7 variations found. LOC_Os08g18850 (hypothetical protein), ranging from 11,251,537 bp to 11,251,841 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811251553 (J) | chr08 | 11251553 | T | C | 91.00% | 0.00% | T -> C | NA |
LOC_Os08g18850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.984; most accessible tissue: Zhenshan97 panicle, score: 24.575 |
| vg0811251629 (J) | chr08 | 11251629 | A | T | 18.20% | 47.33% | A -> T | NA |
LOC_Os08g18850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g18850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g18850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.934; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0811251630 (J) | chr08 | 11251630 | T | C | 17.40% | 53.53% | T -> C |
Heading_date (All); LR P-value: 7.83E-10;
Spikelet_length (All); LR P-value: 2.00E-16; Spikelet_length (Jap_All); LR P-value: 1.25E-12; mr1137 (All); LR P-value: 1.62E-32; mr1137 (Jap_All); LR P-value: 9.48E-09; mr1576 (All); LR P-value: 6.93E-06; mr1708 (All); LR P-value: 1.04E-06; mr1864 (Jap_All); LR P-value: 5.81E-10; mr1043_2 (Jap_All); LR P-value: 5.95E-06; mr1115_2 (All); LR P-value: 1.57E-27; mr1115_2 (Jap_All); LR P-value: 3.55E-15; mr1129_2 (Jap_All); LR P-value: 4.79E-06; mr1137_2 (All); LR P-value: 4.44E-35; mr1229_2 (All); LR P-value: 1.43E-06; mr1229_2 (Jap_All); LR P-value: 7.95E-07; mr1251_2 (Jap_All); LR P-value: 1.40E-09; mr1252_2 (All); LR P-value: 3.23E-07; mr1252_2 (Jap_All); LR P-value: 8.78E-06; mr1404_2 (Jap_All); LR P-value: 4.71E-06; mr1435_2 (Jap_All); LR P-value: 1.45E-09; mr1502_2 (Jap_All); LR P-value: 2.13E-07; mr1521_2 (Jap_All); LR P-value: 3.73E-09; mr1555_2 (All); LR P-value: 2.58E-06; mr1570_2 (Jap_All); LR P-value: 4.68E-07; mr1580_2 (Jap_All); LR P-value: 6.84E-10; mr1596_2 (Jap_All); LR P-value: 7.79E-06; mr1611_2 (All); LR P-value: 4.10E-24; mr1611_2 (Jap_All); LR P-value: 1.63E-12; mr1671_2 (Jap_All); LR P-value: 5.71E-07; mr1693_2 (All); LR P-value: 1.92E-07; mr1693_2 (Jap_All); LR P-value: 1.53E-06; mr1746_2 (All); LR P-value: 1.16E-16; mr1746_2 (Jap_All); LR P-value: 5.05E-09; mr1789_2 (All); LR P-value: 7.22E-29; mr1800_2 (All); LR P-value: 4.80E-14; mr1825_2 (Jap_All); LR P-value: 2.43E-09; mr1844_2 (All); LR P-value: 3.80E-11; mr1880_2 (All); LR P-value: 2.35E-07; mr1880_2 (Jap_All); LR P-value: 1.21E-07 |
LOC_Os08g18850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g18850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g18850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.934; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0811251643 (J) | chr08 | 11251643 | A | G | 53.90% | 0.21% | A -> G | NA |
LOC_Os08g18860.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g18850.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0811251683 (J) | chr08 | 11251683 | G | A | 98.90% | 0.00% | G -> A |
LOC_Os08g18850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 14.368; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
|
| vg0811251725 (J) | chr08 | 11251725 | G | T | 50.50% | 0.02% | T -> G | NA |
LOC_Os08g18850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g18850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.917; most accessible tissue: Zhenshan97 panicle, score: 36.038 |
| vg0811251746 (J) | chr08 | 11251746 | G | T | 98.00% | 0.00% | G -> T,A | NA |
LOC_Os08g18850.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os08g18850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 13.727; most accessible tissue: Zhenshan97 panicle, score: 36.038 |