53 variations found. Os02g0592600/LOC_Os02g37950 (transposon protein; putative; unclassified; expressed), ranging from 22,934,103 bp to 22,940,327 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g37950 | transposon protein, putative, unclassified, expressed; RAP ID: Os02g0592600; MSU ID: LOC_Os02g37950 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0222934217 (J) | chr02 | 22934217 | G | GCCACCG | 94.80% | 0.00% | G -> GCCACCG | NA |
|
| STR0222939332 (J) | chr02 | 22939332 | G | A | 99.00% | 0.00% | G -> A | NA |
|
| vg0222934117 (J) | chr02 | 22934117 | CTT | CT | 91.00% | 0.74% | CTT -> CT,CTTT,C | NA |
LOC_Os02g37950.1 Alt: CTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: CTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: CTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g37950.1 Alt: CT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: CT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.631; most accessible tissue: Zhenshan97 flower, score: 99.501 |
| vg0222934159 (J) | chr02 | 22934159 | ACGCCGG CGCCGCC GCTCTCG TGAGCCA CCGCCAC | A | 90.30% | 0.00% | ACGCCGGCGC CGCCGCTCTC GTGAGCCACC GCCAC -> A | NA |
LOC_Os02g37950.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.802; most accessible tissue: Zhenshan97 flower, score: 99.604 |
| vg0222934188 (J) | chr02 | 22934188 | CGCCACC GCCGGCG CCGCCGC TCTCGTG A | C | 99.50% | 0.00% | CGCCACCGCC GGCGCCGCCG CTCTCGTGA -> C | NA |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.965; most accessible tissue: Zhenshan97 flower, score: 99.625 |
| vg0222934216 (J) | chr02 | 22934216 | A | AGCCACC | 95.90% | 0.00% | A -> AGCCACC | NA |
LOC_Os02g37950.1 Alt: AGCCACC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: AGCCACC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: AGCCACC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: AGCCACC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: AGCCACC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: AGCCACC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 |
| vg0222934232 (J) | chr02 | 22934232 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g37950.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37950.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.738; most accessible tissue: Zhenshan97 flower, score: 99.464 |
| vg0222934233 (J) | chr02 | 22934233 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.730; most accessible tissue: Zhenshan97 flower, score: 99.457 |
| vg0222934249 (J) | chr02 | 22934249 | T | C | 94.80% | 0.00% | T -> C |
mr1095 (All); LMM P-value: 4.67E-09; LR P-value: 1.51E-26;
mr1098 (All); LMM P-value: 7.07E-13; LR P-value: 5.78E-41; mr1099 (All); LMM P-value: 9.77E-08; LR P-value: 1.40E-31; mr1101 (All); LMM P-value: 5.16E-12; LR P-value: 1.29E-38; mr1113 (All); LMM P-value: 6.35E-15; LR P-value: 2.21E-33; mr1114 (All); LMM P-value: 1.13E-19; LR P-value: 2.91E-42; mr1116 (All); LMM P-value: 8.30E-18; LR P-value: 1.72E-35; mr1117 (All); LMM P-value: 2.71E-20; LR P-value: 3.53E-46; mr1118 (All); LMM P-value: 1.36E-15; LR P-value: 3.94E-25; mr1119 (All); LMM P-value: 1.28E-15; LR P-value: 1.17E-37; mr1120 (All); LMM P-value: 3.17E-12; LR P-value: 6.94E-33; mr1123 (All); LMM P-value: 4.73E-23; LR P-value: 7.45E-56; mr1150 (All); LMM P-value: 5.87E-10; LR P-value: 1.20E-23; mr1180 (All); LR P-value: 1.95E-10; mr1240 (All); LMM P-value: 1.11E-15; LR P-value: 8.53E-33; mr1242 (All); LMM P-value: 1.22E-20; LR P-value: 8.93E-44; mr1247 (All); LMM P-value: 7.07E-16; LR P-value: 9.48E-41; mr1495 (All); LMM P-value: 1.46E-17; LR P-value: 5.92E-30; mr1496 (All); LMM P-value: 2.98E-23; LR P-value: 1.42E-43; mr1589 (All); LMM P-value: 5.90E-06; LR P-value: 8.09E-25; mr1612 (All); LR P-value: 5.72E-13; mr1858 (All); LMM P-value: 8.67E-10; LR P-value: 1.42E-32; mr1859 (All); LMM P-value: 8.31E-10; LR P-value: 1.28E-32; mr1868 (All); LMM P-value: 9.51E-07; LR P-value: 4.93E-29; mr1917 (All); LMM P-value: 1.19E-15; LR P-value: 1.58E-35; mr1936 (All); LMM P-value: 7.72E-16; LR P-value: 1.98E-33; mr1961 (All); LMM P-value: 4.80E-09; LR P-value: 1.09E-25; mr1098_2 (All); LMM P-value: 1.76E-08; LR P-value: 7.83E-39; mr1099_2 (All); LMM P-value: 5.64E-08; LR P-value: 7.24E-32; mr1113_2 (All); LMM P-value: 7.35E-19; LR P-value: 8.37E-43; mr1114_2 (All); LMM P-value: 5.59E-19; LR P-value: 9.95E-45; mr1117_2 (All); LMM P-value: 2.68E-20; LR P-value: 1.49E-47; mr1118_2 (All); LMM P-value: 5.50E-19; LR P-value: 1.55E-28; mr1119_2 (All); LMM P-value: 5.41E-18; LR P-value: 2.40E-43; mr1120_2 (All); LMM P-value: 1.17E-15; LR P-value: 9.93E-45; mr1123_2 (All); LMM P-value: 3.13E-21; LR P-value: 2.39E-56; mr1150_2 (All); LMM P-value: 6.17E-06; mr1240_2 (All); LMM P-value: 7.61E-18; LR P-value: 3.54E-40; mr1242_2 (All); LMM P-value: 1.21E-23; LR P-value: 7.24E-49; mr1247_2 (All); LMM P-value: 2.08E-16; LR P-value: 9.67E-48; mr1495_2 (All); LMM P-value: 1.85E-14; LR P-value: 6.39E-25; mr1496_2 (All); LMM P-value: 1.74E-24; LR P-value: 3.53E-43; mr1911_2 (All); LR P-value: 3.20E-15; mr1936_2 (All); LMM P-value: 6.56E-13; LR P-value: 1.54E-31; mr1961_2 (All); LMM P-value: 4.57E-10; LR P-value: 5.50E-24 |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.687; most accessible tissue: Zhenshan97 flower, score: 99.399 |
| vg0222934404 (J) | chr02 | 22934404 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os02g37950.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g37950.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.124; most accessible tissue: Zhenshan97 flag leaf, score: 97.179 |
| vg0222934405 (J) | chr02 | 22934405 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os02g37950.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.128; most accessible tissue: Zhenshan97 flag leaf, score: 97.186 |
| vg0222934463 (J) | chr02 | 22934463 | TCTCCTC | TCTC | 94.80% | 0.00% | TCTCCTC -> TCTC,TCTCC TCCTC,T | NA |
LOC_Os02g37950.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.1 Alt: TCTCCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: TCTCCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: TCTCCTCCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: TCTCCTCCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: TCTCCTCCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: TCTCCTCCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.1 Alt: TCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: TCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: TCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: TCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: TCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: TCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.761; most accessible tissue: Zhenshan97 flag leaf, score: 96.963 |
| vg0222934895 (J) | chr02 | 22934895 | A | C | 99.40% | 0.00% | A -> C | NA |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.717; most accessible tissue: Minghui63 panicle, score: 91.586 |
| vg0222934933 (J) | chr02 | 22934933 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os02g37950.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.023; most accessible tissue: Callus, score: 90.216 |
| vg0222934952 (J) | chr02 | 22934952 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.966; most accessible tissue: Callus, score: 90.216 |
| vg0222935026 (J) | chr02 | 22935026 | T | C | 94.80% | 0.00% | T -> C |
mr1095 (All); LMM P-value: 4.67E-09; LR P-value: 1.51E-26;
mr1098 (All); LMM P-value: 7.07E-13; LR P-value: 5.78E-41; mr1099 (All); LMM P-value: 9.77E-08; LR P-value: 1.40E-31; mr1101 (All); LMM P-value: 5.16E-12; LR P-value: 1.29E-38; mr1113 (All); LMM P-value: 6.35E-15; LR P-value: 2.21E-33; mr1114 (All); LMM P-value: 1.13E-19; LR P-value: 2.91E-42; mr1116 (All); LMM P-value: 8.30E-18; LR P-value: 1.72E-35; mr1117 (All); LMM P-value: 2.71E-20; LR P-value: 3.53E-46; mr1118 (All); LMM P-value: 1.36E-15; LR P-value: 3.94E-25; mr1119 (All); LMM P-value: 1.28E-15; LR P-value: 1.17E-37; mr1120 (All); LMM P-value: 3.17E-12; LR P-value: 6.94E-33; mr1123 (All); LMM P-value: 4.73E-23; LR P-value: 7.45E-56; mr1150 (All); LMM P-value: 5.87E-10; LR P-value: 1.20E-23; mr1180 (All); LR P-value: 1.95E-10; mr1240 (All); LMM P-value: 1.11E-15; LR P-value: 8.53E-33; mr1242 (All); LMM P-value: 1.22E-20; LR P-value: 8.93E-44; mr1247 (All); LMM P-value: 7.07E-16; LR P-value: 9.48E-41; mr1495 (All); LMM P-value: 1.46E-17; LR P-value: 5.92E-30; mr1496 (All); LMM P-value: 2.98E-23; LR P-value: 1.42E-43; mr1589 (All); LMM P-value: 5.90E-06; LR P-value: 8.09E-25; mr1612 (All); LR P-value: 5.72E-13; mr1858 (All); LMM P-value: 8.67E-10; LR P-value: 1.42E-32; mr1859 (All); LMM P-value: 8.31E-10; LR P-value: 1.28E-32; mr1868 (All); LMM P-value: 9.51E-07; LR P-value: 4.93E-29; mr1917 (All); LMM P-value: 1.19E-15; LR P-value: 1.58E-35; mr1936 (All); LMM P-value: 7.72E-16; LR P-value: 1.98E-33; mr1961 (All); LMM P-value: 4.80E-09; LR P-value: 1.09E-25; mr1098_2 (All); LMM P-value: 1.76E-08; LR P-value: 7.83E-39; mr1099_2 (All); LMM P-value: 5.64E-08; LR P-value: 7.24E-32; mr1113_2 (All); LMM P-value: 7.35E-19; LR P-value: 8.37E-43; mr1114_2 (All); LMM P-value: 5.59E-19; LR P-value: 9.95E-45; mr1117_2 (All); LMM P-value: 2.68E-20; LR P-value: 1.49E-47; mr1118_2 (All); LMM P-value: 5.50E-19; LR P-value: 1.55E-28; mr1119_2 (All); LMM P-value: 5.41E-18; LR P-value: 2.40E-43; mr1120_2 (All); LMM P-value: 1.17E-15; LR P-value: 9.93E-45; mr1123_2 (All); LMM P-value: 3.13E-21; LR P-value: 2.39E-56; mr1150_2 (All); LMM P-value: 6.17E-06; mr1240_2 (All); LMM P-value: 7.61E-18; LR P-value: 3.54E-40; mr1242_2 (All); LMM P-value: 1.21E-23; LR P-value: 7.24E-49; mr1247_2 (All); LMM P-value: 2.08E-16; LR P-value: 9.67E-48; mr1495_2 (All); LMM P-value: 1.85E-14; LR P-value: 6.39E-25; mr1496_2 (All); LMM P-value: 1.74E-24; LR P-value: 3.53E-43; mr1911_2 (All); LR P-value: 3.20E-15; mr1936_2 (All); LMM P-value: 6.56E-13; LR P-value: 1.54E-31; mr1961_2 (All); LMM P-value: 4.57E-10; LR P-value: 5.50E-24 |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.687; most accessible tissue: Callus, score: 90.216 |
| vg0222935033 (J) | chr02 | 22935033 | A | G | 94.90% | 0.00% | A -> G |
mr1095 (All); LMM P-value: 4.67E-09; LR P-value: 1.51E-26;
mr1098 (All); LMM P-value: 7.07E-13; LR P-value: 5.78E-41; mr1099 (All); LMM P-value: 9.77E-08; LR P-value: 1.40E-31; mr1101 (All); LMM P-value: 5.16E-12; LR P-value: 1.29E-38; mr1113 (All); LMM P-value: 6.35E-15; LR P-value: 2.21E-33; mr1114 (All); LMM P-value: 1.13E-19; LR P-value: 2.91E-42; mr1116 (All); LMM P-value: 8.30E-18; LR P-value: 1.72E-35; mr1117 (All); LMM P-value: 2.71E-20; LR P-value: 3.53E-46; mr1118 (All); LMM P-value: 1.36E-15; LR P-value: 3.94E-25; mr1119 (All); LMM P-value: 1.28E-15; LR P-value: 1.17E-37; mr1120 (All); LMM P-value: 3.17E-12; LR P-value: 6.94E-33; mr1123 (All); LMM P-value: 4.73E-23; LR P-value: 7.45E-56; mr1150 (All); LMM P-value: 5.87E-10; LR P-value: 1.20E-23; mr1180 (All); LR P-value: 1.95E-10; mr1240 (All); LMM P-value: 1.11E-15; LR P-value: 8.53E-33; mr1242 (All); LMM P-value: 1.22E-20; LR P-value: 8.93E-44; mr1247 (All); LMM P-value: 7.07E-16; LR P-value: 9.48E-41; mr1495 (All); LMM P-value: 1.46E-17; LR P-value: 5.92E-30; mr1496 (All); LMM P-value: 2.98E-23; LR P-value: 1.42E-43; mr1589 (All); LMM P-value: 5.90E-06; LR P-value: 8.09E-25; mr1612 (All); LR P-value: 5.72E-13; mr1858 (All); LMM P-value: 8.67E-10; LR P-value: 1.42E-32; mr1859 (All); LMM P-value: 8.31E-10; LR P-value: 1.28E-32; mr1868 (All); LMM P-value: 9.51E-07; LR P-value: 4.93E-29; mr1917 (All); LMM P-value: 1.19E-15; LR P-value: 1.58E-35; mr1936 (All); LMM P-value: 7.72E-16; LR P-value: 1.98E-33; mr1961 (All); LMM P-value: 4.80E-09; LR P-value: 1.09E-25; mr1098_2 (All); LMM P-value: 1.76E-08; LR P-value: 7.83E-39; mr1099_2 (All); LMM P-value: 5.64E-08; LR P-value: 7.24E-32; mr1113_2 (All); LMM P-value: 7.35E-19; LR P-value: 8.37E-43; mr1114_2 (All); LMM P-value: 5.59E-19; LR P-value: 9.95E-45; mr1117_2 (All); LMM P-value: 2.68E-20; LR P-value: 1.49E-47; mr1118_2 (All); LMM P-value: 5.50E-19; LR P-value: 1.55E-28; mr1119_2 (All); LMM P-value: 5.41E-18; LR P-value: 2.40E-43; mr1120_2 (All); LMM P-value: 1.17E-15; LR P-value: 9.93E-45; mr1123_2 (All); LMM P-value: 3.13E-21; LR P-value: 2.39E-56; mr1150_2 (All); LMM P-value: 6.17E-06; mr1240_2 (All); LMM P-value: 7.61E-18; LR P-value: 3.54E-40; mr1242_2 (All); LMM P-value: 1.21E-23; LR P-value: 7.24E-49; mr1247_2 (All); LMM P-value: 2.08E-16; LR P-value: 9.67E-48; mr1495_2 (All); LMM P-value: 1.85E-14; LR P-value: 6.39E-25; mr1496_2 (All); LMM P-value: 1.74E-24; LR P-value: 3.53E-43; mr1911_2 (All); LR P-value: 3.20E-15; mr1936_2 (All); LMM P-value: 6.56E-13; LR P-value: 1.54E-31; mr1961_2 (All); LMM P-value: 4.57E-10; LR P-value: 5.50E-24 |
LOC_Os02g37950.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.741; most accessible tissue: Callus, score: 90.216 |
| vg0222935049 (J) | chr02 | 22935049 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os02g37950.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37950.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.573; most accessible tissue: Callus, score: 90.216 |
| vg0222935242 (J) | chr02 | 22935242 | T | C | 94.90% | 0.00% | T -> C |
mr1095 (All); LMM P-value: 1.42E-06; LR P-value: 6.67E-23;
mr1098 (All); LMM P-value: 2.14E-10; LR P-value: 5.98E-37; mr1099 (All); LMM P-value: 2.79E-06; LR P-value: 1.80E-29; mr1101 (All); LMM P-value: 2.74E-09; LR P-value: 4.87E-35; mr1113 (All); LMM P-value: 1.30E-12; LR P-value: 2.45E-30; mr1114 (All); LMM P-value: 4.93E-17; LR P-value: 2.36E-39; mr1116 (All); LMM P-value: 4.02E-15; LR P-value: 2.70E-32; mr1117 (All); LMM P-value: 8.85E-18; LR P-value: 1.01E-42; mr1118 (All); LMM P-value: 6.40E-13; LR P-value: 8.31E-22; mr1119 (All); LMM P-value: 6.33E-12; LR P-value: 5.02E-32; mr1120 (All); LMM P-value: 3.94E-10; LR P-value: 7.95E-30; mr1123 (All); LMM P-value: 8.17E-18; LR P-value: 9.01E-49; mr1150 (All); LMM P-value: 3.05E-09; LR P-value: 2.23E-25; mr1240 (All); LMM P-value: 3.16E-13; LR P-value: 4.56E-29; mr1242 (All); LMM P-value: 6.48E-16; LR P-value: 9.88E-37; mr1247 (All); LMM P-value: 1.97E-14; LR P-value: 5.93E-39; mr1495 (All); LMM P-value: 1.85E-13; LR P-value: 1.36E-25; mr1496 (All); LMM P-value: 2.25E-18; LR P-value: 3.77E-37; mr1589 (All); LR P-value: 2.65E-22; mr1612 (All); LR P-value: 8.45E-12; mr1858 (All); LMM P-value: 9.08E-08; LR P-value: 3.32E-29; mr1859 (All); LMM P-value: 8.79E-08; LR P-value: 3.04E-29; mr1868 (All); LR P-value: 4.56E-25; mr1917 (All); LMM P-value: 2.30E-13; LR P-value: 2.84E-32; mr1936 (All); LMM P-value: 7.79E-13; LR P-value: 2.95E-29; mr1961 (All); LMM P-value: 4.50E-08; LR P-value: 6.36E-25; mr1098_2 (All); LMM P-value: 3.72E-06; LR P-value: 3.88E-33; mr1099_2 (All); LMM P-value: 2.31E-06; LR P-value: 1.26E-28; mr1113_2 (All); LMM P-value: 8.82E-16; LR P-value: 2.19E-39; mr1114_2 (All); LMM P-value: 6.15E-16; LR P-value: 5.75E-41; mr1117_2 (All); LMM P-value: 6.19E-17; LR P-value: 5.63E-43; mr1118_2 (All); LMM P-value: 1.03E-14; LR P-value: 1.04E-23; mr1119_2 (All); LMM P-value: 3.29E-15; LR P-value: 7.60E-40; mr1120_2 (All); LMM P-value: 5.97E-13; LR P-value: 8.90E-41; mr1123_2 (All); LMM P-value: 1.47E-16; LR P-value: 1.67E-48; mr1150_2 (All); LMM P-value: 9.12E-06; mr1240_2 (All); LMM P-value: 8.93E-15; LR P-value: 2.17E-35; mr1242_2 (All); LMM P-value: 7.36E-18; LR P-value: 1.27E-41; mr1247_2 (All); LMM P-value: 4.91E-14; LR P-value: 1.24E-44; mr1495_2 (All); LMM P-value: 1.34E-10; mr1496_2 (All); LMM P-value: 4.01E-19; LR P-value: 1.28E-36; mr1936_2 (All); LMM P-value: 6.55E-10; LR P-value: 1.20E-26; mr1961_2 (All); LMM P-value: 6.21E-08; LR P-value: 7.07E-22 |
LOC_Os02g37950.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.129; most accessible tissue: Minghui63 flag leaf, score: 84.227 |
| vg0222935269 (J) | chr02 | 22935269 | AT | A | 94.80% | 0.00% | AT -> A | NA |
LOC_Os02g37950.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.523; most accessible tissue: Minghui63 flag leaf, score: 82.053 |
| vg0222935310 (J) | chr02 | 22935310 | T | A | 96.50% | 0.00% | T -> A | NA |
LOC_Os02g37950.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g37950.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g37950.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289 |
| vg0222935471 (J) | chr02 | 22935471 | G | GT | 99.80% | 0.00% | G -> GT | NA |
LOC_Os02g37950.1 Alt: GT| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g37950.3 Alt: GT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g37940.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: GT| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37930.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g37950.2 Alt: GT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.694; most accessible tissue: Minghui63 flag leaf, score: 81.052 |
| vg0222935587 (J) | chr02 | 22935587 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os02g37950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g37950.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os02g37950.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 70.672; most accessible tissue: Zhenshan97 young leaf, score: 81.841 |
| vg0222935791 (J) | chr02 | 22935791 | C | T | 96.20% | 0.00% | C -> T | NA |
LOC_Os02g37950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g37950.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g37950.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 66.985; most accessible tissue: Minghui63 young leaf, score: 78.443 |
| vg0222935812 (J) | chr02 | 22935812 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g37950.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g37950.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os02g37950.3 Alt: A| missense_variant MODERATE(snpEff) LOC_Os02g37940.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g37940.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.410; most accessible tissue: Minghui63 young leaf, score: 79.191 |
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