307 variations found. LOC_Os11g41990 (armadillo%2Fbeta-catenin-like repeat family protein; expressed), ranging from 25,245,781 bp to 25,252,767 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR1125246770 (J) | chr11 | 25246770 | G | A | 88.50% | 0.00% | G -> A | NA |
|
| STR1125247767 (J) | chr11 | 25247767 | GA | GG | 90.80% | 0.00% | GA -> GG | NA |
|
| STR1125247997 (J) | chr11 | 25247997 | C | T | 82.20% | 0.00% | C -> T | NA |
|
| STR1125250223 (J) | chr11 | 25250223 | A | G | 91.20% | 0.00% | A -> G | NA |
|
| STR1125251815 (J) | chr11 | 25251815 | AAA | AAAA | 54.00% | 0.00% | AAA -> AA,AAAA | NA |
|
| vg1125245809 (J) | chr11 | 25245809 | G | T | 94.40% | 0.00% | G -> T |
mr1484 (All); LMM P-value: 1.36E-08;
mr1484 (Jap_All); LMM P-value: 2.44E-06; mr1530 (All); LMM P-value: 4.41E-11; LR P-value: 1.30E-13; mr1530 (Jap_All); LMM P-value: 6.47E-07; LR P-value: 1.08E-09; mr1745 (All); LMM P-value: 1.42E-10; mr1745 (Jap_All); LMM P-value: 8.36E-07; mr1926 (All); LMM P-value: 4.31E-06; mr1002_2 (All); LR P-value: 6.78E-09; mr1484_2 (All); LMM P-value: 2.00E-07; mr1530_2 (All); LMM P-value: 2.40E-11; mr1530_2 (Jap_All); LMM P-value: 2.29E-08; LR P-value: 1.06E-13; mr1745_2 (All); LMM P-value: 6.31E-07; mr1841_2 (All); LMM P-value: 6.24E-06 |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.471; most accessible tissue: Minghui63 young leaf, score: 85.236 |
| vg1125246022 (J) | chr11 | 25246022 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.430; most accessible tissue: Callus, score: 87.209 |
| vg1125246091 (J) | chr11 | 25246091 | TACA | T | 99.70% | 0.00% | TACA -> T | NA |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.609; most accessible tissue: Zhenshan97 young leaf, score: 83.623 |
| vg1125246115 (J) | chr11 | 25246115 | C | A | 96.00% | 0.00% | C -> A | NA |
LOC_Os11g41990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.483; most accessible tissue: Zhenshan97 young leaf, score: 80.325 |
| vg1125246164 (J) | chr11 | 25246164 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os11g41990.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.149; most accessible tissue: Minghui63 panicle, score: 78.920 |
| vg1125246196 (J) | chr11 | 25246196 | T | C | 98.70% | 0.00% | T -> C | NA |
LOC_Os11g41990.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.271; most accessible tissue: Callus, score: 82.227 |
| vg1125246201 (J) | chr11 | 25246201 | G | A | 96.00% | 0.00% | G -> A |
mr1238 (Ind_All); LMM P-value: 5.45E-16; LR P-value: 5.25E-17;
mr1309 (Ind_All); LMM P-value: 1.66E-10; LR P-value: 2.67E-11; mr1484 (Ind_All); LMM P-value: 8.79E-07; LR P-value: 1.11E-07; mr1841 (Ind_All); LMM P-value: 2.34E-08; LR P-value: 1.08E-08; mr1238_2 (Ind_All); LMM P-value: 2.13E-12; LR P-value: 1.40E-13; mr1484_2 (Ind_All); LMM P-value: 5.95E-12; LR P-value: 1.26E-13; mr1841_2 (Ind_All); LMM P-value: 9.29E-14; LR P-value: 4.18E-14; mr1900_2 (Ind_All); LMM P-value: 3.62E-08; LR P-value: 2.67E-09; mr1945_2 (Ind_All); LMM P-value: 2.27E-08; LR P-value: 2.27E-08 |
LOC_Os11g41990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.308; most accessible tissue: Callus, score: 82.227 |
| vg1125246202 (J) | chr11 | 25246202 | CT | C | 99.30% | 0.00% | CT -> C | NA |
LOC_Os11g41990.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.678; most accessible tissue: Callus, score: 82.227 |
| vg1125246230 (J) | chr11 | 25246230 | C | T | 96.50% | 0.00% | C -> T |
mr1238 (Ind_All); LMM P-value: 5.45E-16; LR P-value: 5.25E-17;
mr1309 (Ind_All); LMM P-value: 1.66E-10; LR P-value: 2.67E-11; mr1484 (Ind_All); LMM P-value: 8.79E-07; LR P-value: 1.11E-07; mr1841 (Ind_All); LMM P-value: 2.34E-08; LR P-value: 1.08E-08; mr1238_2 (Ind_All); LMM P-value: 2.13E-12; LR P-value: 1.40E-13; mr1484_2 (Ind_All); LMM P-value: 5.95E-12; LR P-value: 1.26E-13; mr1841_2 (Ind_All); LMM P-value: 9.29E-14; LR P-value: 4.18E-14; mr1900_2 (Ind_All); LMM P-value: 3.62E-08; LR P-value: 2.67E-09; mr1945_2 (Ind_All); LMM P-value: 2.27E-08; LR P-value: 2.27E-08 |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.505; most accessible tissue: Callus, score: 82.227 |
| vg1125246255 (J) | chr11 | 25246255 | C | T | 90.50% | 0.00% | C -> T |
mr1249 (All); LR P-value: 1.93E-08;
mr1328 (Jap_All); LR P-value: 4.46E-06; mr1596 (All); LR P-value: 7.03E-06; mr1662 (All); LMM P-value: 7.02E-09; LR P-value: 1.71E-08; mr1662 (Jap_All); LR P-value: 1.38E-07; mr1662_2 (All); LMM P-value: 1.10E-10; LR P-value: 2.52E-10; mr1662_2 (Jap_All); LMM P-value: 4.48E-07; LR P-value: 3.17E-09 |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.594; most accessible tissue: Callus, score: 82.227 |
| vg1125246293 (J) | chr11 | 25246293 | G | T | 94.30% | 0.00% | G -> T |
mr1484 (All); LMM P-value: 1.36E-08;
mr1484 (Jap_All); LMM P-value: 2.44E-06; mr1530 (All); LMM P-value: 4.41E-11; LR P-value: 1.30E-13; mr1530 (Jap_All); LMM P-value: 6.47E-07; LR P-value: 1.08E-09; mr1745 (All); LMM P-value: 1.42E-10; mr1745 (Jap_All); LMM P-value: 8.36E-07; mr1926 (All); LMM P-value: 4.31E-06; mr1002_2 (All); LR P-value: 6.78E-09; mr1484_2 (All); LMM P-value: 2.00E-07; mr1530_2 (All); LMM P-value: 2.40E-11; mr1530_2 (Jap_All); LMM P-value: 2.29E-08; LR P-value: 1.06E-13; mr1745_2 (All); LMM P-value: 6.31E-07; mr1841_2 (All); LMM P-value: 6.24E-06 |
LOC_Os11g41990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.989; most accessible tissue: Callus, score: 82.227 |
| vg1125246323 (J) | chr11 | 25246323 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os11g41990.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.860; most accessible tissue: Callus, score: 82.227 |
| vg1125246339 (J) | chr11 | 25246339 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os11g41990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g41990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.533; most accessible tissue: Zhenshan97 young leaf, score: 78.938 |
| vg1125246356 (J) | chr11 | 25246356 | G | A | 99.10% | 0.00% | G -> A | NA |
LOC_Os11g41990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g41990.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 68.450; most accessible tissue: Zhenshan97 young leaf, score: 80.848 |
| vg1125246415 (J) | chr11 | 25246415 | C | T | 96.50% | 0.00% | C -> T,G |
mr1238 (Ind_All); LMM P-value: 5.45E-16; LR P-value: 5.25E-17;
mr1309 (Ind_All); LMM P-value: 1.66E-10; LR P-value: 2.67E-11; mr1484 (Ind_All); LMM P-value: 8.79E-07; LR P-value: 1.11E-07; mr1841 (Ind_All); LMM P-value: 2.34E-08; LR P-value: 1.08E-08; mr1238_2 (Ind_All); LMM P-value: 2.13E-12; LR P-value: 1.40E-13; mr1484_2 (Ind_All); LMM P-value: 5.95E-12; LR P-value: 1.26E-13; mr1841_2 (Ind_All); LMM P-value: 9.29E-14; LR P-value: 4.18E-14; mr1900_2 (Ind_All); LMM P-value: 3.62E-08; LR P-value: 2.67E-09; mr1945_2 (Ind_All); LMM P-value: 2.27E-08; LR P-value: 2.27E-08 |
LOC_Os11g41990.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g41990.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g41990.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.111; most accessible tissue: Zhenshan97 young leaf, score: 78.938 |
| vg1125246449 (J) | chr11 | 25246449 | TG | T | 99.40% | 0.00% | TG -> T | NA |
LOC_Os11g41990.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.286; most accessible tissue: Zhenshan97 young leaf, score: 77.101 |
| vg1125246491 (J) | chr11 | 25246491 | C | G | 99.40% | 0.00% | C -> G | NA |
LOC_Os11g41990.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.668; most accessible tissue: Callus, score: 76.543 |
| vg1125246520 (J) | chr11 | 25246520 | T | C | 95.80% | 0.00% | T -> C,A |
mr1238 (Ind_All); LMM P-value: 5.45E-16; LR P-value: 5.25E-17;
mr1309 (Ind_All); LMM P-value: 1.66E-10; LR P-value: 2.67E-11; mr1484 (Ind_All); LMM P-value: 8.79E-07; LR P-value: 1.11E-07; mr1841 (Ind_All); LMM P-value: 2.34E-08; LR P-value: 1.08E-08; mr1238_2 (Ind_All); LMM P-value: 2.13E-12; LR P-value: 1.40E-13; mr1484_2 (Ind_All); LMM P-value: 5.95E-12; LR P-value: 1.26E-13; mr1841_2 (Ind_All); LMM P-value: 9.29E-14; LR P-value: 4.18E-14; mr1900_2 (Ind_All); LMM P-value: 3.62E-08; LR P-value: 2.67E-09; mr1945_2 (Ind_All); LMM P-value: 2.27E-08; LR P-value: 2.27E-08 |
LOC_Os11g41990.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g41990.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g41990.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.141; most accessible tissue: Callus, score: 76.543 |
| vg1125246522 (J) | chr11 | 25246522 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os11g41990.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.428; most accessible tissue: Callus, score: 76.543 |
| vg1125246561 (J) | chr11 | 25246561 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os11g41990.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g41990.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.324; most accessible tissue: Callus, score: 76.543 |
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