10 variations found. LOC_Os05g41540 (bZIP transcription factor domain containing protein; expressed), ranging from 24,320,999 bp to 24,322,781 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524321117 (J) | chr05 | 24321117 | CTA | CTATATA TATATA | 95.00% | 0.00% | CTA -> CTATATATAT ATA,CTATAT ATATA,C,CT ATATATATAT ATA,CTATAT ATATATATAT ATATATATAT A,CTATATAT ATATATATA | NA |
LOC_Os05g41540.1 Alt: CTATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41530.1 Alt: CTATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: CTATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: CTATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: CTATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: CTATATATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41530.1 Alt: CTATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: CTATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: CTATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: CTATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: CTATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41530.1 Alt: CTATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: CTATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: CTATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: CTATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: CTATATATATATATATATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41530.1 Alt: CTATATATATATATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: CTATATATATATATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: CTATATATATATATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: CTATATATATATATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: CTATATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41530.1 Alt: CTATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: CTATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: CTATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: CTATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g41530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.234; most accessible tissue: Zhenshan97 flag leaf, score: 94.973 |
| vg0524321131 (J) | chr05 | 24321131 | ACACGAG | A | 99.90% | 0.00% | ACACGAG -> A | NA |
LOC_Os05g41540.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g41530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.319; most accessible tissue: Zhenshan97 flag leaf, score: 95.277 |
| vg0524321380 (J) | chr05 | 24321380 | A | C | 64.60% | 0.00% | C -> A |
mr1102 (All); LR P-value: 1.22E-19;
mr1122 (All); LR P-value: 1.26E-24; mr1168 (All); LR P-value: 4.47E-24; mr1194 (All); LR P-value: 1.09E-46; mr1383 (All); LR P-value: 1.22E-25; mr1414 (All); LR P-value: 7.30E-28; mr1695 (All); LR P-value: 8.44E-59; mr1723 (All); LR P-value: 2.53E-28; mr1846 (All); LR P-value: 5.01E-12; mr1889 (All); LMM P-value: 3.02E-09; LR P-value: 1.39E-70; mr1896 (All); LMM P-value: 5.20E-06; LR P-value: 6.08E-87; mr1903 (All); LR P-value: 2.32E-32; mr1907 (All); LMM P-value: 8.34E-11; LR P-value: 5.07E-109; mr1934 (All); LMM P-value: 1.78E-07; LR P-value: 3.02E-98; mr1935 (All); LMM P-value: 1.49E-06; LR P-value: 3.75E-67; mr1962 (All); LR P-value: 4.46E-59; mr1968 (All); LR P-value: 2.19E-17; mr1986 (All); LR P-value: 2.31E-09; mr1105_2 (All); LR P-value: 6.62E-30; mr1150_2 (All); LR P-value: 5.07E-31; mr1162_2 (All); LR P-value: 6.49E-15; mr1168_2 (All); LR P-value: 1.29E-20; mr1191_2 (All); LR P-value: 6.10E-13; mr1448_2 (All); LR P-value: 3.02E-35; mr1607_2 (All); LR P-value: 1.08E-07; mr1712_2 (All); LR P-value: 1.52E-20; mr1717_2 (All); LR P-value: 2.32E-13; mr1889_2 (All); LMM P-value: 7.48E-09; LR P-value: 9.71E-86; mr1893_2 (All); LR P-value: 3.82E-13; mr1896_2 (All); LMM P-value: 6.94E-08; LR P-value: 2.49E-83; mr1907_2 (All); LMM P-value: 3.51E-07; LR P-value: 2.74E-118; mr1934_2 (All); LMM P-value: 2.69E-09; LR P-value: 3.95E-107; mr1962_2 (All); LR P-value: 1.92E-124 |
LOC_Os05g41540.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 85.876; most accessible tissue: Zhenshan97 flag leaf, score: 97.172 |
| vg0524321823 (J) | chr05 | 24321823 | G | A | 99.80% | 0.00% | G -> A,T | NA |
LOC_Os05g41540.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g41530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41540.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os05g41530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.506; most accessible tissue: Zhenshan97 flag leaf, score: 99.112 |
| vg0524321915 (J) | chr05 | 24321915 | G | T | 99.20% | 0.00% | G -> T | NA |
LOC_Os05g41540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.922; most accessible tissue: Zhenshan97 flag leaf, score: 99.108 |
| vg0524322445 (J) | chr05 | 24322445 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os05g41540.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g41550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.718; most accessible tissue: Minghui63 young leaf, score: 99.596 |
| vg0524322502 (J) | chr05 | 24322502 | ACTCTCT CT | A | 53.50% | 0.00% | A -> ACTCTCTCT, ACTCTCTCTC T,ACTCTCT, ACTCTCTCTC TCT,ACTCTC TCTCTCTCT, ACTCTCTCTC TCTCTCTCTC T | NA |
LOC_Os05g41540.1 Alt: ACTCTCTCTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41550.2 Alt: ACTCTCTCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCTCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCTCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: ACTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: ACTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: ACTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: ACTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: ACTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: ACTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: ACTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: ACTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41540.1 Alt: ACTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.2 Alt: ACTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: ACTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: ACTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.382; most accessible tissue: Minghui63 young leaf, score: 99.717 |
| vg0524322517 (J) | chr05 | 24322517 | C | CTCTCT | 99.80% | 0.00% | C -> CTCTCT,CTC TCTCT | NA |
LOC_Os05g41540.1 Alt: CTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g41550.2 Alt: CTCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: CTCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: CTCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41540.1 Alt: CTCTCT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g41550.2 Alt: CTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.5 Alt: CTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41550.3 Alt: CTCTCT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.437; most accessible tissue: Minghui63 young leaf, score: 99.739 |
| vg0524322680 (J) | chr05 | 24322680 | G | T | 93.30% | 0.00% | G -> T |
mr1016 (Jap_All); LR P-value: 2.61E-10;
mr1017 (Jap_All); LR P-value: 6.90E-11; mr1019 (Jap_All); LR P-value: 9.22E-09; mr1055 (Jap_All); LR P-value: 1.25E-12; mr1132 (Jap_All); LR P-value: 5.37E-11; mr1390 (Jap_All); LR P-value: 1.38E-10; mr1490 (Jap_All); LR P-value: 3.44E-12; mr1606 (Jap_All); LR P-value: 2.97E-06; mr1019_2 (All); LMM P-value: 6.06E-06; mr1019_2 (Jap_All); LR P-value: 6.83E-10; mr1132_2 (Jap_All); LR P-value: 1.77E-13; mr1178_2 (Jap_All); LR P-value: 1.36E-13; mr1194_2 (Jap_All); LR P-value: 2.21E-06; mr1390_2 (Jap_All); LR P-value: 2.02E-13; mr1490_2 (Jap_All); LR P-value: 1.72E-13 |
LOC_Os05g41540.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41550.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41550.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.592; most accessible tissue: Minghui63 young leaf, score: 99.823 |
| STR0524322673 (J) | chr05 | 24322673 | TTGATTT G | TTGATTT T | 94.60% | 0.00% | TTGATTTG -> TTGATTTT | NA |
|