77 variations found. LOC_Os04g35700 (STE_MEKK_ste11_MAP3K.16 - STE kinases include homologs to sterile 7; sterile 11 and sterile 20 from yeast; expressed), ranging from 21,752,559 bp to 21,758,662 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0421753716 (J) | chr04 | 21753716 | TCATATT C | TCATATT T | 98.80% | 0.00% | TCATATTC -> TCATATTT | NA |
|
| STR0421755022 (J) | chr04 | 21755022 | AAC | AAA | 96.90% | 0.00% | AAC -> AAA | NA |
|
| STR0421757952 (J) | chr04 | 21757952 | AGAAATA | AGAAATG | 82.90% | 0.00% | AGAAATA -> AGAAATG | NA |
|
| vg0421752654 (J) | chr04 | 21752654 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os04g35700.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.077; most accessible tissue: Minghui63 young leaf, score: 95.256 |
| vg0421752795 (J) | chr04 | 21752795 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os04g35700.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.013; most accessible tissue: Minghui63 flower, score: 95.395 |
| vg0421752849 (J) | chr04 | 21752849 | C | CAG | 89.10% | 0.23% | C -> CAG,G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g35700.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: CAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35690.1 Alt: CAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: CAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.606; most accessible tissue: Minghui63 young leaf, score: 94.233 |
| vg0421753233 (J) | chr04 | 21753233 | T | C | 89.40% | 0.00% | T -> C |
mr1038 (All); LR P-value: 1.40E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 5.37E-08; mr1038_2 (All); LR P-value: 2.17E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 1.95E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
LOC_Os04g35690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35700.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.308; most accessible tissue: Minghui63 flower, score: 93.472 |
| vg0421753291 (J) | chr04 | 21753291 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os04g35700.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.678; most accessible tissue: Minghui63 flower, score: 93.394 |
| vg0421753363 (J) | chr04 | 21753363 | A | G | 96.60% | 0.00% | A -> G | NA |
LOC_Os04g35700.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.314; most accessible tissue: Minghui63 flower, score: 91.725 |
| vg0421753489 (J) | chr04 | 21753489 | A | G | 89.10% | 0.23% | A -> G |
mr1038 (All); LR P-value: 1.12E-07;
mr1038 (Ind_All); LR P-value: 2.05E-06; mr1389 (All); LR P-value: 7.26E-08; mr1038_2 (All); LR P-value: 2.98E-10; mr1038_2 (Ind_All); LR P-value: 3.64E-08; mr1074_2 (Ind_All); LR P-value: 4.20E-06; mr1389_2 (All); LR P-value: 3.79E-09; mr1389_2 (Ind_All); LR P-value: 9.92E-08; mr1723_2 (Ind_All); LR P-value: 6.06E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g35690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.661; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg0421753539 (J) | chr04 | 21753539 | G | A | 89.40% | 0.00% | G -> A |
mr1038 (All); LR P-value: 1.40E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 5.37E-08; mr1038_2 (All); LR P-value: 2.17E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 1.95E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.250; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0421753643 (J) | chr04 | 21753643 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.804; most accessible tissue: Zhenshan97 panicle, score: 91.845 |
| vg0421753669 (J) | chr04 | 21753669 | T | C | 89.20% | 0.00% | T -> C |
mr1038 (All); LR P-value: 1.85E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 1.16E-07; mr1038_2 (All); LR P-value: 4.08E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 3.71E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
LOC_Os04g35690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35700.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.110; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg0421753673 (J) | chr04 | 21753673 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os04g35690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.425; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg0421753723 (J) | chr04 | 21753723 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os04g35690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35700.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.056; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
| vg0421753738 (J) | chr04 | 21753738 | G | T | 99.80% | 0.00% | G -> T,A | NA |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os04g35690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.397; most accessible tissue: Zhenshan97 panicle, score: 93.657 |
| vg0421753760 (J) | chr04 | 21753760 | C | T | 89.70% | 0.23% | C -> T |
mr1038 (All); LR P-value: 1.40E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 5.37E-08; mr1038_2 (All); LR P-value: 2.17E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 1.95E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g35690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.238; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
| vg0421753782 (J) | chr04 | 21753782 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.446; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
| vg0421753795 (J) | chr04 | 21753795 | G | A | 89.60% | 0.23% | G -> A |
mr1038 (All); LR P-value: 1.81E-07;
mr1038 (Ind_All); LR P-value: 3.25E-06; mr1389 (All); LR P-value: 5.38E-08; mr1038_2 (All); LR P-value: 2.79E-10; mr1038_2 (Ind_All); LR P-value: 3.43E-08; mr1074_2 (Ind_All); LR P-value: 1.69E-06; mr1389_2 (All); LR P-value: 4.08E-09; mr1389_2 (Ind_All); LR P-value: 1.06E-07; mr1723_2 (Ind_All); LR P-value: 9.76E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.357; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
| vg0421753826 (J) | chr04 | 21753826 | G | A | 89.10% | 0.21% | G -> A |
mr1038 (All); LR P-value: 1.40E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 5.37E-08; mr1038_2 (All); LR P-value: 2.17E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 1.95E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.861; most accessible tissue: Zhenshan97 panicle, score: 93.845 |
| vg0421753830 (J) | chr04 | 21753830 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.065; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0421753853 (J) | chr04 | 21753853 | AAAAAC | A | 99.80% | 0.00% | AAAAAC -> A | NA |
LOC_Os04g35690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.823; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0421753862 (J) | chr04 | 21753862 | TG | T | 99.80% | 0.00% | TG -> T | NA |
LOC_Os04g35690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.478; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
| vg0421753925 (J) | chr04 | 21753925 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os04g35690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g35700.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g35700.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.646; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0421753967 (J) | chr04 | 21753967 | T | C | 89.40% | 0.00% | T -> C |
mr1038 (All); LR P-value: 1.40E-07;
mr1038 (Ind_All); LR P-value: 2.57E-06; mr1389 (All); LR P-value: 5.37E-08; mr1038_2 (All); LR P-value: 2.17E-10; mr1038_2 (Ind_All); LR P-value: 2.75E-08; mr1074_2 (Ind_All); LR P-value: 2.92E-06; mr1389_2 (All); LR P-value: 1.95E-09; mr1389_2 (Ind_All); LR P-value: 5.29E-08; mr1723_2 (Ind_All); LR P-value: 6.93E-07 |
LOC_Os04g35690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g35700.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g35700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.946; most accessible tissue: Zhenshan97 panicle, score: 93.351 |
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