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=4.993e^-20)
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
wolba	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	109.6159	1.1894e-25
In_2L_t	8.1409	0.0171

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

99 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

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
X	5790742	X_5790742_SNP [dm3] X_5896709_SNP [dm6]	A	C	6.215e^-10	0.001	INTRON CR45668	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6847092	3L_6847092_SNP [dm3] 3L_6853992_SNP [dm6]	C	A	6.107e^-9	0.006	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	16881030	3R_16881030_SNP [dm3] 3R_21055308_SNP [dm6]	A	G	1.080e^-8	0.007	INTRON Mvl
3R	27053219	3R_27053219_SNP [dm3] 3R_31227497_SNP [dm6]	G	A	2.615e^-8	0.012	SYNONYMOUS_CODING CG12054 INTRON CG12054	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1392135	3L_1392135_SNP [dm3] 3L_1392135_SNP [dm6]	T	G	3.099e^-7	0.116	INTRON Ptp61F	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3889922	2L_3889922_SNP [dm3] 2L_3889922_SNP [dm6]	A	T	4.443e^-7	0.139	UTR_5_PRIME capu INTRON capu	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk
X	17046982	X_17046982_SNP [dm3] X_17152949_SNP [dm6]	G	A	6.836e^-7	0.183	INTRON xmas-1
X	18743909	X_18743909_SNP [dm3] X_18849876_SNP [dm6]	T	C	9.858e^-7	0.231	SPLICE_SITE_REGION CG34422 INTRON CG34422
X	21207647	X_21207647_DEL [dm3] X_21336620_DEL [dm6]	TTGGAAATTATTG...	AAAAA	1.341e^-6	0.279	INTRON tty
X	5612373	X_5612373_SNP [dm3] X_5718340_SNP [dm6]	G	T	1.636e^-6	0.307	UPSTREAM CG33080 INTERGENIC
3R	7108951	3R_7108951_SNP [dm3] 3R_11283229_SNP [dm6]	T	C	2.556e^-6	0.434	INTRON CR31386
X	16338819	X_16338819_SNP [dm3] X_16444786_SNP [dm6]	C	A	2.778e^-6	0.434	UTR_3_PRIME rngo DOWNSTREAM eIF-2alpha	TF binding site mE1_TFBS_cad
3L	1273379	3L_1273379_SNP [dm3] 3L_1273379_SNP [dm6]	G	A	3.774e^-6	0.544	INTRON CG9134
3R	7760319	3R_7760319_SNP [dm3] 3R_11934597_SNP [dm6]	C	A	4.582e^-6	0.591	DOWNSTREAM CG14731 INTRON Cad87A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	3062016	X_3062016_SNP [dm3] X_3167983_SNP [dm6]	G	A	4.852e^-6	0.591	SYNONYMOUS_CODING N	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	2683247	3L_2683247_SNP [dm3] 3L_2683247_SNP [dm6]	G	C	5.122e^-6	0.591	INTRON Fife
X	7539133	X_7539133_SNP [dm3] X_7645100_SNP [dm6]	G	T	5.533e^-6	0.591	INTRON ct
X	8436972	X_8436972_SNP [dm3] X_8542939_SNP [dm6]	A	T	5.674e^-6	0.591	INTRON Nrg
X	10126549	X_10126549_DEL [dm3] X_10232516_DEL [dm6]	CC	C	9.869e^-6	0.877	UTR_5_PRIME Ipod UPSTREAM Ipod DOWNSTREAM Hk
X	903384	X_903384_SNP [dm3] X_1009351_SNP [dm6]	G	C	1.204e^-5	0.877	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_chinmo
X	2321563	X_2321563_SNP [dm3] X_2427530_SNP [dm6]	G	A	1.722e^-5	0.877	SYNONYMOUS_CODING gt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi
X	10191703	X_10191703_SNP [dm3] X_10297670_SNP [dm6]	T	A	1.843e^-5	0.877	INTRON alpha-Man-I
X	10041900	X_10041900_SNP [dm3] X_10147867_SNP [dm6]	G	A	1.965e^-5	0.877	INTRON CR44894 & 1 other
3R	15849591	3R_15849591_SNP [dm3] 3R_20023869_SNP [dm6]	T	A	2.482e^-5	0.877	INTRON psidin	TF binding site mE1_TFBS_cad
3L	459685	3L_459685_SNP [dm3] 3L_459685_SNP [dm6]	T	C	2.628e^-5	0.877	INTRON klar
3L	2432308	3L_2432308_SNP [dm3] 3L_2432308_SNP [dm6]	A	C	2.893e^-5	0.877	INTRON CG45186
3L	8758535	3L_8758535_SNP [dm3] 3L_8765435_SNP [dm6]	C	G	3.503e^-5	0.877	INTRON Fhos	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	18464207	X_18464207_SNP [dm3] X_18570174_SNP [dm6]	A	C	4.575e^-5	0.877	INTRON Bx	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo
3R	1795192	3R_1795192_SNP [dm3] 3R_5969470_SNP [dm6]	G	T	5.118e^-5	0.877	UPSTREAM CR44926 INTERGENIC
X	15059199	X_15059199_INS [dm3] X_15165166_INS [dm6]	T	TT	5.463e^-5	0.877	INTERGENIC
3L	9655038	3L_9655038_SNP [dm3] 3L_9661938_SNP [dm6]	T	C	5.809e^-5	0.877	INTRON fry	TF binding site BDTNP1_TFBS_twi
3L	4097139	3L_4097139_INS [dm3] 3L_4097139_INS [dm6]	A	ACA	6.193e^-5	0.877	INTRON CG14995	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
X	9590072	X_9590072_SNP [dm3] X_9696039_SNP [dm6]	T	C	8.424e^-5	0.877	SYNONYMOUS_CODING btd	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	21874117	X_21874117_SNP [dm3] X_22472281_SNP [dm6]	G	A	8.798e^-5	0.877	UPSTREAM CG14613 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	13737890	3R_13737890_SNP [dm3] 3R_17912168_SNP [dm6]	C	A	9.423e^-5	0.877	DOWNSTREAM CG43445 INTRON Rim
X	16947482	X_16947482_SNP [dm3] X_17053449_SNP [dm6]	T	A	9.590e^-5	0.877	INTRON CG45002
X	9495510	X_9495510_SNP [dm3] X_9601477_SNP [dm6]	A	T	9.820e^-5	0.877	INTRON Gga	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	19870398	3R_19870398_SNP [dm3] 3R_24044676_SNP [dm6]	G	A	1.051e^-4	0.877	SYNONYMOUS_CODING Rox8	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	18503149	3L_18503149_DEL [dm3] 3L_18510049_DEL [dm6]	GG	G	1.131e^-4	0.877	INTERGENIC
X	9568501	X_9568501_INS [dm3] X_9674468_INS [dm6]	T	TGTT	1.175e^-4	0.877	INTRON nej	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	6030706	2R_6030706_SNP [dm3] 2R_10143201_SNP [dm6]	G	A	1.275e^-4	0.877	NON_SYNONYMOUS_CODING CG18011	TF binding site BDTNP1_TFBS_ftz mE1_TFBS_sens
X	15554379	X_15554379_SNP [dm3] X_15660346_SNP [dm6]	A	G	1.291e^-4	0.877	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	16192878	X_16192878_SNP [dm3] X_16298845_SNP [dm6]	G	C	1.500e^-4	0.877	SPLICE_SITE_REGION CG3632 INTRON CG3632
X	5800681	X_5800681_SNP [dm3] X_5906648_SNP [dm6]	T	C	1.510e^-4	0.877	SYNONYMOUS_CODING CG4020	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	12848355	X_12848355_SNP [dm3] X_12954322_SNP [dm6]	T	C	1.516e^-4	0.877	INTRON hec
X	7887513	X_7887513_SNP [dm3] X_7993480_SNP [dm6]	G	C	1.541e^-4	0.877	INTERGENIC
3L	19299430	3L_19299430_SNP [dm3] 3L_19306330_SNP [dm6]	C	T	1.557e^-4	0.877	SYNONYMOUS_CODING pip DOWNSTREAM pip INTRON pip
X	5509110	X_5509110_SNP [dm3] X_5615077_SNP [dm6]	C	T	1.575e^-4	0.877	NON_SYNONYMOUS_CODING CG34434 UPSTREAM CG34435	TF binding site mE1_TFBS_chinmo
3R	21831700	3R_21831700_SNP [dm3] 3R_26005978_SNP [dm6]	G	A	1.622e^-4	0.877	START_GAINED E_spl_mbeta-HLH UTR_5_PRIME E_spl_mbeta-HLH DOWNSTREAM CR45039	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	21027486	3R_21027486_SNP [dm3] 3R_25201764_SNP [dm6]	C	T	1.640e^-4	0.877	INTRON CG13654 & 1 other
3L	10280289	3L_10280289_SNP [dm3] 3L_10287189_SNP [dm6]	C	T	1.667e^-4	0.877	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4493835	3L_4493835_SNP [dm3] 3L_4493835_SNP [dm6]	T	C	1.731e^-4	0.877	DOWNSTREAM CR44709 INTERGENIC
2R	6141293	2R_6141293_SNP [dm3] 2R_10253788_SNP [dm6]	G	T	1.779e^-4	0.877	NON_SYNONYMOUS_CODING CG12913	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	15714572	3L_15714572_SNP [dm3] 3L_15721472_SNP [dm6]	A	G	1.935e^-4	0.877	DOWNSTREAM comm INTERGENIC	TF binding site mE1_TFBS_cad
3L	2487396	3L_2487396_SNP [dm3] 3L_2487396_SNP [dm6]	G	C	1.962e^-4	0.877	INTRON CG45186
X	15055033	X_15055033_SNP [dm3] X_15161000_SNP [dm6]	T	C	1.982e^-4	0.877	INTRON CG9095
3R	16880831	3R_16880831_SNP [dm3] 3R_21055109_SNP [dm6]	G	C	1.998e^-4	0.877	INTRON Mvl
X	3342186	X_3342186_INS [dm3] X_3448153_INS [dm6]	T	TGTGT	2.033e^-4	0.877	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA
X	15061129	X_15061129_SNP [dm3] X_15167096_SNP [dm6]	C	T	2.213e^-4	0.877	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25166050	3R_25166050_SNP [dm3] 3R_29340328_SNP [dm6]	C	T	2.306e^-4	0.877	INTERGENIC
3L	622542	3L_622542_INS [dm3] 3L_622542_INS [dm6]	A	AA	2.466e^-4	0.877	UPSTREAM CG43337 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Stat92E
3L	7091834	3L_7091834_SNP [dm3] 3L_7098734_SNP [dm6]	T	A	2.557e^-4	0.877	INTRON form3
X	21134188	X_21134188_SNP [dm3] X_21263161_SNP [dm6]	A	G	2.580e^-4	0.877	INTRON CG32521
3R	24831957	3R_24831957_SNP [dm3] 3R_29006235_SNP [dm6]	C	T	2.695e^-4	0.877	INTRON wat
X	10852007	X_10852007_SNP [dm3] X_10957974_SNP [dm6]	G	T	2.705e^-4	0.877	INTRON Myo10A
3R	26655003	3R_26655003_SNP [dm3] 3R_30829281_SNP [dm6]	T	C	2.881e^-4	0.877	INTRON CG15544
3L	6275044	3L_6275044_SNP [dm3] 3L_6281944_SNP [dm6]	T	A	3.107e^-4	0.877	INTERGENIC
3R	9418485	3R_9418485_SNP [dm3] 3R_13592763_SNP [dm6]	C	A	3.569e^-4	0.877	UPSTREAM CG14369 INTERGENIC
X	1308076	X_1308076_SNP [dm3] X_1414043_SNP [dm6]	C	A	3.648e^-4	0.877	UTR_5_PRIME futsch	TF binding site mE1_TFBS_chinmo
X	21359156	X_21359156_SNP [dm3] X_21488129_SNP [dm6]	G	T	3.659e^-4	0.877	INTERGENIC
3R	23081157	3R_23081157_SNP [dm3] 3R_27255435_SNP [dm6]	A	T	3.720e^-4	0.877	INTRON TfIIA-L
3L	8608451	3L_8608451_SNP [dm3] 3L_8615351_SNP [dm6]	A	G	4.007e^-4	0.877	SYNONYMOUS_CODING CG6282
3L	3902231	3L_3902231_SNP [dm3] 3L_3902231_SNP [dm6]	T	G	4.713e^-4	0.877	UPSTREAM Ubi-p63E INTRON Ubi-p63E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
X	3317365	X_3317365_INS [dm3] X_3423332_INS [dm6]	C	CATGGGCTATCGAGGGGTAG...	4.925e^-4	0.877	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	7937977	X_7937977_SNP [dm3] X_8043944_SNP [dm6]	A	G	5.012e^-4	0.877	SYNONYMOUS_CODING fs_1_h	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4439632	2L_4439632_SNP [dm3] 2L_4439632_SNP [dm6]	T	C	5.252e^-4	0.877	UTR_5_PRIME CG15431 INTRON CG15431
3L	9365361	3L_9365361_SNP [dm3] 3L_9372261_SNP [dm6]	G	A	5.402e^-4	0.877	SYNONYMOUS_CODING Hsp67Bc UPSTREAM Hsp67Bb & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	25994703	3R_25994703_SNP [dm3] 3R_30168981_SNP [dm6]	C	T	5.471e^-4	0.877	SYNONYMOUS_CODING CG31028
3L	8992354	3L_8992354_SNP [dm3] 3L_8999254_SNP [dm6]	T	C	5.623e^-4	0.877	SYNONYMOUS_CODING CG5087	TF binding site mE1_TFBS_sens
3R	26246778	3R_26246778_SNP [dm3] 3R_30421056_SNP [dm6]	A	T	5.719e^-4	0.877	UTR_5_PRIME CG42740 UTR_3_PRIME CG2217 DOWNSTREAM CG2217 INTRON CG42740 & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Kr
3L	15199383	3L_15199383_SNP [dm3] 3L_15206283_SNP [dm6]	C	T	5.726e^-4	0.877	INTERGENIC
3L	750661	3L_750661_SNP [dm3] 3L_750661_SNP [dm6]	A	T	5.826e^-4	0.877	INTRON hng3 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco
X	13635926	X_13635926_SNP [dm3] X_13741893_SNP [dm6]	G	T	5.949e^-4	0.877	SYNONYMOUS_CODING Grip91 UTR_3_PRIME CG11151 DOWNSTREAM CG11151
X	5026815	X_5026815_SNP [dm3] X_5132782_SNP [dm6]	T	G	6.575e^-4	0.877	SYNONYMOUS_CODING Rpn13R INTRON rg & 1 other
X	15056015	X_15056015_SNP [dm3] X_15161982_SNP [dm6]	C	T	6.802e^-4	0.877	INTRON CG9095	TF binding site mE1_TFBS_inv
3L	4489442	3L_4489442_SNP [dm3] 3L_4489442_SNP [dm6]	C	A	6.828e^-4	0.877	INTRON CG13722
3R	11531099	3R_11531099_SNP [dm3] 3R_15705377_SNP [dm6]	A	T	7.317e^-4	0.877	INTRON CG5404
3R	11521201	3R_11521201_SNP [dm3] 3R_15695479_SNP [dm6]	T	C	7.370e^-4	0.877	INTRON CG5399
X	11200085	X_11200085_SNP [dm3] X_11306052_SNP [dm6]	T	A	7.383e^-4	0.877	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	16605452	X_16605452_SNP [dm3] X_16711419_SNP [dm6]	G	A	7.473e^-4	0.877	UTR_5_PRIME CG13008 DOWNSTREAM CG4678
3L	5384138	3L_5384138_SNP [dm3] 3L_5391038_SNP [dm6]	A	T	7.823e^-4	0.877	INTERGENIC
X	15055159	X_15055159_SNP [dm3] X_15161126_SNP [dm6]	T	G	8.184e^-4	0.877	INTRON CG9095
3L	5779393	3L_5779393_INS [dm3] 3L_5786293_INS [dm6]	A	AGA	8.491e^-4	0.877	INTRON Cralbp
X	19942330	X_19942330_SNP [dm3] X_20048297_SNP [dm6]	A	G	8.593e^-4	0.877	INTRON Dop2R
3L	10917624	3L_10917624_DEL [dm3] 3L_10924524_DEL [dm6]	CGCTGCCCGTTGAC...	C	9.017e^-4	0.877	INTERGENIC
3L	16802607	3L_16802607_INS [dm3] 3L_16809507_INS [dm6]	C	GTG	9.039e^-4	0.877	DOWNSTREAM CG13024 INTRON nudC
X	9284433	X_9284433_SNP [dm3] X_9390400_SNP [dm6]	G	T	9.108e^-4	0.877	INTRON mgl
X	15433362	X_15433362_INS [dm3] X_15539329_INS [dm6]	CT	TGGATA	9.351e^-4	0.877	INTRON Ac13E
X	3059946	X_3059946_SNP [dm3] X_3165913_SNP [dm6]	T	C	9.437e^-4	0.877	SYNONYMOUS_CODING N	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens

By genomic position
Variant impact
Gene name

WolbachiaStatus phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results