26 variations found. LOC_Os07g42400 (transposon protein; putative; unclassified; expressed), ranging from 25,371,993 bp to 25,376,165 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725372026 (J) | chr07 | 25372026 | A | T | 91.90% | 0.00% | A -> T |
mr1055 (Jap_All); LR P-value: 8.12E-11;
mr1132 (Jap_All); LR P-value: 2.05E-10; mr1248 (All); LR P-value: 1.40E-06; mr1301 (All); LR P-value: 2.87E-18; mr1563 (Jap_All); LR P-value: 3.85E-09; mr1825 (Jap_All); LR P-value: 7.09E-08; mr1993 (All); LR P-value: 1.37E-06; mr1178_2 (Jap_All); LR P-value: 1.38E-13; mr1498_2 (Jap_All); LR P-value: 5.96E-06; mr1769_2 (All); LR P-value: 1.14E-11; mr1769_2 (Jap_All); LR P-value: 9.95E-14; mr1993_2 (All); LR P-value: 2.95E-11 |
LOC_Os07g42400.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.450; most accessible tissue: Callus, score: 99.825 |
| vg0725372203 (J) | chr07 | 25372203 | GT | G | 77.80% | 0.00% | GT -> G,GTT,TT,G TTT | NA |
LOC_Os07g42400.1 Alt: GTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: GTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: GTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: GTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: TT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: TT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: TT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: TT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.656; most accessible tissue: Zhenshan97 panicle, score: 99.042 |
| vg0725372255 (J) | chr07 | 25372255 | GT | G | 78.50% | 3.75% | GT -> G | NA |
LOC_Os07g42400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42400.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g42400.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os07g42400.2 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 97.999; most accessible tissue: Zhenshan97 flower, score: 98.591 |
| vg0725372256 (J) | chr07 | 25372256 | TGG | T | 68.00% | 0.00% | T -> TGG | NA |
LOC_Os07g42400.1 Alt: TGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os07g42400.2 Alt: TGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 97.998; most accessible tissue: Zhenshan97 flower, score: 98.588 |
| vg0725372439 (J) | chr07 | 25372439 | G | C | 69.90% | 0.00% | C -> G |
mr1386 (All); LR P-value: 4.45E-12;
mr1563 (Jap_All); LR P-value: 3.20E-09; mr1825 (Jap_All); LR P-value: 9.24E-08; mr1170_2 (Jap_All); LR P-value: 8.76E-06; mr1178_2 (Jap_All); LR P-value: 3.27E-13; mr1498_2 (Jap_All); LR P-value: 3.17E-06; mr1563_2 (Jap_All); LR P-value: 5.10E-08; mr1769_2 (Jap_All); LR P-value: 1.86E-13 |
LOC_Os07g42395.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42395.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.820; most accessible tissue: Zhenshan97 flower, score: 97.917 |
| vg0725372759 (J) | chr07 | 25372759 | G | A | 97.00% | 0.00% | G -> A,T | NA |
LOC_Os07g42400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g42400.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g42400.1 Alt: T| synonymous_variant LOW(snpEff) LOC_Os07g42400.2 Alt: T| synonymous_variant LOW(snpEff) LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.644; most accessible tissue: Zhenshan97 flower, score: 88.675 |
| vg0725372947 (J) | chr07 | 25372947 | C | T | 80.90% | 0.00% | C -> T |
mr1094 (Ind_All); LR P-value: 2.44E-06;
mr1215_2 (Ind_All); LR P-value: 7.82E-07; mr1218_2 (Ind_All); LR P-value: 5.52E-09; mr1232_2 (Ind_All); LR P-value: 1.65E-06; mr1380_2 (All); LR P-value: 2.03E-06; mr1380_2 (Ind_All); LR P-value: 4.77E-06; mr1422_2 (Ind_All); LR P-value: 1.91E-06; mr1561_2 (All); LR P-value: 2.13E-06; mr1954_2 (Ind_All); LR P-value: 3.92E-06 |
LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.669; most accessible tissue: Callus, score: 81.460 |
| vg0725372962 (J) | chr07 | 25372962 | C | T | 61.80% | 0.00% | T -> C |
mr1070 (All); LR P-value: 1.58E-11;
mr1386 (All); LR P-value: 1.51E-13; mr1414 (All); LR P-value: 5.21E-28; mr1514 (All); LR P-value: 1.45E-08; mr1542 (All); LR P-value: 2.00E-35; mr1632 (All); LR P-value: 2.54E-26; mr1683 (All); LR P-value: 1.08E-10; mr1751 (All); LR P-value: 1.64E-11; mr1039_2 (All); LR P-value: 3.17E-27; mr1632_2 (All); LR P-value: 2.72E-33 |
LOC_Os07g42395.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42395.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.896; most accessible tissue: Callus, score: 81.460 |
| vg0725373324 (J) | chr07 | 25373324 | G | C | 61.80% | 0.00% | C -> G |
mr1039 (All); LR P-value: 2.45E-25;
mr1070 (All); LR P-value: 1.03E-11; mr1128 (All); LR P-value: 4.17E-10; mr1386 (All); LR P-value: 1.12E-13; mr1414 (All); LR P-value: 2.10E-28; mr1514 (All); LR P-value: 1.00E-08; mr1542 (All); LR P-value: 5.19E-36; mr1632 (All); LR P-value: 1.70E-27; mr1683 (All); LR P-value: 9.04E-11; mr1751 (All); LR P-value: 1.30E-11; mr1039_2 (All); LR P-value: 3.91E-28; mr1128_2 (All); LR P-value: 2.03E-12; mr1632_2 (All); LR P-value: 3.51E-34 |
LOC_Os07g42400.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os07g42400.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 47.181; most accessible tissue: Callus, score: 84.092 |
| vg0725373501 (J) | chr07 | 25373501 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os07g42400.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g42400.2 Alt: T| synonymous_variant LOW(snpEff) LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.715; most accessible tissue: Callus, score: 83.547 |
| vg0725373636 (J) | chr07 | 25373636 | C | T | 70.10% | 0.00% | T -> C |
mr1052 (Ind_All); LR P-value: 9.39E-06;
mr1055 (Jap_All); LR P-value: 8.12E-11; mr1132 (Jap_All); LR P-value: 2.05E-10; mr1386 (All); LR P-value: 1.59E-12; mr1563 (Jap_All); LR P-value: 3.85E-09; mr1825 (Jap_All); LR P-value: 7.09E-08; mr1178_2 (Jap_All); LR P-value: 1.38E-13; mr1498_2 (Jap_All); LR P-value: 5.96E-06; mr1769_2 (Jap_All); LR P-value: 9.95E-14 |
LOC_Os07g42400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g42400.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 38.747; most accessible tissue: Zhenshan97 young leaf, score: 59.009 |
| vg0725374504 (J) | chr07 | 25374504 | A | G | 70.20% | 0.00% | G -> A |
LOC_Os07g42400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os07g42400.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 64.450; most accessible tissue: Zhenshan97 panicle, score: 76.605 |
|
| vg0725374509 (J) | chr07 | 25374509 | C | A | 97.00% | 0.00% | C -> A | NA |
LOC_Os07g42400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g42400.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 64.920; most accessible tissue: Zhenshan97 panicle, score: 76.605 |
| vg0725374751 (J) | chr07 | 25374751 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os07g42400.2 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42400.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.381; most accessible tissue: Callus, score: 71.998 |
| vg0725374896 (J) | chr07 | 25374896 | A | G | 92.00% | 0.00% | A -> G |
mr1055 (Jap_All); LR P-value: 8.12E-11;
mr1132 (Jap_All); LR P-value: 2.05E-10; mr1248 (All); LR P-value: 1.40E-06; mr1301 (All); LR P-value: 2.87E-18; mr1563 (Jap_All); LR P-value: 3.85E-09; mr1825 (Jap_All); LR P-value: 7.09E-08; mr1993 (All); LR P-value: 1.37E-06; mr1178_2 (Jap_All); LR P-value: 1.38E-13; mr1498_2 (Jap_All); LR P-value: 5.96E-06; mr1769_2 (All); LR P-value: 1.14E-11; mr1769_2 (Jap_All); LR P-value: 9.95E-14; mr1993_2 (All); LR P-value: 2.95E-11 |
LOC_Os07g42395.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42395.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.591; most accessible tissue: Zhenshan97 flower, score: 65.164 |
| vg0725374902 (J) | chr07 | 25374902 | G | A | 63.60% | 0.00% | G -> A |
mr1094 (Ind_All); LR P-value: 9.48E-07;
mr1352 (All); LR P-value: 3.49E-09; mr1627 (Ind_All); LR P-value: 3.11E-06; mr1755 (Ind_All); LR P-value: 7.15E-06; mr1172_2 (All); LR P-value: 3.26E-11; mr1215_2 (All); LR P-value: 9.78E-11; mr1215_2 (Ind_All); LR P-value: 1.37E-07; mr1218_2 (All); LR P-value: 4.04E-20; mr1218_2 (Ind_All); LR P-value: 4.25E-08; mr1220_2 (All); LR P-value: 1.33E-10; mr1220_2 (Ind_All); LR P-value: 5.58E-06; mr1260_2 (All); LR P-value: 2.70E-18; mr1260_2 (Ind_All); LR P-value: 2.18E-06; mr1277_2 (Ind_All); LR P-value: 3.77E-06; mr1302_2 (All); LR P-value: 2.92E-07; mr1319_2 (All); LR P-value: 6.70E-09; mr1327_2 (All); LR P-value: 2.18E-08; mr1327_2 (Ind_All); LR P-value: 4.20E-09; mr1330_2 (All); LR P-value: 9.69E-13; mr1352_2 (All); LR P-value: 1.25E-17; mr1362_2 (Ind_All); LR P-value: 1.21E-06; mr1378_2 (Ind_All); LR P-value: 1.52E-07; mr1422_2 (All); LR P-value: 7.86E-24; mr1422_2 (Ind_All); LR P-value: 3.27E-07; mr1428_2 (All); LR P-value: 5.69E-07; mr1428_2 (Ind_All); LR P-value: 4.42E-06; mr1454_2 (All); LR P-value: 3.47E-15; mr1511_2 (Ind_All); LR P-value: 4.07E-06; mr1604_2 (All); LR P-value: 1.83E-07; mr1627_2 (All); LR P-value: 2.76E-20; mr1739_2 (Ind_All); LR P-value: 4.44E-09; mr1751_2 (All); LR P-value: 9.73E-11; mr1824_2 (All); LR P-value: 4.60E-07; mr1836_2 (Ind_All); LR P-value: 6.67E-06; mr1885_2 (All); LR P-value: 3.52E-08; mr1954_2 (Ind_All); LR P-value: 8.16E-06 |
LOC_Os07g42395.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42395.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42400.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.192; most accessible tissue: Zhenshan97 flower, score: 65.164 |
| vg0725375322 (J) | chr07 | 25375322 | G | A | 61.90% | 0.00% | A -> G |
mr1039 (All); LR P-value: 1.23E-25;
mr1070 (All); LR P-value: 8.37E-12; mr1128 (All); LR P-value: 1.72E-10; mr1386 (All); LR P-value: 1.12E-13; mr1414 (All); LR P-value: 2.74E-28; mr1514 (All); LR P-value: 1.03E-08; mr1542 (All); LR P-value: 3.04E-36; mr1632 (All); LR P-value: 3.95E-28; mr1683 (All); LR P-value: 1.50E-10; mr1751 (All); LR P-value: 2.44E-11; mr1039_2 (All); LR P-value: 1.26E-28; mr1128_2 (All); LR P-value: 1.42E-12; mr1632_2 (All); LR P-value: 1.52E-34 |
LOC_Os07g42400.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.580; most accessible tissue: Zhenshan97 flower, score: 82.236 |
| vg0725375330 (J) | chr07 | 25375330 | C | T | 70.10% | 0.00% | T -> C |
mr1052 (Ind_All); LR P-value: 9.39E-06;
mr1386 (All); LR P-value: 1.38E-12; mr1518 (Jap_All); LR P-value: 3.05E-06; mr1563 (Jap_All); LR P-value: 3.40E-09; mr1676 (Jap_All); LR P-value: 1.13E-06; mr1769 (Jap_All); LR P-value: 9.96E-14; mr1825 (Jap_All); LR P-value: 7.73E-08; mr1498_2 (Jap_All); LR P-value: 5.49E-06; mr1563_2 (Jap_All); LR P-value: 8.10E-08; mr1769_2 (Jap_All); LR P-value: 7.92E-15 |
LOC_Os07g42400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.556; most accessible tissue: Zhenshan97 flower, score: 82.236 |
| vg0725375360 (J) | chr07 | 25375360 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os07g42400.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g42400.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os07g42395.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42395.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.075; most accessible tissue: Zhenshan97 flower, score: 83.812 |
| vg0725375367 (J) | chr07 | 25375367 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os07g42400.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g42400.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os07g42395.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42395.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.176; most accessible tissue: Zhenshan97 flower, score: 83.061 |
| vg0725375507 (J) | chr07 | 25375507 | G | A | 66.40% | 0.00% | G -> A |
mr1215 (All); LR P-value: 3.19E-06;
mr1215 (Ind_All); LR P-value: 7.16E-06; mr1218 (Ind_All); LR P-value: 4.25E-06; mr1352 (All); LR P-value: 6.03E-11; mr1352 (Ind_All); LR P-value: 3.53E-06; mr1450 (All); LR P-value: 2.24E-06; mr1622 (All); LR P-value: 9.13E-07; mr1627 (Ind_All); LR P-value: 4.63E-07; mr1041_2 (All); LR P-value: 4.86E-06; mr1084_2 (All); LR P-value: 2.53E-08; mr1114_2 (Ind_All); LR P-value: 1.53E-06; mr1115_2 (Ind_All); LR P-value: 5.34E-07; mr1172_2 (All); LR P-value: 8.78E-09; mr1205_2 (All); LR P-value: 2.15E-07; mr1215_2 (All); LR P-value: 4.69E-12; mr1215_2 (Ind_All); LR P-value: 8.44E-10; mr1218_2 (All); LR P-value: 9.71E-22; mr1218_2 (Ind_All); LR P-value: 1.83E-10; mr1220_2 (All); LR P-value: 3.17E-12; mr1220_2 (Ind_All); LR P-value: 2.77E-08; mr1232_2 (Ind_All); LR P-value: 2.79E-06; mr1236_2 (All); LR P-value: 1.64E-06; mr1236_2 (Ind_All); LR P-value: 6.36E-08; mr1277_2 (Ind_All); LR P-value: 8.00E-07; mr1302_2 (All); LR P-value: 1.36E-07; mr1304_2 (Ind_All); LR P-value: 5.81E-06; mr1345_2 (Ind_All); LR P-value: 5.85E-06; mr1362_2 (Ind_All); LR P-value: 2.89E-06; mr1378_2 (Ind_All); LR P-value: 1.71E-06; mr1407_2 (All); LR P-value: 8.73E-06; mr1422_2 (All); LR P-value: 2.49E-24; mr1422_2 (Ind_All); LR P-value: 4.44E-09; mr1424_2 (Ind_All); LMM P-value: 9.10E-06; LR P-value: 9.09E-06; mr1511_2 (Ind_All); LR P-value: 5.59E-07; mr1583_2 (All); LR P-value: 6.44E-14; mr1583_2 (Ind_All); LR P-value: 5.91E-09; mr1604_2 (All); LR P-value: 5.27E-08; mr1624_2 (Ind_All); LR P-value: 1.95E-07; mr1653_2 (Ind_All); LR P-value: 1.16E-06; mr1700_2 (Ind_All); LR P-value: 4.66E-06; mr1713_2 (Ind_All); LR P-value: 7.18E-06; mr1751_2 (All); LR P-value: 2.00E-11; mr1751_2 (Ind_All); LR P-value: 2.17E-06; mr1771_2 (Ind_All); LR P-value: 8.18E-08; mr1784_2 (Ind_All); LR P-value: 3.89E-06; mr1800_2 (Ind_All); LR P-value: 2.67E-06; mr1824_2 (All); LR P-value: 1.38E-07; mr1844_2 (Ind_All); LR P-value: 5.38E-06; mr1850_2 (All); LR P-value: 6.19E-12; mr1850_2 (Ind_All); LR P-value: 5.96E-09; mr1885_2 (All); LR P-value: 9.28E-08 |
LOC_Os07g42400.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.715; most accessible tissue: Callus, score: 91.724 |
| vg0725375553 (J) | chr07 | 25375553 | A | C | 97.00% | 0.00% | A -> C | NA |
LOC_Os07g42400.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.653; most accessible tissue: Callus, score: 91.724 |
| vg0725375735 (J) | chr07 | 25375735 | A | G | 96.50% | 0.00% | A -> G |
LOC_Os07g42400.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.317; most accessible tissue: Callus, score: 97.594 |
|
| vg0725375781 (J) | chr07 | 25375781 | G | A | 66.30% | 0.00% | G -> A |
mr1215 (All); LR P-value: 1.57E-06;
mr1215 (Ind_All); LR P-value: 3.41E-06; mr1218 (Ind_All); LR P-value: 1.88E-06; mr1352 (All); LR P-value: 2.29E-11; mr1352 (Ind_All); LR P-value: 2.62E-06; mr1450 (All); LR P-value: 5.13E-07; mr1622 (All); LR P-value: 2.59E-07; mr1627 (Ind_All); LR P-value: 5.61E-07; mr1041_2 (All); LR P-value: 1.72E-06; mr1084_2 (All); LR P-value: 1.04E-08; mr1114_2 (Ind_All); LR P-value: 3.05E-06; mr1115_2 (Ind_All); LR P-value: 3.86E-07; mr1128_2 (Ind_All); LR P-value: 6.65E-06; mr1159_2 (Ind_All); LR P-value: 4.65E-06; mr1172_2 (All); LR P-value: 3.68E-09; mr1205_2 (All); LR P-value: 1.42E-07; mr1215_2 (All); LR P-value: 1.18E-12; mr1215_2 (Ind_All); LR P-value: 8.19E-10; mr1218_2 (All); LR P-value: 4.85E-22; mr1218_2 (Ind_All); LR P-value: 3.91E-10; mr1220_2 (All); LR P-value: 6.66E-13; mr1220_2 (Ind_All); LR P-value: 1.39E-08; mr1232_2 (Ind_All); LR P-value: 3.52E-06; mr1236_2 (All); LR P-value: 5.39E-07; mr1236_2 (Ind_All); LR P-value: 3.48E-08; mr1277_2 (Ind_All); LR P-value: 1.95E-06; mr1299_2 (Ind_All); LR P-value: 7.43E-06; mr1302_2 (All); LR P-value: 4.58E-08; mr1304_2 (Ind_All); LR P-value: 5.66E-06; mr1345_2 (Ind_All); LR P-value: 8.32E-06; mr1352_2 (All); LR P-value: 1.79E-16; mr1362_2 (Ind_All); LR P-value: 1.53E-06; mr1378_2 (Ind_All); LR P-value: 8.80E-07; mr1407_2 (All); LR P-value: 4.32E-06; mr1420_2 (All); LR P-value: 9.94E-06; mr1422_2 (All); LR P-value: 2.95E-25; mr1422_2 (Ind_All); LR P-value: 5.49E-09; mr1488_2 (All); LR P-value: 1.20E-06; mr1511_2 (Ind_All); LR P-value: 5.53E-07; mr1583_2 (All); LR P-value: 2.17E-14; mr1583_2 (Ind_All); LR P-value: 8.90E-09; mr1604_2 (All); LR P-value: 1.45E-08; mr1624_2 (Ind_All); LR P-value: 3.70E-07; mr1646_2 (Ind_All); LR P-value: 7.42E-06; mr1653_2 (Ind_All); LR P-value: 5.69E-07; mr1700_2 (Ind_All); LR P-value: 2.40E-06; mr1713_2 (Ind_All); LR P-value: 4.03E-06; mr1739_2 (Ind_All); LR P-value: 7.04E-09; mr1751_2 (All); LR P-value: 1.04E-11; mr1751_2 (Ind_All); LR P-value: 3.38E-06; mr1771_2 (Ind_All); LR P-value: 1.14E-07; mr1784_2 (Ind_All); LR P-value: 4.14E-06; mr1800_2 (Ind_All); LR P-value: 2.66E-06; mr1824_2 (All); LR P-value: 3.85E-08; mr1844_2 (Ind_All); LR P-value: 2.89E-06; mr1850_2 (All); LR P-value: 1.68E-12; mr1850_2 (Ind_All); LR P-value: 4.40E-09; mr1885_2 (All); LR P-value: 5.63E-08 |
LOC_Os07g42400.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.640; most accessible tissue: Callus, score: 97.594 |
| vg0725375828 (J) | chr07 | 25375828 | T | C | 97.00% | 0.00% | T -> C | NA |
LOC_Os07g42400.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.716; most accessible tissue: Callus, score: 95.025 |
| vg0725375847 (J) | chr07 | 25375847 | A | G | 61.90% | 0.00% | G -> A |
mr1070 (All); LR P-value: 3.01E-11;
mr1386 (All); LR P-value: 2.73E-13; mr1414 (All); LR P-value: 1.29E-27; mr1514 (All); LR P-value: 1.21E-08; mr1542 (All); LR P-value: 1.46E-35; mr1632 (All); LR P-value: 2.86E-27; mr1683 (All); LR P-value: 2.55E-10; mr1751 (All); LR P-value: 2.73E-11; mr1039_2 (All); LR P-value: 1.10E-27; mr1632_2 (All); LR P-value: 1.60E-33 |
LOC_Os07g42400.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42400.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42395.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.884; most accessible tissue: Callus, score: 95.025 |