39 variations found. Os12g0106600/LOC_Os12g01580 (MATE efflux protein; putative; expressed), ranging from 350,765 bp to 355,106 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g01580 | MATE efflux protein, putative, expressed; RAP ID: Os12g0106600; MSU ID: LOC_Os12g01580 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200350840 (J) | chr12 | 350840 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g01580.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.671; most accessible tissue: Minghui63 flag leaf, score: 99.269 |
| vg1200350861 (J) | chr12 | 350861 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g01580.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.585; most accessible tissue: Minghui63 flag leaf, score: 99.212 |
| vg1200350898 (J) | chr12 | 350898 | G | T | 99.40% | 0.00% | G -> T | NA |
LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g01580.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.237; most accessible tissue: Minghui63 flag leaf, score: 99.020 |
| vg1200350921 (J) | chr12 | 350921 | C | A | 79.90% | 0.00% | C -> A |
Grain_length (All); LR P-value: 9.36E-17;
Grain_length (Ind_All); LR P-value: 8.33E-18; mr1174 (All); LR P-value: 2.10E-09; mr1174_2 (All); LR P-value: 4.02E-09 |
LOC_Os12g01580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 97.014; most accessible tissue: Minghui63 flag leaf, score: 98.970 |
| vg1200350923 (J) | chr12 | 350923 | T | A | 94.00% | 0.00% | T -> A | NA |
LOC_Os12g01580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.871; most accessible tissue: Minghui63 flag leaf, score: 98.899 |
| vg1200351020 (J) | chr12 | 351020 | A | T | 93.90% | 0.00% | A -> T | NA |
LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.631; most accessible tissue: Minghui63 flag leaf, score: 98.190 |
| vg1200351026 (J) | chr12 | 351026 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g01580.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.555; most accessible tissue: Minghui63 flag leaf, score: 98.215 |
| vg1200351085 (J) | chr12 | 351085 | A | C | 93.80% | 0.00% | A -> C | NA |
LOC_Os12g01580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.606; most accessible tissue: Minghui63 flag leaf, score: 98.288 |
| vg1200351516 (J) | chr12 | 351516 | A | G | 50.00% | 0.15% | A -> G | NA |
LOC_Os12g01580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g01580.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 66.760; most accessible tissue: Minghui63 flag leaf, score: 89.523 |
| vg1200351630 (J) | chr12 | 351630 | G | T | 94.00% | 0.00% | G -> T | NA |
LOC_Os12g01580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.569; most accessible tissue: Minghui63 flag leaf, score: 89.325 |
| vg1200351852 (J) | chr12 | 351852 | G | A | 94.00% | 0.00% | G -> A | NA |
LOC_Os12g01580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g01580.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 60.706; most accessible tissue: Minghui63 flag leaf, score: 87.326 |
| vg1200351909 (J) | chr12 | 351909 | C | A | 60.70% | 0.04% | C -> A,T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g01580.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.278; most accessible tissue: Minghui63 flag leaf, score: 88.687 |
| vg1200352034 (J) | chr12 | 352034 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g01570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01580.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os12g01580.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566 |
| vg1200352075 (J) | chr12 | 352075 | CA | C | 56.60% | 0.00% | CA -> C | NA |
LOC_Os12g01574.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.270; most accessible tissue: Minghui63 flag leaf, score: 79.676 |
| vg1200352164 (J) | chr12 | 352164 | T | C | 50.10% | 0.00% | T -> C | NA |
LOC_Os12g01574.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.469; most accessible tissue: Minghui63 flag leaf, score: 77.153 |
| vg1200352221 (J) | chr12 | 352221 | A | G | 94.00% | 0.00% | A -> G | NA |
LOC_Os12g01574.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.811; most accessible tissue: Callus, score: 81.076 |
| vg1200352243 (J) | chr12 | 352243 | G | C | 93.80% | 0.00% | G -> C | NA |
LOC_Os12g01574.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.293; most accessible tissue: Callus, score: 81.076 |
| vg1200352276 (J) | chr12 | 352276 | A | G | 94.00% | 0.00% | A -> G | NA |
LOC_Os12g01574.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.936; most accessible tissue: Callus, score: 81.076 |
| vg1200352341 (J) | chr12 | 352341 | C | T | 61.00% | 0.11% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.577; most accessible tissue: Minghui63 flag leaf, score: 76.091 |
| vg1200352442 (J) | chr12 | 352442 | A | T | 99.10% | 0.00% | A -> T | NA |
LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.103; most accessible tissue: Callus, score: 83.049 |
| vg1200352550 (J) | chr12 | 352550 | T | A | 93.80% | 0.00% | T -> A | NA |
LOC_Os12g01580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g01580.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 59.373; most accessible tissue: Callus, score: 83.049 |
| vg1200352586 (J) | chr12 | 352586 | G | A | 81.30% | 0.00% | G -> A | NA |
LOC_Os12g01580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g01580.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 56.908; most accessible tissue: Minghui63 flag leaf, score: 74.955 |
| vg1200352652 (J) | chr12 | 352652 | G | A | 79.90% | 0.15% | G -> A |
Grain_length (All); LR P-value: 9.36E-17;
Grain_length (Ind_All); LR P-value: 8.33E-18; mr1174 (All); LR P-value: 2.10E-09; mr1174_2 (All); LR P-value: 4.02E-09 |
LOC_Os12g01580.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g01580.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g01580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g01580.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 53.669; most accessible tissue: Minghui63 flag leaf, score: 74.563 |
| vg1200352663 (J) | chr12 | 352663 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os12g01580.1 Alt: A| splice_donor_variant&intron_variant HIGH(snpEff)
LOC_Os12g01580.2 Alt: A| splice_donor_variant&intron_variant HIGH(snpEff) LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.705; most accessible tissue: Minghui63 flag leaf, score: 74.955 |
| vg1200352786 (J) | chr12 | 352786 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g01570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g01580.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os12g01580.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.621; most accessible tissue: Callus, score: 79.309 |
| vg1200352804 (J) | chr12 | 352804 | T | G | 93.80% | 0.00% | T -> G | NA |
LOC_Os12g01574.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.936; most accessible tissue: Callus, score: 79.309 |
| vg1200352883 (J) | chr12 | 352883 | C | G | 93.90% | 0.00% | C -> G | NA |
LOC_Os12g01574.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.475; most accessible tissue: Callus, score: 56.838 |
| vg1200353021 (J) | chr12 | 353021 | A | AT | 93.80% | 0.00% | A -> AT | NA |
LOC_Os12g01574.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.144; most accessible tissue: Callus, score: 79.374 |
| vg1200353183 (J) | chr12 | 353183 | T | G | 60.90% | 0.02% | T -> G | NA |
LOC_Os12g01580.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g01580.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g01580.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g01580.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 49.878; most accessible tissue: Callus, score: 77.663 |
| vg1200353257 (J) | chr12 | 353257 | A | T | 93.80% | 0.00% | A -> T | NA |
LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.191; most accessible tissue: Callus, score: 77.663 |
| vg1200353430 (J) | chr12 | 353430 | G | A | 62.40% | 0.15% | G -> A |
Heading_date (Jap_All); LR P-value: 1.18E-13;
Plant_height (Jap_All); LR P-value: 6.56E-16; Spikelet_length (Jap_All); LR P-value: 1.25E-16; mr1097 (Jap_All); LR P-value: 2.58E-06; mr1042_2 (Jap_All); LR P-value: 1.21E-07; mr1043_2 (Jap_All); LR P-value: 3.49E-07; mr1045_2 (Jap_All); LR P-value: 6.31E-07; mr1074_2 (Jap_All); LMM P-value: 7.25E-06; LR P-value: 7.25E-06; mr1092_2 (Jap_All); LR P-value: 3.55E-06; mr1097_2 (Jap_All); LR P-value: 1.24E-07; mr1185_2 (Jap_All); LR P-value: 2.73E-06; mr1204_2 (Jap_All); LR P-value: 1.48E-06; mr1252_2 (Jap_All); LR P-value: 4.63E-06; mr1263_2 (Jap_All); LR P-value: 3.11E-07; mr1269_2 (Jap_All); LR P-value: 1.86E-06; mr1359_2 (Jap_All); LR P-value: 2.90E-07; mr1502_2 (Jap_All); LR P-value: 8.95E-09; mr1567_2 (Jap_All); LR P-value: 5.62E-06; mr1638_2 (Jap_All); LR P-value: 3.78E-06; mr1680_2 (Jap_All); LR P-value: 3.07E-07; mr1798_2 (Jap_All); LR P-value: 6.90E-07; mr1865_2 (Jap_All); LR P-value: 9.42E-06; mr1896_2 (Jap_All); LR P-value: 7.10E-06; mr1912_2 (Jap_All); LR P-value: 2.62E-06 |
LOC_Os12g01580.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g01580.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g01580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os12g01580.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 44.876; most accessible tissue: Callus, score: 81.742 |
| vg1200353613 (J) | chr12 | 353613 | CA | CAA | 63.70% | 0.00% | CAAA -> CA,CAA,CAA AA,C | NA |
LOC_Os12g01574.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: CAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: CAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01570.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 |
| vg1200353813 (J) | chr12 | 353813 | G | T | 79.90% | 0.15% | G -> T |
Grain_length (All); LR P-value: 9.99E-17;
Grain_length (Ind_All); LR P-value: 8.33E-18; mr1174 (All); LR P-value: 6.59E-09 |
LOC_Os12g01580.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g01580.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g01580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os12g01580.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 66.181; most accessible tissue: Callus, score: 84.591 |
| vg1200354503 (J) | chr12 | 354503 | G | A | 95.80% | 0.00% | G -> A | NA |
LOC_Os12g01580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g01580.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 79.048; most accessible tissue: Minghui63 flower, score: 87.958 |
| vg1200354572 (J) | chr12 | 354572 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os12g01580.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g01580.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g01590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.937; most accessible tissue: Minghui63 flower, score: 85.666 |
| vg1200354737 (J) | chr12 | 354737 | C | T | 49.90% | 0.08% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g01580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.386; most accessible tissue: Callus, score: 87.414 |
| vg1200354871 (J) | chr12 | 354871 | G | C | 93.80% | 0.00% | G -> C | NA |
LOC_Os12g01580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01580.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.041; most accessible tissue: Minghui63 flag leaf, score: 88.342 |
| vg1200354988 (J) | chr12 | 354988 | G | A | 79.90% | 0.17% | G -> A |
Grain_length (All); LR P-value: 3.05E-16;
Grain_length (Ind_All); LR P-value: 3.75E-17; mr1174 (All); LR P-value: 1.33E-09; mr1174_2 (All); LR P-value: 2.53E-09 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g01580.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01580.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.838; most accessible tissue: Callus, score: 91.978 |
| vg1200355096 (J) | chr12 | 355096 | C | T | 93.90% | 0.00% | C -> T | NA |
LOC_Os12g01580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g01580.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01574.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g01590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.081; most accessible tissue: Zhenshan97 panicle, score: 91.206 |