26 variations found. LOC_Os03g17700 (CGMC_MAPKCGMC_2_ERK.2 - CGMC includes CDA; MAPK; GSK3; and CLKC kinases; expressed), ranging from 9,847,699 bp to 9,850,473 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0309849316 (J) | chr03 | 9849316 | AA | AAA | 62.40% | 0.00% | AAA -> AA | NA |
|
| STR0309850205 (J) | chr03 | 9850205 | C | CCTC | 63.60% | 0.00% | CCTC -> C | NA |
|
| vg0309847749 (J) | chr03 | 9847749 | C | G | 95.80% | 0.00% | C -> G | NA |
LOC_Os03g17700.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.115; most accessible tissue: Zhenshan97 young leaf, score: 98.859 |
| vg0309847767 (J) | chr03 | 9847767 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os03g17700.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g17690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17690.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17710.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.930; most accessible tissue: Zhenshan97 young leaf, score: 98.819 |
| vg0309847925 (J) | chr03 | 9847925 | A | T | 65.20% | 0.00% | T -> A | NA |
LOC_Os03g17700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.371; most accessible tissue: Zhenshan97 young leaf, score: 98.829 |
| vg0309848266 (J) | chr03 | 9848266 | G | C | 65.00% | 0.00% | C -> G,A | NA |
LOC_Os03g17690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g17710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17690.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17710.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17700.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os03g17690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.863; most accessible tissue: Callus, score: 99.733 |
| vg0309848359 (J) | chr03 | 9848359 | T | A | 65.00% | 0.00% | A -> T | NA |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.586; most accessible tissue: Zhenshan97 young leaf, score: 99.139 |
| vg0309848417 (J) | chr03 | 9848417 | C | T | 87.80% | 0.23% | C -> T | NA |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.673; most accessible tissue: Zhenshan97 young leaf, score: 99.186 |
| vg0309848464 (J) | chr03 | 9848464 | A | G | 65.20% | 0.00% | G -> A | NA |
LOC_Os03g17690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.989; most accessible tissue: Callus, score: 99.852 |
| vg0309848511 (J) | chr03 | 9848511 | T | C | 65.10% | 0.02% | C -> T | NA |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.319; most accessible tissue: Callus, score: 99.852 |
| vg0309848706 (J) | chr03 | 9848706 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os03g17700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 96.816; most accessible tissue: Zhenshan97 young leaf, score: 99.429 |
| vg0309848837 (J) | chr03 | 9848837 | G | T | 97.90% | 0.00% | G -> T | NA |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.044; most accessible tissue: Zhenshan97 young leaf, score: 99.499 |
| vg0309848861 (J) | chr03 | 9848861 | G | C | 65.00% | 0.25% | G -> C | NA |
LOC_Os03g17690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 94.659; most accessible tissue: Zhenshan97 young leaf, score: 99.466 |
| vg0309849047 (J) | chr03 | 9849047 | C | T | 87.80% | 0.23% | C -> T | NA |
LOC_Os03g17700.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g17700.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.399; most accessible tissue: Zhenshan97 young leaf, score: 99.331 |
| vg0309849247 (J) | chr03 | 9849247 | T | C | 51.90% | 0.34% | C -> T |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.154; most accessible tissue: Zhenshan97 young leaf, score: 98.991 |
|
| vg0309849252 (J) | chr03 | 9849252 | T | C | 65.10% | 0.00% | C -> T | NA |
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.086; most accessible tissue: Zhenshan97 young leaf, score: 98.978 |
| vg0309849291 (J) | chr03 | 9849291 | C | T | 65.10% | 0.00% | T -> C | NA |
LOC_Os03g17690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.370; most accessible tissue: Zhenshan97 young leaf, score: 98.938 |
| vg0309849315 (J) | chr03 | 9849315 | GA | GAA | 60.20% | 0.00% | GAA -> GA,G | NA |
LOC_Os03g17690.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.257; most accessible tissue: Zhenshan97 young leaf, score: 98.849 |
| vg0309849480 (J) | chr03 | 9849480 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os03g17700.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.629; most accessible tissue: Zhenshan97 young leaf, score: 98.812 |
| vg0309849999 (J) | chr03 | 9849999 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os03g17690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.556; most accessible tissue: Zhenshan97 young leaf, score: 98.809 |
| vg0309850204 (J) | chr03 | 9850204 | C | CCCT | 65.00% | 0.00% | CCCT -> C | NA |
LOC_Os03g17700.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.014; most accessible tissue: Zhenshan97 young leaf, score: 99.599 |
| vg0309850243 (J) | chr03 | 9850243 | C | A | 85.40% | 0.00% | A -> C,T |
Heading_date (All); LR P-value: 2.28E-14;
Heading_date (Jap_All); LR P-value: 2.46E-13; Plant_height (Jap_All); LR P-value: 2.05E-13; Spikelet_length (All); LR P-value: 8.68E-14; mr1031 (Jap_All); LR P-value: 1.87E-06; mr1056 (All); LR P-value: 4.87E-13; mr1056 (Jap_All); LR P-value: 4.14E-06; mr1163 (Jap_All); LR P-value: 1.01E-06; mr1252 (All); LR P-value: 6.12E-07; mr1952 (Jap_All); LMM P-value: 6.96E-06; LR P-value: 6.95E-06; mr1002_2 (All); LR P-value: 1.19E-10; mr1002_2 (Jap_All); LR P-value: 1.85E-08; mr1010_2 (Jap_All); LR P-value: 1.58E-07; mr1011_2 (All); LR P-value: 3.67E-11; mr1011_2 (Jap_All); LR P-value: 7.78E-08; mr1031_2 (Jap_All); LR P-value: 2.62E-08; mr1330_2 (Jap_All); LR P-value: 2.49E-08; mr1449_2 (Jap_All); LR P-value: 3.38E-07; mr1454_2 (Jap_All); LR P-value: 1.10E-08; mr1730_2 (Jap_All); LR P-value: 4.33E-06 |
LOC_Os03g17700.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g17700.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17700.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.561; most accessible tissue: Zhenshan97 young leaf, score: 99.728 |
| vg0309850311 (J) | chr03 | 9850311 | A | G | 65.30% | 0.00% | G -> A | NA |
LOC_Os03g17700.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.117; most accessible tissue: Zhenshan97 young leaf, score: 99.850 |
| vg0309850312 (J) | chr03 | 9850312 | T | G | 65.10% | 0.00% | G -> T | NA |
LOC_Os03g17700.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.121; most accessible tissue: Zhenshan97 young leaf, score: 99.851 |
| vg0309850413 (J) | chr03 | 9850413 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os03g17700.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g17690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g17710.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.358; most accessible tissue: Zhenshan97 young leaf, score: 99.920 |
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