74 variations found. LOC_Os03g06230 (galactose mutarotase-like; putative; expressed), ranging from 3,119,830 bp to 3,123,758 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0303120168 (J) | chr03 | 3120168 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os03g06220.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g06230.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g06210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.552; most accessible tissue: Minghui63 panicle, score: 89.444 |
| vg0303120321 (J) | chr03 | 3120321 | C | T | 64.20% | 0.21% | T -> C | NA |
LOC_Os03g06220.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06230.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.174; most accessible tissue: Callus, score: 92.010 |
| vg0303120357 (J) | chr03 | 3120357 | A | C | 64.30% | 0.25% | C -> A | NA |
LOC_Os03g06220.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.583; most accessible tissue: Zhenshan97 flower, score: 91.158 |
| vg0303120371 (J) | chr03 | 3120371 | C | A | 98.80% | 0.00% | C -> A | NA |
LOC_Os03g06220.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.878; most accessible tissue: Zhenshan97 flower, score: 91.191 |
| vg0303120450 (J) | chr03 | 3120450 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g06220.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g06230.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g06210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.463; most accessible tissue: Callus, score: 94.191 |
| vg0303120493 (J) | chr03 | 3120493 | A | C | 64.50% | 0.19% | C -> A | NA |
LOC_Os03g06220.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.731; most accessible tissue: Callus, score: 94.191 |
| vg0303120517 (J) | chr03 | 3120517 | GA | G | 56.90% | 0.02% | G -> GA,GAA | NA |
LOC_Os03g06220.1 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06230.1 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g06220.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06210.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.912; most accessible tissue: Callus, score: 94.191 |
| vg0303120595 (J) | chr03 | 3120595 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os03g06230.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os03g06220.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g06210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.349; most accessible tissue: Zhenshan97 flower, score: 93.121 |
| vg0303120656 (J) | chr03 | 3120656 | T | C | 64.60% | 0.08% | C -> T | NA |
LOC_Os03g06230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g06230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.581; most accessible tissue: Minghui63 panicle, score: 91.586 |
| vg0303120925 (J) | chr03 | 3120925 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os03g06220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g06230.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.427; most accessible tissue: Callus, score: 88.675 |
| vg0303120936 (J) | chr03 | 3120936 | C | CTTCAAA TGT | 57.40% | 0.17% | CTTCAAATGT -> C | NA |
LOC_Os03g06220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.606; most accessible tissue: Callus, score: 88.675 |
| vg0303120958 (J) | chr03 | 3120958 | T | C | 57.40% | 0.00% | C -> T |
mr1026 (All); LR P-value: 1.42E-34;
mr1063 (All); LR P-value: 3.12E-56; mr1088 (All); LR P-value: 1.89E-62; mr1125 (All); LR P-value: 1.39E-49; mr1161 (All); LR P-value: 4.21E-35; mr1200 (All); LR P-value: 8.73E-42; mr1220 (All); LR P-value: 8.18E-07; mr1221 (All); LR P-value: 5.55E-30; mr1225 (All); LR P-value: 4.22E-31; mr1246 (All); LR P-value: 3.40E-63; mr1249 (All); LR P-value: 8.71E-08; mr1260 (All); LR P-value: 2.43E-08; mr1571 (All); LR P-value: 2.40E-23; mr1583 (All); LR P-value: 3.66E-15; mr1598 (All); LR P-value: 6.57E-19; mr1870 (All); LR P-value: 2.91E-15; mr1943 (All); LR P-value: 1.33E-22; mr1037_2 (All); LR P-value: 3.18E-31; mr1063_2 (All); LR P-value: 1.12E-56; mr1065_2 (All); LR P-value: 2.54E-63; mr1088_2 (All); LR P-value: 1.02E-73; mr1091_2 (All); LR P-value: 5.90E-49; mr1125_2 (All); LR P-value: 1.92E-66; mr1161_2 (All); LR P-value: 3.47E-34; mr1221_2 (All); LR P-value: 6.68E-35; mr1323_2 (All); LR P-value: 1.71E-25; mr1422_2 (All); LR P-value: 5.50E-25; mr1580_2 (All); LR P-value: 2.30E-29; mr1745_2 (All); LR P-value: 7.13E-39; mr1751_2 (All); LR P-value: 3.79E-09; mr1798_2 (All); LR P-value: 8.43E-68; mr1825_2 (All); LR P-value: 4.26E-29; mr1924_2 (All); LR P-value: 1.64E-21; mr1943_2 (All); LR P-value: 1.42E-25 |
LOC_Os03g06220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.101; most accessible tissue: Minghui63 panicle, score: 89.702 |
| vg0303120960 (J) | chr03 | 3120960 | G | A | 64.60% | 0.11% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g06220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.101; most accessible tissue: Minghui63 panicle, score: 89.702 |
| vg0303120980 (J) | chr03 | 3120980 | C | A | 64.60% | 0.23% | A -> C | NA |
LOC_Os03g06220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.184; most accessible tissue: Minghui63 panicle, score: 89.949 |
| vg0303120988 (J) | chr03 | 3120988 | T | G | 64.50% | 0.17% | G -> T | NA |
LOC_Os03g06220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.503; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg0303121010 (J) | chr03 | 3121010 | G | A | 83.00% | 0.00% | G -> A |
Heading_date (Jap_All); LR P-value: 9.82E-10;
Plant_height (Jap_All); LR P-value: 1.27E-15; mr1010 (Jap_All); LR P-value: 1.86E-06; mr1082 (Jap_All); LR P-value: 2.97E-06; mr1097 (All); LR P-value: 1.26E-10; mr1137 (Jap_All); LR P-value: 4.28E-10; mr1183 (Jap_All); LR P-value: 4.04E-06; mr1503 (Jap_All); LR P-value: 4.51E-06; mr1554 (All); LR P-value: 3.61E-07; mr1602 (All); LR P-value: 5.90E-07; mr1617 (Jap_All); LR P-value: 2.94E-07; mr1668 (All); LR P-value: 8.88E-08; mr1715 (All); LR P-value: 4.44E-19; mr1729 (All); LR P-value: 8.96E-06; mr1729 (Jap_All); LR P-value: 3.51E-06; mr1871 (All); LR P-value: 1.44E-13; mr1991 (All); LR P-value: 6.64E-06; mr1010_2 (Jap_All); LR P-value: 1.30E-07; mr1042_2 (All); LR P-value: 5.64E-20; mr1072_2 (Jap_All); LR P-value: 7.75E-06; mr1097_2 (All); LR P-value: 7.41E-14; mr1129_2 (Jap_All); LR P-value: 5.99E-06; mr1137_2 (Jap_All); LR P-value: 6.95E-11; mr1164_2 (Jap_All); LR P-value: 6.55E-06; mr1205_2 (All); LR P-value: 1.59E-07; mr1206_2 (All); LR P-value: 6.26E-06; mr1252_2 (Jap_All); LR P-value: 1.08E-06; mr1369_2 (All); LR P-value: 8.60E-07; mr1405_2 (All); LR P-value: 1.46E-06; mr1418_2 (All); LR P-value: 7.86E-07; mr1419_2 (All); LR P-value: 2.84E-06; mr1420_2 (All); LR P-value: 3.78E-06; mr1441_2 (Jap_All); LR P-value: 3.43E-06; mr1453_2 (All); LR P-value: 2.16E-07; mr1488_2 (All); LR P-value: 3.99E-07; mr1521_2 (All); LR P-value: 4.35E-13; mr1521_2 (Jap_All); LR P-value: 2.10E-07; mr1554_2 (All); LR P-value: 2.15E-07; mr1574_2 (All); LR P-value: 5.19E-06; mr1596_2 (Jap_All); LR P-value: 5.37E-06; mr1611_2 (Jap_All); LR P-value: 3.12E-11; mr1617_2 (Jap_All); LR P-value: 1.69E-08; mr1668_2 (All); LR P-value: 9.81E-08; mr1671_2 (Jap_All); LR P-value: 8.99E-07; mr1680_2 (All); LR P-value: 3.23E-12; mr1683_2 (All); LR P-value: 3.02E-07; mr1715_2 (All); LR P-value: 6.75E-17; mr1742_2 (All); LR P-value: 8.73E-13; mr1851_2 (All); LR P-value: 7.98E-10; mr1864_2 (All); LR P-value: 1.79E-13; mr1871_2 (All); LR P-value: 2.60E-21 |
LOC_Os03g06220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.161; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0303121023 (J) | chr03 | 3121023 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g06220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.235; most accessible tissue: Minghui63 panicle, score: 90.624 |
| vg0303121028 (J) | chr03 | 3121028 | G | T | 64.60% | 0.25% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g06220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.055; most accessible tissue: Minghui63 panicle, score: 91.034 |
| vg0303121030 (J) | chr03 | 3121030 | A | T | 64.60% | 0.25% | T -> A | NA |
LOC_Os03g06220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 81.741; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg0303121032 (J) | chr03 | 3121032 | A | C | 64.60% | 0.25% | C -> A | NA |
LOC_Os03g06220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 81.760; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg0303121051 (J) | chr03 | 3121051 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g06220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.910; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0303121055 (J) | chr03 | 3121055 | C | T | 64.60% | 0.21% | T -> C | NA |
LOC_Os03g06220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.421; most accessible tissue: Minghui63 panicle, score: 90.624 |
| vg0303121077 (J) | chr03 | 3121077 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g06220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g06240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g06240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g06230.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.701; most accessible tissue: Minghui63 panicle, score: 90.833 |
| vg0303121087 (J) | chr03 | 3121087 | T | C | 64.60% | 0.19% | C -> T | NA |
LOC_Os03g06220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.463; most accessible tissue: Minghui63 panicle, score: 91.034 |
| vg0303121088 (J) | chr03 | 3121088 | C | T | 64.60% | 0.19% | T -> C | NA |
LOC_Os03g06220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g06240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g06230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.479; most accessible tissue: Minghui63 panicle, score: 91.034 |
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