39 variations found. Os12g0561500/LOC_Os12g37480 (invertase%2Fpectin methylesterase inhibitor family protein; putative; expressed), ranging from 22,999,867 bp to 23,000,959 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g37480 | invertase/pectin methylesterase inhibitor family protein, putative, expressed; RAP ID: Os12g0561500; MSU ID: LOC_Os12g37480 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999884 (J) | chr12 | 22999884 | C | CTAATTA CT | 43.50% | 47.48% | C -> CTAATTACT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: CTAATTACT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: CTAATTACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: CTAATTACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 28.602; most accessible tissue: Zhenshan97 flower, score: 45.068 |
| vg1222999887 (J) | chr12 | 22999887 | C | T | 21.40% | 55.25% | C -> T,CTCT | NA |
LOC_Os12g37480.1 Alt: CTCT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: CTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: CTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 28.694; most accessible tissue: Zhenshan97 flower, score: 45.068 |
| vg1222999892 (J) | chr12 | 22999892 | CAT | C | 43.80% | 44.05% | CAT -> C,TAT | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g37480.1 Alt: TAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: TAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: TAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.340; most accessible tissue: Zhenshan97 flower, score: 45.068 |
| vg1222999902 (J) | chr12 | 22999902 | A | G | 26.10% | 47.25% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.592; most accessible tissue: Zhenshan97 flower, score: 44.193 |
| vg1222999904 (J) | chr12 | 22999904 | C | T | 45.00% | 44.03% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.622; most accessible tissue: Zhenshan97 flower, score: 44.193 |
| vg1222999908 (J) | chr12 | 22999908 | G | A | 41.00% | 44.92% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.240; most accessible tissue: Zhenshan97 flower, score: 44.193 |
| vg1222999909 (J) | chr12 | 22999909 | T | C | 39.10% | 42.62% | T -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 29.240; most accessible tissue: Zhenshan97 flower, score: 44.193 |
| vg1222999916 (J) | chr12 | 22999916 | G | A | 13.20% | 60.60% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.563; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg1222999919 (J) | chr12 | 22999919 | C | A | 43.30% | 44.69% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.836; most accessible tissue: Zhenshan97 flower, score: 49.964 |
| vg1222999944 (J) | chr12 | 22999944 | CT | C | 12.10% | 69.78% | CT -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 34.032; most accessible tissue: Callus, score: 65.184 |
| vg1222999973 (J) | chr12 | 22999973 | A | C | 4.20% | 73.70% | A -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 36.897; most accessible tissue: Callus, score: 65.184 |
| vg1222999984 (J) | chr12 | 22999984 | CATATAT ATATAT | C | 3.40% | 73.21% | CATATATATA TAT -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 36.367; most accessible tissue: Callus, score: 65.184 |
| vg1222999986 (J) | chr12 | 22999986 | T | C | 5.00% | 81.61% | T -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 36.472; most accessible tissue: Callus, score: 65.184 |
| vg1222999998 (J) | chr12 | 22999998 | T | C | 0.50% | 89.89% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.015; most accessible tissue: Minghui63 root, score: 65.927 |
| vg1223000001 (J) | chr12 | 23000001 | A | G | 1.00% | 82.20% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.870; most accessible tissue: Minghui63 root, score: 66.549 |
| vg1223000007 (J) | chr12 | 23000007 | A | G | 0.90% | 84.30% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.086; most accessible tissue: Zhenshan97 flower, score: 69.089 |
| vg1223000011 (J) | chr12 | 23000011 | ATACATA TATATAT ATATTAT ATATATA TATATAT AATATAT ATATATA TATG | GTACATA TATATAT ATATTAT ATATATA TATATAT AATATAT ATATATA TATG | 1.00% | 79.98% | ATACATATAT ATATATATTA TATATATATA TATATAATAT ATATATATAT ATG -> GTACATATAT ATATATATTA TATATATATA TATATAATAT ATATATATAT ATG,A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37480.1 Alt: GTACATATATATATATATTATATATATATATATATAATATATATATATATATG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: GTACATATATATATATATTATATATATATATATATAATATATATATATATATG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: GTACATATATATATATATTATATATATATATATATAATATATATATATATATG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.593; most accessible tissue: Minghui63 panicle, score: 74.563 |
| vg1223000053 (J) | chr12 | 23000053 | A | G | 55.10% | 34.28% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.731; most accessible tissue: Zhenshan97 flower, score: 81.047 |
| vg1223000075 (J) | chr12 | 23000075 | T | C | 95.90% | 0.00% | T -> C | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.641; most accessible tissue: Zhenshan97 flower, score: 82.718 |
| vg1223000091 (J) | chr12 | 23000091 | C | T | 43.40% | 39.50% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.093; most accessible tissue: Zhenshan97 flower, score: 83.283 |
| vg1223000128 (J) | chr12 | 23000128 | C | A | 93.70% | 0.00% | C -> A |
mr1006 (All); LR P-value: 2.08E-06;
mr1006 (Ind_All); LR P-value: 7.72E-06; mr1052 (All); LR P-value: 4.33E-06; mr1074 (Ind_All); LR P-value: 5.00E-06; mr1081 (Ind_All); LR P-value: 6.64E-06; mr1098 (Ind_All); LR P-value: 6.57E-06; mr1130 (Ind_All); LR P-value: 1.25E-06; mr1498 (All); LR P-value: 5.14E-11; mr1498 (Ind_All); LR P-value: 1.61E-10; mr1749 (All); LR P-value: 5.84E-06; mr1769 (All); LR P-value: 1.97E-13; mr1769 (Ind_All); LR P-value: 8.70E-13; mr1887 (All); LR P-value: 9.22E-06; mr1887 (Ind_All); LR P-value: 4.14E-06; mr1951 (All); LR P-value: 9.82E-10; mr1951 (Ind_All); LR P-value: 6.52E-08; mr1986 (Ind_All); LR P-value: 9.58E-07; mr1074_2 (Ind_All); LR P-value: 1.49E-06; mr1155_2 (Ind_All); LR P-value: 6.62E-08; mr1222_2 (Ind_All); LR P-value: 9.41E-06; mr1498_2 (All); LR P-value: 4.71E-10; mr1498_2 (Ind_All); LR P-value: 7.59E-07; mr1679_2 (Ind_All); LR P-value: 9.77E-06; mr1720_2 (Ind_All); LR P-value: 7.40E-06; mr1769_2 (Ind_All); LR P-value: 2.03E-08; mr1925_2 (All); LR P-value: 3.86E-07; mr1951_2 (All); LR P-value: 2.64E-09; mr1951_2 (Ind_All); LR P-value: 6.44E-09 |
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.990; most accessible tissue: Zhenshan97 flower, score: 84.119 |
| vg1223000134 (J) | chr12 | 23000134 | C | T | 71.20% | 0.00% | C -> T | NA |
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.338; most accessible tissue: Zhenshan97 flower, score: 84.598 |
| vg1223000136 (J) | chr12 | 23000136 | T | G | 48.00% | 11.38% | T -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.162; most accessible tissue: Zhenshan97 flower, score: 84.598 |
|
| vg1223000137 (J) | chr12 | 23000137 | AG | A | 99.30% | 0.00% | AG -> A | NA |
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.352; most accessible tissue: Zhenshan97 flower, score: 84.598 |
| vg1223000139 (J) | chr12 | 23000139 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.650; most accessible tissue: Zhenshan97 flower, score: 84.964 |
| vg1223000145 (J) | chr12 | 23000145 | A | T | 97.70% | 0.00% | A -> T | NA |
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.076; most accessible tissue: Zhenshan97 flower, score: 85.053 |
| vg1223000154 (J) | chr12 | 23000154 | G | T | 93.70% | 0.00% | G -> T |
mr1006 (All); LR P-value: 2.50E-06;
mr1006 (Ind_All); LR P-value: 8.97E-06; mr1052 (All); LR P-value: 5.29E-06; mr1498 (All); LR P-value: 1.66E-10; mr1498 (Ind_All); LR P-value: 4.83E-10; mr1769 (All); LR P-value: 1.03E-12; mr1769 (Ind_All); LR P-value: 6.23E-12; mr1951 (All); LR P-value: 1.31E-09; mr1951 (Ind_All); LR P-value: 7.97E-08; mr1986 (Ind_All); LR P-value: 3.32E-06; mr1155_2 (Ind_All); LR P-value: 2.25E-07; mr1498_2 (All); LR P-value: 1.87E-09; mr1925_2 (All); LR P-value: 1.72E-06; mr1951_2 (All); LR P-value: 6.35E-09; mr1951_2 (Ind_All); LR P-value: 1.55E-08 |
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.696; most accessible tissue: Zhenshan97 flower, score: 85.314 |
| vg1223000181 (J) | chr12 | 23000181 | C | T | 71.80% | 0.00% | C -> T | NA |
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.449; most accessible tissue: Zhenshan97 flower, score: 86.041 |
| vg1223000183 (J) | chr12 | 23000183 | CTA | C | 60.90% | 0.00% | CTA -> C,CTATA,AT A | NA |
LOC_Os12g37480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37480.1 Alt: ATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: ATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: ATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37480.1 Alt: CTATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: CTATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: CTATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.108; most accessible tissue: Zhenshan97 flower, score: 86.194 |
| vg1223000209 (J) | chr12 | 23000209 | A | G | 83.70% | 0.00% | A -> G |
mr1038 (All); LR P-value: 1.06E-06;
mr1038 (Ind_All); LR P-value: 9.44E-07; mr1389 (All); LR P-value: 1.11E-06; mr1389 (Ind_All); LR P-value: 1.96E-06; mr1970 (Ind_All); LR P-value: 7.97E-06; mr1038_2 (All); LMM P-value: 1.59E-06; LR P-value: 1.58E-07; mr1038_2 (Ind_All); LMM P-value: 2.53E-06; LR P-value: 4.92E-07; mr1389_2 (All); LMM P-value: 8.71E-07; LR P-value: 4.05E-07; mr1389_2 (Ind_All); LMM P-value: 1.81E-06; LR P-value: 2.85E-07 |
LOC_Os12g37480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.853; most accessible tissue: Zhenshan97 flower, score: 88.247 |
| vg1223000245 (J) | chr12 | 23000245 | C | A | 65.40% | 9.25% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.280; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg1223000255 (J) | chr12 | 23000255 | C | T | 78.80% | 8.72% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.186; most accessible tissue: Minghui63 panicle, score: 90.624 |
| vg1223000286 (J) | chr12 | 23000286 | A | T | 55.60% | 16.04% | A -> T | NA |
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 79.252; most accessible tissue: Zhenshan97 flower, score: 90.197 |
| vg1223000337 (J) | chr12 | 23000337 | T | A | 70.80% | 18.26% | T -> A | NA |
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 79.694; most accessible tissue: Minghui63 panicle, score: 92.078 |
| vg1223000349 (J) | chr12 | 23000349 | G | A | 68.60% | 19.68% | G -> A | NA |
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.134; most accessible tissue: Minghui63 panicle, score: 92.078 |
| vg1223000364 (J) | chr12 | 23000364 | T | C | 73.70% | 21.71% | T -> C | NA |
LOC_Os12g37480.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.161; most accessible tissue: Minghui63 panicle, score: 92.231 |
| vg1223000624 (J) | chr12 | 23000624 | C | T | 52.50% | 9.06% | C -> T | NA |
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 80.689; most accessible tissue: Minghui63 panicle, score: 93.521 |
| vg1223000666 (J) | chr12 | 23000666 | C | G | 85.60% | 1.61% | C -> G | NA |
LOC_Os12g37480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37480.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 80.241; most accessible tissue: Minghui63 panicle, score: 93.837 |
| vg1223000853 (J) | chr12 | 23000853 | T | A | 99.80% | 0.00% | T -> A | NA |
LOC_Os12g37480.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g37470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g37490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.339; most accessible tissue: Zhenshan97 flower, score: 91.124 |