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=1.844e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

868 significant hits at p-value < 0.001.

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
3R	13895133	3R_13895133_SNP [dm3] 3R_18069411_SNP [dm6]	T	A	1.128e^-6	1	INTERGENIC
3R	13895159	3R_13895159_SNP [dm3] 3R_18069437_SNP [dm6]	A	C	1.455e^-6	1	INTERGENIC
3R	25135771	3R_25135771_SNP [dm3] 3R_29310049_SNP [dm6]	G	A	2.863e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco
2L	920946	2L_920946_SNP [dm3] 2L_920946_SNP [dm6]	T	C	6.511e^-6	1	INTERGENIC
2L	1107120	2L_1107120_SNP [dm3] 2L_1107120_SNP [dm6]	C	T	6.791e^-6	1	INTRON mtRNApol	TF binding site mE1_TFBS_sens
3R	25135805	3R_25135805_SNP [dm3] 3R_29310083_SNP [dm6]	T	A	8.079e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco
2R	8563519	2R_8563519_SNP [dm3] 2R_12676014_SNP [dm6]	T	G	1.075e^-5	1	UPSTREAM CG42708 INTRON CG42708	TF binding site mE1_TFBS_inv
3L	11383402	3L_11383402_SNP [dm3] 3L_11390302_SNP [dm6]	A	C	1.289e^-5	1	INTERGENIC
2L	7022271	2L_7022271_SNP [dm3] 2L_7022271_SNP [dm6]	T	A	1.302e^-5	1	SYNONYMOUS_CODING Pcp INTRON ade3
3L	13395572	3L_13395572_SNP [dm3] 3L_13402472_SNP [dm6]	C	T	1.305e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	13294440	2L_13294440_SNP [dm3] 2L_13294440_SNP [dm6]	A	G	1.365e^-5	1	INTRON CG31729	TF binding site BDTNP1_TFBS_twi
3L	12128460	3L_12128460_SNP [dm3] 3L_12135360_SNP [dm6]	G	A	1.389e^-5	1	SYNONYMOUS_CODING CG5645	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	11978780	3R_11978780_SNP [dm3] 3R_16153058_SNP [dm6]	G	T	1.461e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	21222505	3L_21222505_SNP [dm3] 3L_21229405_SNP [dm6]	T	C	1.548e^-5	1	INTRON Eip78C
2R	11168103	2R_11168103_SNP [dm3] 2R_15280598_SNP [dm6]	C	T	2.005e^-5	1	INTRON Trpm
2L	4659746	2L_4659746_SNP [dm3] 2L_4659746_SNP [dm6]	C	G	2.085e^-5	1	INTERGENIC
2L	921008	2L_921008_INS [dm3] 2L_921008_INS [dm6]	A	AAATA	2.092e^-5	1	INTERGENIC
2R	13770012	2R_13770012_SNP [dm3] 2R_17882507_SNP [dm6]	T	C	2.102e^-5	1	UPSTREAM CG30110 INTRON Elk
X	6005925	X_6005925_SNP [dm3] X_6111892_SNP [dm6]	T	A	2.146e^-5	1	INTRON Ca-alpha1T	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13395571	3L_13395571_SNP [dm3] 3L_13402471_SNP [dm6]	A	T	2.227e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2R	11168109	2R_11168109_SNP [dm3] 2R_15280604_SNP [dm6]	C	T	2.314e^-5	1	INTRON Trpm
2R	14889390	2R_14889390_SNP [dm3] 2R_19001885_SNP [dm6]	A	G	2.525e^-5	1	INTRON tn	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	24579641	3R_24579641_SNP [dm3] 3R_28753919_SNP [dm6]	C	A	2.576e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
2L	2837302	2L_2837302_SNP [dm3] 2L_2837302_SNP [dm6]	A	T	2.655e^-5	1	INTRON CG3119	TF binding site mE1_TFBS_cad
3L	7633219	3L_7633219_SNP [dm3] 3L_7640119_SNP [dm6]	A	G	2.918e^-5	1	SPLICE_SITE_REGION CG33276 DOWNSTREAM CG33275 & 2 others INTRON CG33276	TF binding site mE1_TFBS_Ubx
2R	19788814	2R_19788814_SNP [dm3] 2R_23901291_SNP [dm6]	G	A	2.931e^-5	1	SYNONYMOUS_CODING Lpt
3L	13272412	3L_13272412_SNP [dm3] 3L_13279312_SNP [dm6]	G	T	3.046e^-5	1	UTR_3_PRIME caps UPSTREAM tRNA:CR32123:Psi
2L	2308920	2L_2308920_SNP [dm3] 2L_2308920_SNP [dm6]	T	G	3.359e^-5	1	NON_SYNONYMOUS_CODING CG9967 DOWNSTREAM CG16995	TF binding site mE1_TFBS_chinmo
X	15360930	X_15360930_SNP [dm3] X_15466897_SNP [dm6]	G	A	3.364e^-5	1	NON_SYNONYMOUS_CODING CG15642 UPSTREAM CG15641 DOWNSTREAM CG6299 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_chinmo mE1_TFBS_HSA
3L	16962274	3L_16962274_SNP [dm3] 3L_16969174_SNP [dm6]	T	A	3.513e^-5	1	UPSTREAM Exn DOWNSTREAM Nc73EF INTERGENIC
3L	16962282	3L_16962282_SNP [dm3] 3L_16969182_SNP [dm6]	T	G	3.513e^-5	1	UPSTREAM Exn DOWNSTREAM Nc73EF INTERGENIC
2L	4161698	2L_4161698_SNP [dm3] 2L_4161698_SNP [dm6]	T	C	3.540e^-5	1	INTERGENIC
3L	13272545	3L_13272545_SNP [dm3] 3L_13279445_SNP [dm6]	C	G	3.603e^-5	1	UTR_3_PRIME caps UPSTREAM tRNA:CR32123:Psi
3R	13895203	3R_13895203_SNP [dm3] 3R_18069481_SNP [dm6]	A	G	3.605e^-5	1	INTERGENIC
3R	13895201	3R_13895201_SNP [dm3] 3R_18069479_SNP [dm6]	T	A	3.776e^-5	1	INTERGENIC
X	2579429	X_2579429_SNP [dm3] X_2685396_SNP [dm6]	G	A	3.904e^-5	1	UPSTREAM per INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	13384483	3L_13384483_SNP [dm3] 3L_13391383_SNP [dm6]	C	G	4.109e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_Kr
3R	20915327	3R_20915327_DEL [dm3] 3R_25089605_DEL [dm6]	TT	T	4.239e^-5	1	INTERGENIC
2R	20006383	2R_20006383_SNP [dm3] 2R_24118860_SNP [dm6]	T	A	4.428e^-5	1	INTRON CG3257	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
3R	18164960	3R_18164960_SNP [dm3] 3R_22339238_SNP [dm6]	G	A	4.463e^-5	1	INTRON CG5388	TF binding site mE1_TFBS_Trl
3L	10286066	3L_10286066_SNP [dm3] 3L_10292966_SNP [dm6]	G	A	4.513e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1040564	3L_1040564_SNP [dm3] 3L_1040564_SNP [dm6]	T	C	4.898e^-5	1	INTRON bab1	TF binding site mE1_TFBS_cad
3R	16027008	3R_16027008_SNP [dm3] 3R_20201286_SNP [dm6]	C	T	4.924e^-5	1	INTERGENIC
X	2579441	X_2579441_SNP [dm3] X_2685408_SNP [dm6]	C	T	4.967e^-5	1	UPSTREAM per INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	4162676	2L_4162676_SNP [dm3] 2L_4162676_SNP [dm6]	T	G	5.080e^-5	1	INTERGENIC
2L	2969058	2L_2969058_SNP [dm3] 2L_2969058_SNP [dm6]	G	A	5.104e^-5	1	SYNONYMOUS_CODING Ts DOWNSTREAM Rbp9 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	1746707	2L_1746707_SNP [dm3] 2L_1746707_SNP [dm6]	T	C	5.299e^-5	1	INTRON CG17646
3L	4509910	3L_4509910_SNP [dm3] 3L_4509910_SNP [dm6]	A	C	5.314e^-5	1	DOWNSTREAM Tie INTERGENIC
2L	3821084	2L_3821084_SNP [dm3] 2L_3821084_SNP [dm6]	G	A	5.410e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad
2R	6089561	2R_6089561_SNP [dm3] 2R_10202056_SNP [dm6]	C	T	5.468e^-5	1	INTERGENIC
2L	8781605	2L_8781605_SNP [dm3] 2L_8781605_SNP [dm6]	A	G	5.530e^-5	1	UPSTREAM CG9468 DOWNSTREAM CG42710 INTERGENIC
2L	16338419	2L_16338419_SNP [dm3] 2L_16338419_SNP [dm6]	A	T	5.722e^-5	1	SYNONYMOUS_CODING CG42266 UPSTREAM CG31817	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1040526	3L_1040526_SNP [dm3] 3L_1040526_SNP [dm6]	C	A	5.813e^-5	1	INTRON bab1	TF binding site mE1_TFBS_cad
X	6007635	X_6007635_SNP [dm3] X_6113602_SNP [dm6]	G	A	5.961e^-5	1	SYNONYMOUS_CODING Ca-alpha1T	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19558138	2R_19558138_SNP [dm3] 2R_23670615_SNP [dm6]	G	A	6.456e^-5	1	INTRON Pde8	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	25138178	3R_25138178_SNP [dm3] 3R_29312456_SNP [dm6]	T	A	6.548e^-5	1	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_hkb mE1_TFBS_sens
2R	20477099	2R_20477099_SNP [dm3] 2R_24589576_SNP [dm6]	G	T	6.675e^-5	1	INTRON pio
3L	12529233	3L_12529233_SNP [dm3] 3L_12536133_SNP [dm6]	C	T	7.040e^-5	1	SYNONYMOUS_CODING CG4069 DOWNSTREAM CG10688	TF binding site mE1_TFBS_cad
3L	15223405	3L_15223405_INS [dm3] 3L_15230305_INS [dm6]	A	AA	7.206e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
3L	10286073	3L_10286073_SNP [dm3] 3L_10292973_SNP [dm6]	A	G	7.480e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	19224838	3R_19224838_SNP [dm3] 3R_23399116_SNP [dm6]	G	A	7.571e^-5	1	DOWNSTREAM CR44323 INTERGENIC
2R	11566897	2R_11566897_SNP [dm3] 2R_15679392_SNP [dm6]	T	C	8.063e^-5	1	UPSTREAM CG8207 DOWNSTREAM Vha14-1 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	20518050	2R_20518050_SNP [dm3] 2R_24630527_SNP [dm6]	A	T	8.277e^-5	1	UPSTREAM Cyp9c1 DOWNSTREAM CR43787 INTRON CG13594
2L	921028	2L_921028_INS [dm3] 2L_921028_INS [dm6]	A	ACA	8.379e^-5	1	INTERGENIC
2L	921047	2L_921047_SNP [dm3] 2L_921047_SNP [dm6]	T	C	8.379e^-5	1	INTERGENIC
2R	8562576	2R_8562576_SNP [dm3] 2R_12675071_SNP [dm6]	A	T	8.762e^-5	1	SYNONYMOUS_CODING CG42708 UPSTREAM CG42708 INTRON CG42708
3R	5225240	3R_5225240_SNP [dm3] 3R_9399518_SNP [dm6]	G	C	9.208e^-5	1	SYNONYMOUS_CODING Or85f DOWNSTREAM CG34117 & 1 other	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	13771343	2R_13771343_SNP [dm3] 2R_17883838_SNP [dm6]	T	C	9.622e^-5	1	INTRON Elk
2R	20425599	2R_20425599_SNP [dm3] 2R_24538076_SNP [dm6]	A	G	9.811e^-5	1	INTRON CG4622 & 1 other
2L	1107210	2L_1107210_SNP [dm3] 2L_1107210_SNP [dm6]	T	A	9.825e^-5	1	NON_SYNONYMOUS_CODING mtRNApol	TF binding site mE1_TFBS_sens
2R	8438940	2R_8438940_SNP [dm3] 2R_12551435_SNP [dm6]	T	A	9.852e^-5	1	INTRON fra
2R	8438944	2R_8438944_SNP [dm3] 2R_12551439_SNP [dm6]	G	C	9.852e^-5	1	INTRON fra
2L	4659832	2L_4659832_SNP [dm3] 2L_4659832_SNP [dm6]	T	C	9.951e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	8563587	2R_8563587_SNP [dm3] 2R_12676082_SNP [dm6]	A	G	9.957e^-5	1	UPSTREAM CG42708 INTRON CG42708	TF binding site mE1_TFBS_inv
2R	8563592	2R_8563592_SNP [dm3] 2R_12676087_SNP [dm6]	A	G	9.957e^-5	1	UPSTREAM CG42708 INTRON CG42708	TF binding site mE1_TFBS_inv
3L	6179603	3L_6179603_SNP [dm3] 3L_6186503_SNP [dm6]	G	A	1.011e^-4	1	SYNONYMOUS_CODING D19A DOWNSTREAM CG43293	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10630439	2L_10630439_SNP [dm3] 2L_10630439_SNP [dm6]	T	C	1.017e^-4	1	SYNONYMOUS_CODING CG7329	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	20518051	2R_20518051_SNP [dm3] 2R_24630528_SNP [dm6]	C	T	1.035e^-4	1	UPSTREAM Cyp9c1 DOWNSTREAM CR43787 INTRON CG13594
3L	1142391	3L_1142391_SNP [dm3] 3L_1142391_SNP [dm6]	T	C	1.085e^-4	1	SYNONYMOUS_CODING bab2	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
X	4433154	X_4433154_SNP [dm3] X_4539121_SNP [dm6]	C	T	1.086e^-4	1	SYNONYMOUS_CODING rb INTRON CR32773	TF binding site mE1_TFBS_sens
3R	11860790	3R_11860790_SNP [dm3] 3R_16035068_SNP [dm6]	T	C	1.106e^-4	1	UTR_5_PRIME pnr INTRON pnr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll mE1_TFBS_HSA
2L	4659873	2L_4659873_SNP [dm3] 2L_4659873_SNP [dm6]	A	T	1.111e^-4	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	19426809	2R_19426809_SNP [dm3] 2R_23539286_SNP [dm6]	A	C	1.118e^-4	1	SYNONYMOUS_CODING ppk3 UPSTREAM bw	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13384485	3L_13384485_SNP [dm3] 3L_13391385_SNP [dm6]	G	T	1.127e^-4	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_Kr
2R	7376323	2R_7376323_SNP [dm3] 2R_11488818_SNP [dm6]	G	T	1.149e^-4	1	INTRON inv
X	16131469	X_16131469_SNP [dm3] X_16237436_SNP [dm6]	G	T	1.176e^-4	1	INTERGENIC
3L	1850676	3L_1850676_SNP [dm3] 3L_1850676_SNP [dm6]	T	A	1.176e^-4	1	DOWNSTREAM CG13936 INTERGENIC
2L	6902654	2L_6902654_SNP [dm3] 2L_6902654_SNP [dm6]	G	T	1.179e^-4	1	DOWNSTREAM mir-932 INTRON Nlg2
X	10809696	X_10809696_SNP [dm3] X_10915663_SNP [dm6]	C	G	1.180e^-4	1	SYNONYMOUS_CODING CG43901 INTRON CG43901	TF binding site mE1_TFBS_chinmo
3R	13817840	3R_13817840_SNP [dm3] 3R_17992118_SNP [dm6]	A	T	1.185e^-4	1	INTRON cpo
3R	5225193	3R_5225193_SNP [dm3] 3R_9399471_SNP [dm6]	T	C	1.193e^-4	1	DOWNSTREAM CG34117 & 1 other INTRON Or85f	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	9523928	3L_9523928_SNP [dm3] 3L_9530828_SNP [dm6]	A	T	1.205e^-4	1	SYNONYMOUS_CODING Or67a
X	6007458	X_6007458_SNP [dm3] X_6113425_SNP [dm6]	A	G	1.207e^-4	1	SYNONYMOUS_CODING Ca-alpha1T	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12961774	2L_12961774_INS [dm3] 2L_12961774_INS [dm6]	A	AA	1.207e^-4	1	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	10809504	3R_10809504_SNP [dm3] 3R_14983782_SNP [dm6]	T	A	1.213e^-4	1	INTERGENIC
2L	19899604	2L_19899604_SNP [dm3] 2L_19899604_SNP [dm6]	T	C	1.265e^-4	1	INTRON sick	TF binding site mE1_TFBS_HSA
2L	3328783	2L_3328783_SNP [dm3] 2L_3328783_SNP [dm6]	A	C	1.270e^-4	1	NON_SYNONYMOUS_CODING CG33282
3R	11293692	3R_11293692_SNP [dm3] 3R_15467970_SNP [dm6]	T	C	1.273e^-4	1	INTRON AdamTS-A
2L	922510	2L_922510_DEL [dm3] 2L_922510_DEL [dm6]	AAATATA	A	1.279e^-4	1	UPSTREAM CG4341 INTERGENIC
2R	14825880	2R_14825880_SNP [dm3] 2R_18938375_SNP [dm6]	T	C	1.295e^-4	1	INTRON sano

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Missing results

By genomic position
Variant impact
Gene name

pc_KP_PElem_GC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results