 (All); LR P-value: 7.70E-30;
mr1606 (All); LR P-value: 2.16E-07; mr1866 (All); LR P-value: 3.42E-09; mr1115_2 (All); LR P-value: 8.02E-25; mr1137_2 (All); LR P-value: 6.30E-36; mr1180_2 (Jap_All); LR P-value: 5.38E-07; mr1183_2 (Jap_All); LR P-value: 7.66E-07; mr1554_2 (Jap_All); LR P-value: 9.52E-07; mr1730_2 (Jap_All); LR P-value: 2.77E-06; mr1794_2 (Jap_All); LR P-value: 2.69E-08; mr1879_2 (All); LR P-value: 3.68E-12 |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.353; most accessible tissue: Minghui63 root, score: 79.740 |
| vg0335310116 (J) | chr03 | 35310116 | C | T | 95.90% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.444; most accessible tissue: Minghui63 root, score: 79.740 |
| vg0335310117 (J) | chr03 | 35310117 | C | A | 81.40% | 0.00% | C -> A,T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.444; most accessible tissue: Minghui63 root, score: 79.740 |
| vg0335310118 (J) | chr03 | 35310118 | G | A | 64.60% | 0.00% | A -> T,G |
mr1099 (Ind_All); LR P-value: 9.53E-06;
mr1180 (Ind_All); LR P-value: 1.80E-06; mr1911 (Ind_All); LR P-value: 5.99E-06; mr1918 (Ind_All); LR P-value: 9.71E-07; mr1942 (All); LR P-value: 2.46E-08; mr1095_2 (Ind_All); LR P-value: 1.91E-07; mr1099_2 (Ind_All); LR P-value: 3.30E-07; mr1180_2 (Jap_All); LR P-value: 5.38E-07; mr1183_2 (Jap_All); LR P-value: 7.66E-07; mr1222_2 (Ind_All); LR P-value: 1.76E-06; mr1554_2 (Jap_All); LR P-value: 9.52E-07; mr1730_2 (Jap_All); LR P-value: 2.77E-06; mr1794_2 (Jap_All); LR P-value: 2.69E-08; mr1815_2 (All); LR P-value: 1.02E-09; mr1879_2 (All); LR P-value: 3.36E-12; mr1942_2 (All); LR P-value: 5.07E-11; mr1977_2 (All); LR P-value: 1.37E-06 |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.444; most accessible tissue: Minghui63 root, score: 79.740 |
| vg0335310132 (J) | chr03 | 35310132 | A | G | 75.80% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.593; most accessible tissue: Minghui63 root, score: 84.686 |
| vg0335310135 (J) | chr03 | 35310135 | A | G | 95.90% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.820; most accessible tissue: Minghui63 root, score: 85.142 |
| vg0335310141 (J) | chr03 | 35310141 | G | A | 93.90% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.027; most accessible tissue: Minghui63 root, score: 85.968 |
| vg0335310143 (J) | chr03 | 35310143 | G | A | 75.70% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.044; most accessible tissue: Minghui63 root, score: 85.968 |
| vg0335310156 (J) | chr03 | 35310156 | C | T | 96.00% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.521; most accessible tissue: Minghui63 root, score: 87.745 |
| vg0335310167 (J) | chr03 | 35310167 | T | C | 58.30% | 0.00% | T -> C | NA |
LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.286; most accessible tissue: Minghui63 root, score: 88.244 |
| vg0335310174 (J) | chr03 | 35310174 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.340; most accessible tissue: Minghui63 root, score: 88.448 |
| vg0335310202 (J) | chr03 | 35310202 | G | A | 95.20% | 1.23% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 69.464; most accessible tissue: Minghui63 root, score: 88.578 |
| vg0335310206 (J) | chr03 | 35310206 | AG | A | 73.60% | 0.55% | AG -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 69.921; most accessible tissue: Minghui63 root, score: 88.767 |
| vg0335310207 (J) | chr03 | 35310207 | G | A | 95.70% | 1.04% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.017; most accessible tissue: Minghui63 root, score: 88.767 |
| vg0335310210 (J) | chr03 | 35310210 | T | A | 79.80% | 0.53% | T -> A,TA | NA |
LOC_Os03g62330.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.660; most accessible tissue: Minghui63 root, score: 89.013 |
| vg0335310225 (J) | chr03 | 35310225 | A | AT | 64.50% | 0.00% | A -> AT,G,T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.300; most accessible tissue: Minghui63 root, score: 90.465 |
| vg0335310240 (J) | chr03 | 35310240 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.427; most accessible tissue: Minghui63 root, score: 91.142 |
| vg0335310245 (J) | chr03 | 35310245 | C | T | 81.50% | 0.00% | C -> T |
mr1095 (Ind_All); LR P-value: 8.12E-06;
mr1099 (Ind_All); LR P-value: 2.99E-06; mr1180 (All); LR P-value: 3.11E-10; mr1918 (Ind_All); LR P-value: 3.92E-07; mr1929 (All); LR P-value: 2.91E-09; mr1095_2 (Ind_All); LR P-value: 2.72E-08; mr1099_2 (Ind_All); LR P-value: 2.27E-07; mr1222_2 (Ind_All); LR P-value: 1.52E-06; mr1449_2 (All); LR P-value: 2.95E-08; mr1929_2 (All); LR P-value: 5.04E-06 |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.649; most accessible tissue: Minghui63 root, score: 91.220 |
| vg0335310249 (J) | chr03 | 35310249 | C | T | 95.90% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.810; most accessible tissue: Minghui63 root, score: 91.258 |
| vg0335310254 (J) | chr03 | 35310254 | A | G | 75.80% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.828; most accessible tissue: Minghui63 root, score: 91.370 |
| vg0335310262 (J) | chr03 | 35310262 | A | G | 75.80% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.057; most accessible tissue: Minghui63 root, score: 91.370 |
| vg0335310275 (J) | chr03 | 35310275 | G | A | 75.80% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.825; most accessible tissue: Minghui63 root, score: 91.296 |
| vg0335310280 (J) | chr03 | 35310280 | A | T | 99.60% | 0.00% | A -> T | NA |
LOC_Os03g62330.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.615; most accessible tissue: Minghui63 root, score: 91.258 |
| vg0335310287 (J) | chr03 | 35310287 | G | A | 87.60% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.069; most accessible tissue: Minghui63 root, score: 91.181 |
| vg0335310288 (J) | chr03 | 35310288 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.114; most accessible tissue: Minghui63 root, score: 91.181 |
| vg0335310289 (J) | chr03 | 35310289 | G | A | 72.20% | 0.00% | G -> A | NA |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.114; most accessible tissue: Minghui63 root, score: 91.181 |
| vg0335310293 (J) | chr03 | 35310293 | G | A | 82.50% | 0.00% | A -> G |
mr1115 (All); LR P-value: 4.79E-22;
mr1137 (All); LR P-value: 1.29E-30; mr1606 (All); LR P-value: 3.23E-07; mr1611 (All); LR P-value: 2.70E-22; mr1866 (All); LR P-value: 1.01E-09; mr1920 (All); LR P-value: 1.22E-21; mr1115_2 (All); LR P-value: 7.09E-27; mr1137_2 (All); LR P-value: 1.65E-37; mr1180_2 (Jap_All); LR P-value: 5.38E-07; mr1183_2 (Jap_All); LR P-value: 7.66E-07; mr1554_2 (Jap_All); LR P-value: 9.52E-07; mr1611_2 (All); LR P-value: 1.82E-22; mr1617_2 (All); LR P-value: 8.16E-27; mr1730_2 (All); LR P-value: 1.51E-16; mr1730_2 (Jap_All); LR P-value: 2.77E-06; mr1794_2 (Jap_All); LR P-value: 2.69E-08 |
LOC_Os03g62330.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.111; most accessible tissue: Minghui63 root, score: 91.481 |
| vg0335310300 (J) | chr03 | 35310300 | T | C | 97.60% | 0.00% | T -> C | NA |
LOC_Os03g62330.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.119; most accessible tissue: Minghui63 root, score: 91.517 |
| vg0335310303 (J) | chr03 | 35310303 | G | A | 59.40% | 0.00% | G -> A |
LOC_Os03g62330.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.362; most accessible tissue: Minghui63 root, score: 91.589 |
|
| vg0335310367 (J) | chr03 | 35310367 | T | G | 99.00% | 0.00% | T -> G | NA |
LOC_Os03g62330.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.247; most accessible tissue: Minghui63 root, score: 93.365 |
| vg0335310403 (J) | chr03 | 35310403 | A | G | 97.60% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.228; most accessible tissue: Minghui63 root, score: 93.821 |
| vg0335310429 (J) | chr03 | 35310429 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os03g62330.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.698; most accessible tissue: Minghui63 root, score: 94.172 |
| vg0335310482 (J) | chr03 | 35310482 | C | T | 96.00% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.481; most accessible tissue: Minghui63 root, score: 94.959 |
| vg0335310534 (J) | chr03 | 35310534 | A | T | 75.80% | 0.00% | A -> T | NA |
LOC_Os03g62330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.359; most accessible tissue: Zhenshan97 root, score: 96.259 |