32 variations found. Os02g0195600/LOC_Os02g10200 (zinc finger A20 and AN1 domain-containing stress-associated protein; putative; expressed), ranging from 5,345,589 bp to 5,347,486 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g10200 | zinc finger A20 and AN1 domain-containing stress-associated protein, putative, expressed; RAP ID: Os02g0195600; MSU ID: LOC_Os02g10200 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0205345612 (J) | chr02 | 5345612 | A | C | 99.80% | 0.00% | A -> C | NA |
LOC_Os02g10200.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g10200.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g10210.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.551; most accessible tissue: Zhenshan97 root, score: 88.851 |
| vg0205345816 (J) | chr02 | 5345816 | C | T | 58.40% | 0.17% | C -> T |
mr1077 (All); LR P-value: 1.73E-20;
mr1077 (Ind_All); LR P-value: 6.80E-06; mr1080 (Ind_All); LR P-value: 4.85E-06; mr1592 (All); LR P-value: 7.98E-14; mr1598 (All); LR P-value: 1.90E-18; mr1609 (All); LR P-value: 3.38E-12; mr1610 (All); LR P-value: 8.83E-08; mr1619 (Ind_All); LR P-value: 6.09E-06; mr1860 (All); LR P-value: 1.75E-08; mr1036_2 (Ind_All); LR P-value: 6.62E-07; mr1072_2 (Ind_All); LR P-value: 1.21E-07; mr1075_2 (Ind_All); LR P-value: 7.55E-08; mr1077_2 (All); LR P-value: 2.63E-23; mr1077_2 (Ind_All); LR P-value: 9.27E-10; mr1080_2 (Ind_All); LR P-value: 5.61E-09; mr1149_2 (Ind_All); LR P-value: 4.06E-07; mr1321_2 (All); LR P-value: 8.08E-08; mr1598_2 (All); LR P-value: 5.03E-36; mr1619_2 (Ind_All); LR P-value: 2.79E-11; mr1795_2 (Ind_All); LR P-value: 6.06E-07; mr1829_2 (Ind_All); LR P-value: 4.09E-11; mr1842_2 (Ind_All); LR P-value: 1.62E-08; mr1861_2 (Ind_All); LR P-value: 5.71E-08; mr1902_2 (Ind_All); LR P-value: 2.34E-09; mr1933_2 (Ind_All); LR P-value: 1.43E-07; mr1962_2 (Ind_All); LR P-value: 1.28E-10 |
LOC_Os02g10200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 78.072; most accessible tissue: Minghui63 young leaf, score: 84.814 |
| vg0205345960 (J) | chr02 | 5345960 | A | AG | 76.20% | 0.34% | A -> AG | NA |
LOC_Os02g10200.1 Alt: AG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: AG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.973; most accessible tissue: Minghui63 young leaf, score: 89.337 |
| vg0205345992 (J) | chr02 | 5345992 | G | A | 60.50% | 0.00% | G -> A |
mr1077 (All); LR P-value: 3.42E-19;
mr1598 (All); LR P-value: 2.81E-19; mr1609 (All); LR P-value: 1.27E-12; mr1610 (All); LR P-value: 1.06E-07; mr1655 (All); LR P-value: 4.79E-13; mr1036_2 (Ind_All); LR P-value: 1.53E-06; mr1072_2 (Ind_All); LR P-value: 2.66E-07; mr1075_2 (Ind_All); LR P-value: 1.83E-07; mr1077_2 (Ind_All); LR P-value: 1.77E-09; mr1080_2 (Ind_All); LR P-value: 1.59E-08; mr1253_2 (All); LR P-value: 9.57E-21; mr1321_2 (All); LR P-value: 3.99E-07; mr1598_2 (All); LR P-value: 2.60E-36; mr1619_2 (Ind_All); LR P-value: 1.60E-10; mr1795_2 (Ind_All); LR P-value: 4.44E-07; mr1829_2 (Ind_All); LR P-value: 2.06E-10; mr1842_2 (Ind_All); LR P-value: 7.38E-08; mr1897_2 (Ind_All); LR P-value: 8.34E-06; mr1933_2 (Ind_All); LR P-value: 8.03E-07; mr1962_2 (Ind_All); LR P-value: 9.22E-10 |
LOC_Os02g10200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.904; most accessible tissue: Minghui63 young leaf, score: 89.871 |
| vg0205346005 (J) | chr02 | 5346005 | A | T | 60.40% | 0.00% | A -> T |
mr1077 (All); LR P-value: 3.42E-19;
mr1598 (All); LR P-value: 2.81E-19; mr1609 (All); LR P-value: 1.27E-12; mr1610 (All); LR P-value: 1.06E-07; mr1655 (All); LR P-value: 4.79E-13; mr1036_2 (Ind_All); LR P-value: 1.53E-06; mr1072_2 (Ind_All); LR P-value: 2.66E-07; mr1075_2 (Ind_All); LR P-value: 1.83E-07; mr1077_2 (Ind_All); LR P-value: 1.77E-09; mr1080_2 (Ind_All); LR P-value: 1.59E-08; mr1253_2 (All); LR P-value: 9.57E-21; mr1321_2 (All); LR P-value: 3.99E-07; mr1598_2 (All); LR P-value: 2.60E-36; mr1619_2 (Ind_All); LR P-value: 1.60E-10; mr1795_2 (Ind_All); LR P-value: 4.44E-07; mr1829_2 (Ind_All); LR P-value: 2.06E-10; mr1842_2 (Ind_All); LR P-value: 7.38E-08; mr1897_2 (Ind_All); LR P-value: 8.34E-06; mr1933_2 (Ind_All); LR P-value: 8.03E-07; mr1962_2 (Ind_All); LR P-value: 9.22E-10 |
LOC_Os02g10200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.714; most accessible tissue: Minghui63 young leaf, score: 90.072 |
| vg0205346100 (J) | chr02 | 5346100 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os02g10200.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g10200.2 Alt: G| synonymous_variant LOW(snpEff) LOC_Os02g10210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.000; most accessible tissue: Zhenshan97 young leaf, score: 91.151 |
| vg0205346136 (J) | chr02 | 5346136 | G | A | 76.20% | 0.30% | G -> A |
mr1004 (All); LR P-value: 5.42E-06;
mr1006 (All); LR P-value: 3.61E-06; mr1007 (All); LR P-value: 8.34E-07; mr1052 (All); LR P-value: 2.91E-06; mr1077 (Ind_All); LR P-value: 1.74E-06; mr1445 (All); LR P-value: 1.77E-06; mr1619 (Ind_All); LR P-value: 6.32E-06; mr1036_2 (All); LR P-value: 9.58E-06; mr1036_2 (Ind_All); LR P-value: 1.60E-08; mr1072_2 (Ind_All); LR P-value: 1.18E-08; mr1075_2 (Ind_All); LR P-value: 4.22E-09; mr1077_2 (Ind_All); LR P-value: 2.51E-11; mr1080_2 (Ind_All); LR P-value: 1.81E-08; mr1149_2 (Ind_All); LR P-value: 1.36E-08; mr1158_2 (All); LR P-value: 1.65E-06; mr1169_2 (All); LR P-value: 6.59E-06; mr1169_2 (Ind_All); LR P-value: 1.81E-06; mr1441_2 (Ind_All); LR P-value: 1.24E-08; mr1567_2 (All); LR P-value: 1.22E-07; mr1592_2 (Ind_All); LR P-value: 9.79E-07; mr1598_2 (Ind_All); LR P-value: 2.93E-09; mr1619_2 (Ind_All); LR P-value: 1.78E-11; mr1795_2 (Ind_All); LR P-value: 5.17E-07; mr1829_2 (Ind_All); LR P-value: 1.89E-13; mr1842_2 (Ind_All); LR P-value: 1.03E-09; mr1897_2 (All); LR P-value: 2.80E-10; mr1897_2 (Ind_All); LR P-value: 9.32E-06; mr1902_2 (Ind_All); LR P-value: 2.39E-11; mr1921_2 (All); LR P-value: 1.57E-07; mr1933_2 (Ind_All); LR P-value: 4.45E-07; mr1962_2 (Ind_All); LR P-value: 8.59E-10 |
LOC_Os02g10200.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g10200.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g10200.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g10200.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.251; most accessible tissue: Zhenshan97 young leaf, score: 91.830 |
| vg0205346277 (J) | chr02 | 5346277 | G | A | 76.20% | 0.11% | G -> A |
mr1004 (All); LR P-value: 7.70E-06;
mr1007 (All); LR P-value: 1.07E-06; mr1052 (All); LR P-value: 6.11E-06; mr1077 (Ind_All); LR P-value: 2.62E-06; mr1445 (All); LR P-value: 2.90E-06; mr1036_2 (All); LR P-value: 5.52E-06; mr1036_2 (Ind_All); LR P-value: 7.89E-08; mr1072_2 (Ind_All); LR P-value: 5.15E-08; mr1075_2 (Ind_All); LR P-value: 2.43E-08; mr1077_2 (Ind_All); LR P-value: 1.84E-10; mr1149_2 (Ind_All); LR P-value: 3.75E-08; mr1158_2 (All); LR P-value: 1.74E-06; mr1169_2 (All); LR P-value: 3.42E-06; mr1169_2 (Ind_All); LR P-value: 5.18E-06; mr1441_2 (Ind_All); LR P-value: 5.31E-08; mr1567_2 (All); LR P-value: 3.76E-08; mr1592_2 (Ind_All); LR P-value: 3.28E-06; mr1598_2 (Ind_All); LR P-value: 3.93E-09; mr1619_2 (Ind_All); LR P-value: 1.41E-10; mr1715_2 (All); LR P-value: 2.07E-16; mr1735_2 (All); LR P-value: 4.11E-06; mr1795_2 (Ind_All); LR P-value: 3.38E-06; mr1829_2 (Ind_All); LR P-value: 1.29E-13; mr1842_2 (Ind_All); LR P-value: 1.45E-09; mr1902_2 (Ind_All); LR P-value: 1.39E-11; mr1921_2 (All); LR P-value: 1.25E-07; mr1933_2 (Ind_All); LR P-value: 6.99E-07; mr1962_2 (Ind_All); LR P-value: 2.21E-09 |
LOC_Os02g10200.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g10200.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g10200.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g10200.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.961; most accessible tissue: Zhenshan97 young leaf, score: 93.722 |
| vg0205346325 (J) | chr02 | 5346325 | T | C | 65.30% | 0.00% | C -> T | NA |
LOC_Os02g10200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g10200.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.478; most accessible tissue: Zhenshan97 young leaf, score: 93.764 |
| vg0205346496 (J) | chr02 | 5346496 | A | G | 65.40% | 0.00% | G -> A | NA |
LOC_Os02g10200.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g10200.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.063; most accessible tissue: Zhenshan97 young leaf, score: 89.772 |
| vg0205346587 (J) | chr02 | 5346587 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g10200.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os02g10200.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001 |
| vg0205346933 (J) | chr02 | 5346933 | A | AC | 99.80% | 0.00% | A -> AC | NA |
LOC_Os02g10210.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g10220.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g10200.1 Alt: AC| intron_variant MODIFIER(snpEff) LOC_Os02g10200.2 Alt: AC| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.326; most accessible tissue: Zhenshan97 flower, score: 93.030 |
| vg0205346969 (J) | chr02 | 5346969 | C | A | 76.20% | 0.00% | C -> A |
mr1004 (All); LR P-value: 4.68E-06;
mr1006 (All); LR P-value: 3.83E-06; mr1007 (All); LR P-value: 4.85E-07; mr1052 (All); LR P-value: 3.14E-06; mr1077 (Ind_All); LR P-value: 2.77E-06; mr1445 (All); LR P-value: 5.64E-07; mr1633 (All); LR P-value: 4.28E-06; mr1036_2 (All); LR P-value: 9.48E-07; mr1036_2 (Ind_All); LR P-value: 4.49E-09; mr1072_2 (Ind_All); LR P-value: 1.36E-08; mr1075_2 (Ind_All); LR P-value: 3.63E-09; mr1077_2 (Ind_All); LR P-value: 5.01E-11; mr1149_2 (Ind_All); LR P-value: 1.40E-08; mr1158_2 (All); LR P-value: 4.08E-07; mr1169_2 (All); LR P-value: 6.20E-07; mr1169_2 (Ind_All); LR P-value: 5.28E-07; mr1402_2 (Ind_All); LR P-value: 4.11E-06; mr1441_2 (Ind_All); LR P-value: 8.88E-09; mr1567_2 (All); LR P-value: 1.99E-08; mr1592_2 (Ind_All); LR P-value: 4.62E-07; mr1598_2 (Ind_All); LR P-value: 2.61E-09; mr1619_2 (Ind_All); LR P-value: 5.77E-11; mr1715_2 (All); LR P-value: 5.93E-17; mr1735_2 (All); LR P-value: 3.11E-06; mr1795_2 (Ind_All); LR P-value: 2.84E-07; mr1806_2 (All); LR P-value: 4.61E-10; mr1829_2 (Ind_All); LR P-value: 1.98E-13; mr1842_2 (Ind_All); LR P-value: 5.53E-10; mr1902_2 (Ind_All); LR P-value: 3.54E-11; mr1921_2 (All); LR P-value: 2.73E-08; mr1933_2 (Ind_All); LR P-value: 2.06E-06; mr1962_2 (Ind_All); LR P-value: 5.50E-09 |
LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.109; most accessible tissue: Zhenshan97 flower, score: 93.298 |
| vg0205347059 (J) | chr02 | 5347059 | GAA | GAAA | 37.80% | 0.00% | GAA -> GAAA,GA,G | NA |
LOC_Os02g10210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10220.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.029; most accessible tissue: Zhenshan97 flower, score: 94.175 |
| vg0205347265 (J) | chr02 | 5347265 | A | G | 65.30% | 0.00% | G -> A | NA |
LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.107; most accessible tissue: Zhenshan97 flower, score: 98.198 |
| vg0205347298 (J) | chr02 | 5347298 | AG | AGG | 28.40% | 6.05% | AG -> AGG,AGGGG, A,AGGG,AGG GGG | NA |
LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: AGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: AGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: AGGGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: AGGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: AGGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: AGGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: AGGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: AGGGGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: AGGGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: AGGGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: AGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: AGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: AGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: AGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: AGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: AGGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: AGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: AGGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.971; most accessible tissue: Zhenshan97 flower, score: 98.855 |
| vg0205347308 (J) | chr02 | 5347308 | T | G | 92.90% | 0.68% | T -> G | NA |
LOC_Os02g10210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10220.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 98.246; most accessible tissue: Zhenshan97 flower, score: 99.113 |
| vg0205347344 (J) | chr02 | 5347344 | AC | A | 60.60% | 0.00% | AC -> A | NA |
LOC_Os02g10200.1 Alt: A| splice_donor_variant&intron_variant HIGH(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.115; most accessible tissue: Zhenshan97 flower, score: 99.257 |
| vg0205347354 (J) | chr02 | 5347354 | CGGCGGC GGCGGAG GCCGA | C | 99.90% | 0.00% | CGGCGGCGGC GGAGGCCGA -> C | NA |
LOC_Os02g10200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g10200.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g10210.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10220.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.143; most accessible tissue: Zhenshan97 flower, score: 99.278 |
| vg0205347357 (J) | chr02 | 5347357 | CGGCGGC GGAGGCC GA | CGGCGGC GGAGGCC GAGGCGG CGGAGGC CGA | 99.90% | 0.00% | CGGCGGCGGA GGCCGA -> CGGCGGCGGA GGCCGAGGCG GCGGAGGCCG A,C | NA |
LOC_Os02g10200.1 Alt: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g10200.2 Alt: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g10210.1 Alt: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10220.1 Alt: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g10200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g10200.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g10210.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10220.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.228; most accessible tissue: Zhenshan97 flower, score: 99.344 |
| vg0205347438 (J) | chr02 | 5347438 | CCTCTCT | CCTCTCT CT | 49.30% | 16.29% | CCTCTCT -> CCTCT,CGTC TCTCT,CCT, CCTCTCTCT, C,CCTCTCTC TCTCTCT | NA |
LOC_Os02g10200.1 Alt: CCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: CCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: CGTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: CGTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: CGTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: CGTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: CGTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: CCTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: CCTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: CCTCTCTCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: CCTCTCTCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: CCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: CCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: CCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: CCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: CCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.427; most accessible tissue: Minghui63 root, score: 99.702 |
| vg0205347439 (J) | chr02 | 5347439 | G | C | 65.30% | 0.02% | C -> G | NA |
LOC_Os02g10200.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.462; most accessible tissue: Minghui63 root, score: 99.731 |
| vg0205347448 (J) | chr02 | 5347448 | TCTCTCT CTCTCTC TCA | ACTCTCT CTCTCTC TCA | 66.50% | 21.63% | TCTCTCTCTC TCTCTCA -> ACTCTCTCTC TCTCTCA,T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.1 Alt: ACTCTCTCTCTCTCTCA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10200.2 Alt: ACTCTCTCTCTCTCTCA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: ACTCTCTCTCTCTCTCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: ACTCTCTCTCTCTCTCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: ACTCTCTCTCTCTCTCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.516; most accessible tissue: Minghui63 root, score: 99.774 |
| vg0205347450 (J) | chr02 | 5347450 | TCTCTCT CTCTCTC A | T | 86.00% | 3.87% | TCTCTCTCTC TCTCA -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.516; most accessible tissue: Minghui63 root, score: 99.775 |
| vg0205347452 (J) | chr02 | 5347452 | TCTCTCT CTCTCA | T | 75.80% | 11.32% | TCTCTCTCTC TCA -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.521; most accessible tissue: Minghui63 root, score: 99.779 |
| vg0205347454 (J) | chr02 | 5347454 | TCTCTCT CTCA | T | 60.70% | 1.29% | TCTCTCTCTC A -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.529; most accessible tissue: Minghui63 root, score: 99.783 |
| vg0205347456 (J) | chr02 | 5347456 | TCTCTCT CA | T | 90.00% | 2.41% | TCTCTCTCA -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.529; most accessible tissue: Minghui63 root, score: 99.783 |
| vg0205347458 (J) | chr02 | 5347458 | TCTCTCA | T | 76.90% | 0.25% | TCTCTCA -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.530; most accessible tissue: Minghui63 root, score: 99.783 |
| vg0205347460 (J) | chr02 | 5347460 | TCTCA | T | 44.40% | 38.30% | TCTCA -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.531; most accessible tissue: Minghui63 root, score: 99.784 |
| vg0205347464 (J) | chr02 | 5347464 | A | T | 94.10% | 1.29% | A -> T | NA |
LOC_Os02g10200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.546; most accessible tissue: Minghui63 root, score: 99.794 |
| vg0205347483 (J) | chr02 | 5347483 | AG | A | 87.10% | 6.98% | AG -> A | NA |
LOC_Os02g10200.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10200.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.572; most accessible tissue: Minghui63 root, score: 99.825 |
| STR0205347337 (J) | chr02 | 5347337 | AACCCTA ACCCT | AACCCTA ACCC | 51.00% | 0.00% | AACCCTAACC CT -> AACCCTAACC C | NA |
|