DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=1.132e^-2)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_2L_t	0.01208
In_2R_NS	0.02021

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.3914	0.0151
In_2R_NS	6.1328	0.0466

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1999 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	16532066	3L_16532066_DEL [dm3] 3L_16538966_DEL [dm6]	CA	C	6.559e^-7	0.292	INTRON CG43373
2R	15248610	2R_15248610_SNP [dm3] 2R_19361105_SNP [dm6]	A	C	6.770e^-7	0.292	SYNONYMOUS_CODING CG11961
2R	15248616	2R_15248616_SNP [dm3] 2R_19361111_SNP [dm6]	T	C	6.770e^-7	0.292	SYNONYMOUS_CODING CG11961
3L	16532158	3L_16532158_SNP [dm3] 3L_16539058_SNP [dm6]	C	G	6.961e^-7	0.292	INTRON CG43373
X	10855844	X_10855844_SNP [dm3] X_10961811_SNP [dm6]	G	A	8.863e^-7	0.292	INTRON Myo10A
3R	11018344	3R_11018344_SNP [dm3] 3R_15192622_SNP [dm6]	T	G	1.061e^-6	0.292	SYNONYMOUS_CODING CG6752 UPSTREAM mir-3644
2L	9405390	2L_9405390_SNP [dm3] 2L_9405390_SNP [dm6]	G	A	1.091e^-6	0.292	INTRON Shawl
2R	16304273	2R_16304273_SNP [dm3] 2R_20416768_SNP [dm6]	C	A	3.948e^-6	0.843	INTERGENIC
2L	580962	2L_580962_SNP [dm3] 2L_580962_SNP [dm6]	A	G	4.048e^-6	0.843	INTERGENIC
2L	7958966	2L_7958966_SNP [dm3] 2L_7958966_SNP [dm6]	G	T	4.997e^-6	0.876	INTRON Snoo
3L	16532177	3L_16532177_SNP [dm3] 3L_16539077_SNP [dm6]	C	A	5.153e^-6	0.876	INTRON CG43373
2R	12680355	2R_12680355_SNP [dm3] 2R_16792850_SNP [dm6]	T	A	5.793e^-6	0.876	DOWNSTREAM CG15615 & 1 other INTRON CG15919
2R	10178671	2R_10178671_SNP [dm3] 2R_14291166_SNP [dm6]	T	C	6.579e^-6	0.876	NON_SYNONYMOUS_CODING Ih UTR_5_PRIME Ih UPSTREAM Ih	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_inv
2R	16114803	2R_16114803_SNP [dm3] 2R_20227298_SNP [dm6]	A	G	6.695e^-6	0.876	INTERGENIC
2R	15248685	2R_15248685_SNP [dm3] 2R_19361180_SNP [dm6]	C	G	7.347e^-6	0.876	SYNONYMOUS_CODING CG11961
2R	17397098	2R_17397098_SNP [dm3] 2R_21509593_SNP [dm6]	G	T	8.149e^-6	0.876	INTRON MESK2
2R	10536054	2R_10536054_SNP [dm3] 2R_14648549_SNP [dm6]	C	G	8.155e^-6	0.876	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18104074	3L_18104074_SNP [dm3] 3L_18110974_SNP [dm6]	A	G	8.405e^-6	0.876	SYNONYMOUS_CODING mus304	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	19129166	2L_19129166_INS [dm3] 2L_19129166_INS [dm6]	T	TGATTT	8.984e^-6	0.887	UTR_3_PRIME l_2_37Cd DOWNSTREAM Aats-asn	TF binding site mE1_TFBS_cad
3L	8949995	3L_8949995_SNP [dm3] 3L_8956895_SNP [dm6]	T	A	9.887e^-6	0.895	DOWNSTREAM GNBP3 INTRON mRpL12	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	12680354	2R_12680354_SNP [dm3] 2R_16792849_SNP [dm6]	C	T	1.206e^-5	0.895	DOWNSTREAM CG15615 & 1 other INTRON CG15919
3R	10807234	3R_10807234_SNP [dm3] 3R_14981512_SNP [dm6]	C	G	1.356e^-5	0.895	INTERGENIC
2R	14753586	2R_14753586_SNP [dm3] 2R_18866081_SNP [dm6]	G	A	1.515e^-5	0.895	SYNONYMOUS_CODING Dpt UPSTREAM CG43071
2L	16303852	2L_16303852_SNP [dm3] 2L_16303852_SNP [dm6]	C	T	1.571e^-5	0.895	SYNONYMOUS_CODING c_2_M UPSTREAM CG5869
2R	6975347	2R_6975347_INS [dm3] 2R_11087842_INS [dm6]	T	TCGTCTAGGTT...	1.627e^-5	0.895	UPSTREAM CG43189 INTRON luna & 1 other	TF binding site mE1_TFBS_Kr
2R	17685083	2R_17685083_DEL [dm3] 2R_21797578_DEL [dm6]	GTC	G	1.699e^-5	0.895	DOWNSTREAM CG34204 & 1 other INTERGENIC
2L	3222769	2L_3222769_SNP [dm3] 2L_3222769_SNP [dm6]	T	A	1.738e^-5	0.895	INTERGENIC
X	9803224	X_9803224_DEL [dm3] X_9909191_DEL [dm6]	ATCTTAAGTA	A	1.788e^-5	0.895	UTR_3_PRIME CG1986 DOWNSTREAM CG1986	insulator Insulator_Class_II.mE01
2R	12786317	2R_12786317_SNP [dm3] 2R_16898812_SNP [dm6]	A	G	1.804e^-5	0.895	SYNONYMOUS_CODING inaC
X	8578764	X_8578764_INS [dm3] X_8684731_INS [dm6]	T	TC	1.816e^-5	0.895	UPSTREAM CG11284 INTRON CG11284
2L	11937868	2L_11937868_SNP [dm3] 2L_11937868_SNP [dm6]	G	A	1.920e^-5	0.895	UPSTREAM Or33c DOWNSTREAM Or33b INTERGENIC	TF binding site mE1_TFBS_cad
3R	18590013	3R_18590013_SNP [dm3] 3R_22764291_SNP [dm6]	A	C	1.955e^-5	0.895	SYNONYMOUS_CODING CG4721 UPSTREAM CG4723 INTRON Usp12-46 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	14753589	2R_14753589_SNP [dm3] 2R_18866084_SNP [dm6]	C	A	2.067e^-5	0.895	NON_SYNONYMOUS_CODING Dpt UPSTREAM CG43071
X	9803405	X_9803405_SNP [dm3] X_9909372_SNP [dm6]	C	T	2.175e^-5	0.895	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
3L	16282719	3L_16282719_SNP [dm3] 3L_16289619_SNP [dm6]	T	G	2.192e^-5	0.895	DOWNSTREAM CG13045 INTERGENIC
2R	17378918	2R_17378918_SNP [dm3] 2R_21491413_SNP [dm6]	T	G	2.211e^-5	0.895	INTRON Fkbp14
2L	533659	2L_533659_SNP [dm3] 2L_533659_SNP [dm6]	T	C	2.242e^-5	0.895	INTRON ush	TF binding site mE1_TFBS_inv
X	5516317	X_5516317_SNP [dm3] X_5622284_SNP [dm6]	G	A	2.273e^-5	0.895	SPLICE_SITE_REGION Mlc-c UPSTREAM l_1_G0045 DOWNSTREAM mir-3645 INTRON Mlc-c EXON mir-3645	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	18038355	2R_18038355_INS [dm3] 2R_22150850_INS [dm6]	A	ATA	2.293e^-5	0.895	INTRON a
2R	3529348	2R_3529348_SNP [dm3] 2R_7641843_SNP [dm6]	A	G	2.311e^-5	0.895	NON_SYNONYMOUS_CODING CG43340 INTRON CG43340	TF binding site mE1_TFBS_cad
2L	11158255	2L_11158255_SNP [dm3] 2L_11158255_SNP [dm6]	G	A	2.376e^-5	0.895	UTR_3_PRIME Ca-beta DOWNSTREAM Ca-beta
2R	18452463	2R_18452463_SNP [dm3] 2R_22564958_SNP [dm6]	C	T	2.465e^-5	0.895	SYNONYMOUS_CODING dnr1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26080981	3R_26080981_SNP [dm3] 3R_30255259_SNP [dm6]	C	A	2.539e^-5	0.895	INTERGENIC
2R	15248383	2R_15248383_SNP [dm3] 2R_19360878_SNP [dm6]	T	C	2.545e^-5	0.895	SYNONYMOUS_CODING CG11961	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	7402798	2R_7402798_SNP [dm3] 2R_11515293_SNP [dm6]	A	T	2.705e^-5	0.895	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	19037162	3R_19037162_SNP [dm3] 3R_23211440_SNP [dm6]	G	T	2.748e^-5	0.895	INTRON cnc	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	7619434	2L_7619434_SNP [dm3] 2L_7619434_SNP [dm6]	C	A	2.868e^-5	0.895	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	17230695	2R_17230695_SNP [dm3] 2R_21343190_SNP [dm6]	C	A	2.886e^-5	0.895	SYNONYMOUS_CODING CG15666
2R	17924105	2R_17924105_SNP [dm3] 2R_22036600_SNP [dm6]	A	C	2.902e^-5	0.895	DOWNSTREAM CG9308 INTRON CG34370
2L	20958231	2L_20958231_SNP [dm3] 2L_20958231_SNP [dm6]	T	A	2.954e^-5	0.895	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	17231213	2R_17231213_SNP [dm3] 2R_21343708_SNP [dm6]	T	A	2.972e^-5	0.895	INTRON CG15666
X	11667828	X_11667828_SNP [dm3] X_11773795_SNP [dm6]	T	A	3.028e^-5	0.895	INTRON dy
2R	14752617	2R_14752617_SNP [dm3] 2R_18865112_SNP [dm6]	T	G	3.072e^-5	0.895	UPSTREAM Dpt DOWNSTREAM CG43070 INTRON CG43071
3L	18115607	3L_18115607_SNP [dm3] 3L_18122507_SNP [dm6]	A	T	3.076e^-5	0.895	UPSTREAM CG42853 INTERGENIC
2R	20128717	2R_20128717_SNP [dm3] 2R_24241194_SNP [dm6]	C	A	3.081e^-5	0.895	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	15248394	2R_15248394_SNP [dm3] 2R_19360889_SNP [dm6]	T	C	3.082e^-5	0.895	SYNONYMOUS_CODING CG11961	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	7231135	3L_7231135_SNP [dm3] 3L_7238035_SNP [dm6]	A	T	3.126e^-5	0.895	NON_SYNONYMOUS_CODING CG14829 UPSTREAM BHD	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	9886390	3L_9886390_SNP [dm3] 3L_9893290_SNP [dm6]	C	T	3.183e^-5	0.895	UTR_3_PRIME CalpB & 2 others DOWNSTREAM CG14164 & 1 other
2R	18182229	2R_18182229_SNP [dm3] 2R_22294724_SNP [dm6]	T	G	3.196e^-5	0.895	SYNONYMOUS_CODING CG5819	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	6340801	2R_6340801_SNP [dm3] 2R_10453296_SNP [dm6]	C	T	3.269e^-5	0.895	UPSTREAM Cyp49a1 INTRON Galphao & 1 other
2R	15248382	2R_15248382_SNP [dm3] 2R_19360877_SNP [dm6]	T	C	3.291e^-5	0.895	SYNONYMOUS_CODING CG11961	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	16258329	X_16258329_SNP [dm3] X_16364296_SNP [dm6]	T	C	3.305e^-5	0.895	SYNONYMOUS_CODING nonA	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	12681104	2R_12681104_SNP [dm3] 2R_16793599_SNP [dm6]	C	A	3.306e^-5	0.895	SYNONYMOUS_CODING CG15615 DOWNSTREAM CG15919
3R	10807767	3R_10807767_SNP [dm3] 3R_14982045_SNP [dm6]	G	A	3.307e^-5	0.895	INTERGENIC
3L	1363811	3L_1363811_INS [dm3] 3L_1363811_INS [dm6]	C	CT	3.308e^-5	0.895	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2R	16175836	2R_16175836_SNP [dm3] 2R_20288331_SNP [dm6]	T	G	3.369e^-5	0.895	UTR_3_PRIME CG34199 DOWNSTREAM Cpr56F
2L	16628423	2L_16628423_SNP [dm3] 2L_16628423_SNP [dm6]	T	C	3.378e^-5	0.895	DOWNSTREAM CR44151 INTRON CG42389	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	15248486	2R_15248486_SNP [dm3] 2R_19360981_SNP [dm6]	A	C	3.404e^-5	0.895	INTRON CG11961	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	9803183	X_9803183_SNP [dm3] X_9909150_SNP [dm6]	A	G	3.458e^-5	0.895	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
3L	4074310	3L_4074310_SNP [dm3] 3L_4074310_SNP [dm6]	T	C	3.471e^-5	0.895	UTR_3_PRIME Gad1 UPSTREAM Faa
2R	15248397	2R_15248397_SNP [dm3] 2R_19360892_SNP [dm6]	C	T	3.528e^-5	0.895	SYNONYMOUS_CODING CG11961	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	581295	2L_581295_SNP [dm3] 2L_581295_SNP [dm6]	T	C	3.537e^-5	0.895	INTERGENIC
3L	2292149	3L_2292149_SNP [dm3] 3L_2292149_SNP [dm6]	T	G	3.564e^-5	0.895	INTRON MsR2
2L	7781627	2L_7781627_SNP [dm3] 2L_7781627_SNP [dm6]	G	A	3.633e^-5	0.895	UTR_5_PRIME CG7164 DOWNSTREAM Uro	TF binding site mE1_TFBS_cad
X	10681768	X_10681768_SNP [dm3] X_10787735_SNP [dm6]	A	T	3.670e^-5	0.895	UPSTREAM sesB & 1 other DOWNSTREAM Imp INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	6026096	2L_6026096_SNP [dm3] 2L_6026096_SNP [dm6]	G	A	3.733e^-5	0.895	INTRON CG9109
3R	7125049	3R_7125049_SNP [dm3] 3R_11299327_SNP [dm6]	A	T	3.745e^-5	0.895	INTRON CR31386
2R	16114766	2R_16114766_SNP [dm3] 2R_20227261_SNP [dm6]	G	T	3.814e^-5	0.895	INTERGENIC
3L	15077130	3L_15077130_SNP [dm3] 3L_15084030_SNP [dm6]	T	C	3.816e^-5	0.895	NON_SYNONYMOUS_CODING cp309	TF binding site mE1_TFBS_cad
X	11687956	X_11687956_SNP [dm3] X_11793923_SNP [dm6]	C	A	3.904e^-5	0.895	INTRON CkIIbeta	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_sens
3R	24863791	3R_24863791_SNP [dm3] 3R_29038069_SNP [dm6]	C	A	3.931e^-5	0.895	INTRON Slu7	TF binding site mE1_TFBS_sens
2R	8822651	2R_8822651_SNP [dm3] 2R_12935146_SNP [dm6]	A	C	3.956e^-5	0.895	INTRON CG13322	TF binding site mE1_TFBS_inv mE1_TFBS_sens
3L	11628555	3L_11628555_SNP [dm3] 3L_11635455_SNP [dm6]	C	T	3.960e^-5	0.895	INTRON CG32091
3L	11390032	3L_11390032_SNP [dm3] 3L_11396932_SNP [dm6]	C	T	4.009e^-5	0.895	UPSTREAM CG44362 INTERGENIC
X	9803438	X_9803438_SNP [dm3] X_9909405_SNP [dm6]	G	A	4.168e^-5	0.902	UTR_3_PRIME CG1986
2L	12516588	2L_12516588_SNP [dm3] 2L_12516588_SNP [dm6]	A	G	4.182e^-5	0.902	SYNONYMOUS_CODING bun INTRON bun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12883596	3L_12883596_SNP [dm3] 3L_12890496_SNP [dm6]	C	T	4.265e^-5	0.902	UPSTREAM CR45748 INTRON CG43894
3L	12883597	3L_12883597_SNP [dm3] 3L_12890497_SNP [dm6]	G	A	4.265e^-5	0.902	UPSTREAM CR45748 INTRON CG43894
3R	19431888	3R_19431888_SNP [dm3] 3R_23606166_SNP [dm6]	T	G	4.315e^-5	0.902	UTR_3_PRIME CG31145 UPSTREAM CG10184 DOWNSTREAM CG31145
3L	5495045	3L_5495045_SNP [dm3] 3L_5501945_SNP [dm6]	G	A	4.620e^-5	0.902	UPSTREAM CR44519 INTERGENIC
2R	1316513	2R_1316513_SNP [dm3] 2R_5429008_SNP [dm6]	G	A	4.728e^-5	0.902	INTRON laccase2	transposable element FlyBase
X	6965031	X_6965031_SNP [dm3] X_7070998_SNP [dm6]	T	C	4.729e^-5	0.902	INTRON CG4607
2R	12085705	2R_12085705_SNP [dm3] 2R_16198200_SNP [dm6]	C	T	4.734e^-5	0.902	SYNONYMOUS_CODING CG44243 UTR_3_PRIME CG42837	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8467604	2R_8467604_SNP [dm3] 2R_12580099_SNP [dm6]	A	T	4.782e^-5	0.902	INTRON Sin3A
2L	901470	2L_901470_SNP [dm3] 2L_901470_SNP [dm6]	T	A	4.786e^-5	0.902	DOWNSTREAM snRNA:U1:21D & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	1710777	3L_1710777_SNP [dm3] 3L_1710777_SNP [dm6]	G	T	4.862e^-5	0.902	INTRON CG7991	TF binding site mE1_TFBS_chinmo
X	19887748	X_19887748_SNP [dm3] X_19993715_SNP [dm6]	A	G	4.972e^-5	0.902	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	9714769	3L_9714769_SNP [dm3] 3L_9721669_SNP [dm6]	T	G	5.113e^-5	0.902	SYNONYMOUS_CODING nbs UTR_3_PRIME nbs	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	13980790	2L_13980790_SNP [dm3] 2L_13980790_SNP [dm6]	T	G	5.134e^-5	0.902	SYNONYMOUS_CODING NimC2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_cad
2L	9646224	2L_9646224_SNP [dm3] 2L_9646224_SNP [dm6]	T	C	5.189e^-5	0.902	INTRON Apoltp

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By genomic position
Variant impact
Gene name

pc_Surv_PRettgeriADJ phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results