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=6.006e^-3)
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

1655 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
2R	14313870	2R_14313870_SNP [dm3] 2R_18426365_SNP [dm6]	A	T	3.429e^-6	1	UPSTREAM CG12263 DOWNSTREAM CG5174 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Ubx
3L	7696796	3L_7696796_SNP [dm3] 3L_7703696_SNP [dm6]	G	A	3.736e^-6	1	INTRON CG32373 & 1 other
2R	14313837	2R_14313837_SNP [dm3] 2R_18426332_SNP [dm6]	C	T	4.964e^-6	1	UPSTREAM CG12263 DOWNSTREAM CG5174 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Ubx
3R	22248828	3R_22248828_SNP [dm3] 3R_26423106_SNP [dm6]	C	T	5.528e^-6	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	6747597	2R_6747597_SNP [dm3] 2R_10860092_SNP [dm6]	C	A	5.944e^-6	1	INTRON CG30015 EXON CR44302	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10916450	2R_10916450_SNP [dm3] 2R_15028945_SNP [dm6]	C	A	6.317e^-6	1	INTRON hbs
3L	7434902	3L_7434902_SNP [dm3] 3L_7441802_SNP [dm6]	T	C	6.941e^-6	1	INTRON CG42458
3R	11833326	3R_11833326_SNP [dm3] 3R_16007604_SNP [dm6]	A	G	7.040e^-6	1	EXON CR42839	TF binding site BDTNP1_TFBS_twi
2L	19799896	2L_19799896_SNP [dm3] 2L_19799896_SNP [dm6]	C	T	7.105e^-6	1	INTRON sick	TF binding site mE1_TFBS_cad
X	10426224	X_10426224_SNP [dm3] X_10532191_SNP [dm6]	T	C	7.171e^-6	1	INTRON spri
3L	842921	3L_842921_SNP [dm3] 3L_842921_SNP [dm6]	C	T	7.948e^-6	1	SYNONYMOUS_CODING Gr61a UTR_3_PRIME Gr61a
X	3316039	X_3316039_SNP [dm3] X_3422006_SNP [dm6]	G	C	8.171e^-6	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	3407678	2L_3407678_SNP [dm3] 2L_3407678_SNP [dm6]	G	A	8.785e^-6	1	SYNONYMOUS_CODING pgant2
2R	19458332	2R_19458332_SNP [dm3] 2R_23570809_SNP [dm6]	C	T	9.644e^-6	1	INTRON apt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	13258614	2L_13258614_SNP [dm3] 2L_13258614_SNP [dm6]	A	G	1.022e^-5	1	UTR_3_PRIME CG31851 DOWNSTREAM CG31730 & 1 other
3L	7432289	3L_7432289_SNP [dm3] 3L_7439189_SNP [dm6]	G	A	1.135e^-5	1	SYNONYMOUS_CODING sphinx1 DOWNSTREAM sphinx2 INTRON CG42458	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	4053115	2R_4053115_SNP [dm3] 2R_8165610_SNP [dm6]	C	T	1.232e^-5	1	SYNONYMOUS_CODING Rs1 UPSTREAM CG30373 & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2L	2558637	2L_2558637_SNP [dm3] 2L_2558637_SNP [dm6]	A	C	1.240e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
2R	18903949	2R_18903949_SNP [dm3] 2R_23016426_SNP [dm6]	A	T	1.242e^-5	1	INTRON twi & 1 other
X	3316093	X_3316093_SNP [dm3] X_3422060_SNP [dm6]	G	A	1.387e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	6854815	2R_6854815_SNP [dm3] 2R_10967310_SNP [dm6]	T	A	1.460e^-5	1	INTERGENIC
2L	757289	2L_757289_SNP [dm3] 2L_757289_SNP [dm6]	A	G	1.484e^-5	1	SYNONYMOUS_CODING GABA-B-R3 UTR_3_PRIME GABA-B-R3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	17909739	3R_17909739_SNP [dm3] 3R_22084017_SNP [dm6]	G	C	1.516e^-5	1	DOWNSTREAM CG13408 INTERGENIC
X	12801338	X_12801338_SNP [dm3] X_12907305_SNP [dm6]	G	A	1.527e^-5	1	DOWNSTREAM Brms1 INTRON mRpL49	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
X	3316026	X_3316026_SNP [dm3] X_3421993_SNP [dm6]	T	G	1.617e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	7339668	3L_7339668_SNP [dm3] 3L_7346568_SNP [dm6]	T	C	1.676e^-5	1	NON_SYNONYMOUS_CODING CG14834 DOWNSTREAM Srp19	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	16001993	2L_16001993_SNP [dm3] 2L_16001993_SNP [dm6]	T	C	1.711e^-5	1	DOWNSTREAM CG34167 INTRON beat-Ic EXON CR43825
3R	16234552	3R_16234552_SNP [dm3] 3R_20408830_SNP [dm6]	A	G	1.800e^-5	1	SYNONYMOUS_CODING CG10881 UPSTREAM CG4335 INTRON Gfrl
2R	17901586	2R_17901586_DEL [dm3] 2R_22014081_DEL [dm6]	ATGACA	A	1.811e^-5	1	INTRON CG34370
X	3316025	X_3316025_SNP [dm3] X_3421992_SNP [dm6]	T	A	1.852e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	6918386	3R_6918386_SNP [dm3] 3R_11092664_SNP [dm6]	G	T	2.132e^-5	1	INTERGENIC
3R	21228943	3R_21228943_SNP [dm3] 3R_25403221_SNP [dm6]	C	T	2.134e^-5	1	INTRON Fur1
3L	1562852	3L_1562852_SNP [dm3] 3L_1562852_SNP [dm6]	A	C	2.203e^-5	1	NON_SYNONYMOUS_CODING CG7879	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2R	7070074	2R_7070074_DEL [dm3] 2R_11182569_DEL [dm6]	CTC	C	2.287e^-5	1	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	834376	3L_834376_SNP [dm3] 3L_834376_SNP [dm6]	A	T	2.340e^-5	1	UPSTREAM CG13900 INTRON CG42553	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	2229349	3R_2229349_SNP [dm3] 3R_6403627_SNP [dm6]	A	G	2.406e^-5	1	INTRON Dmtn	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
3R	16234726	3R_16234726_SNP [dm3] 3R_20409004_SNP [dm6]	C	G	2.447e^-5	1	SYNONYMOUS_CODING CG10881 INTRON Gfrl
2R	14561844	2R_14561844_SNP [dm3] 2R_18674339_SNP [dm6]	T	C	2.451e^-5	1	UPSTREAM edl INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb
3L	9352877	3L_9352877_SNP [dm3] 3L_9359777_SNP [dm6]	A	T	2.608e^-5	1	UTR_3_PRIME CG32039 UPSTREAM UGP & 1 other DOWNSTREAM CG32039	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_inv
2L	19732797	2L_19732797_SNP [dm3] 2L_19732797_SNP [dm6]	G	A	2.686e^-5	1	SYNONYMOUS_CODING CG10462 DOWNSTREAM Lar
2R	6752115	2R_6752115_SNP [dm3] 2R_10864610_SNP [dm6]	A	T	2.889e^-5	1	INTRON CG30015
2L	3097371	2L_3097371_SNP [dm3] 2L_3097371_SNP [dm6]	G	A	2.941e^-5	1	INTRON toc
2L	18811826	2L_18811826_SNP [dm3] 2L_18811826_SNP [dm6]	C	T	2.966e^-5	1	UPSTREAM CG10570 & 3 others INTERGENIC
3R	27102755	3R_27102755_SNP [dm3] 3R_31277033_SNP [dm6]	A	T	2.967e^-5	1	INTERGENIC
3R	12318228	3R_12318228_SNP [dm3] 3R_16492506_SNP [dm6]	G	A	3.030e^-5	1	SYNONYMOUS_CODING Cad89D
3R	24579869	3R_24579869_SNP [dm3] 3R_28754147_SNP [dm6]	A	T	3.031e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
3R	21228927	3R_21228927_SNP [dm3] 3R_25403205_SNP [dm6]	G	A	3.044e^-5	1	INTRON Fur1
2L	8349019	2L_8349019_SNP [dm3] 2L_8349019_SNP [dm6]	T	C	3.363e^-5	1	INTRON CG7778
2L	16250169	2L_16250169_SNP [dm3] 2L_16250169_SNP [dm6]	G	T	3.429e^-5	1	INTRON PRL-1
X	3316015	X_3316015_SNP [dm3] X_3421982_SNP [dm6]	G	T	3.465e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	12369490	2L_12369490_SNP [dm3] 2L_12369490_SNP [dm6]	C	G	3.471e^-5	1	UPSTREAM bru-2 INTRON bru-2
2R	6856063	2R_6856063_SNP [dm3] 2R_10968558_SNP [dm6]	A	G	3.703e^-5	1	INTERGENIC
2R	12180115	2R_12180115_SNP [dm3] 2R_16292610_SNP [dm6]	C	T	3.819e^-5	1	SYNONYMOUS_CODING CG7747 DOWNSTREAM CG30100 & 1 other
2L	2246113	2L_2246113_SNP [dm3] 2L_2246113_SNP [dm6]	G	T	3.898e^-5	1	DOWNSTREAM CG4267 & 1 other EXON CR42859
2R	1924021	2R_1924021_SNP [dm3] 2R_6036516_SNP [dm6]	A	G	3.987e^-5	1	UPSTREAM SCAP DOWNSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Ubx
2R	19892507	2R_19892507_SNP [dm3] 2R_24004984_SNP [dm6]	T	C	4.037e^-5	1	INTRON Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	12398136	2L_12398136_SNP [dm3] 2L_12398136_SNP [dm6]	G	C	4.087e^-5	1	UPSTREAM Pkd2 DOWNSTREAM bru-2 INTERGENIC
2L	12315669	2L_12315669_SNP [dm3] 2L_12315669_SNP [dm6]	T	A	4.089e^-5	1	DOWNSTREAM CR45282 & 1 other INTERGENIC
2R	6748790	2R_6748790_INS [dm3] 2R_10861285_INS [dm6]	A	AC	4.368e^-5	1	UTR_5_PRIME CG30015 INTRON CG30015	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	26259010	3R_26259010_SNP [dm3] 3R_30433288_SNP [dm6]	A	C	4.397e^-5	1	SYNONYMOUS_CODING CG15534	TF binding site BDTNP1_TFBS_twi
3R	13754639	3R_13754639_SNP [dm3] 3R_17928917_SNP [dm6]	T	C	4.425e^-5	1	INTRON cpo	TF binding site mE1_TFBS_inv
2L	16250464	2L_16250464_SNP [dm3] 2L_16250464_SNP [dm6]	C	T	4.496e^-5	1	INTRON PRL-1
2R	6745153	2R_6745153_INS [dm3] 2R_10857648_INS [dm6]	C	CT	4.540e^-5	1	INTRON CG30015
2R	14310108	2R_14310108_SNP [dm3] 2R_18422603_SNP [dm6]	A	G	4.670e^-5	1	UPSTREAM CG5174 INTRON CG5174
2L	7207680	2L_7207680_SNP [dm3] 2L_7207680_SNP [dm6]	C	T	4.694e^-5	1	SYNONYMOUS_CODING CG13784 UTR_3_PRIME CG13784
3L	5011261	3L_5011261_SNP [dm3] 3L_5011261_SNP [dm6]	T	G	4.730e^-5	1	DOWNSTREAM CG12027 INTRON Con	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	5554599	3R_5554599_SNP [dm3] 3R_9728877_SNP [dm6]	T	G	4.767e^-5	1	INTRON FoxP	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	2229374	3R_2229374_SNP [dm3] 3R_6403652_SNP [dm6]	C	T	4.879e^-5	1	INTRON Dmtn	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
3L	17050455	3L_17050455_SNP [dm3] 3L_17057355_SNP [dm6]	G	A	4.891e^-5	1	SPLICE_SITE_REGION CG7724 INTRON CG7724	TF binding site mE1_TFBS_cad mE1_TFBS_cnc
X	8980081	X_8980081_SNP [dm3] X_9086048_SNP [dm6]	G	A	4.923e^-5	1	NON_SYNONYMOUS_CODING CG32708 DOWNSTREAM APC4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2R	7074227	2R_7074227_SNP [dm3] 2R_11186722_SNP [dm6]	A	G	4.966e^-5	1	INTRON shn
2R	19892510	2R_19892510_SNP [dm3] 2R_24004987_SNP [dm6]	T	A	5.046e^-5	1	INTRON Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	19689535	3L_19689535_SNP [dm3] 3L_19696435_SNP [dm6]	A	G	5.120e^-5	1	INTERGENIC
3R	25166664	3R_25166664_SNP [dm3] 3R_29340942_SNP [dm6]	T	A	5.202e^-5	1	INTERGENIC
3R	20514548	3R_20514548_SNP [dm3] 3R_24688826_SNP [dm6]	A	G	5.279e^-5	1	INTRON slo
2R	7074241	2R_7074241_SNP [dm3] 2R_11186736_SNP [dm6]	T	G	5.293e^-5	1	INTRON shn
2R	7067231	2R_7067231_SNP [dm3] 2R_11179726_SNP [dm6]	A	T	5.436e^-5	1	INTRON shn
3L	7925042	3L_7925042_SNP [dm3] 3L_7931942_SNP [dm6]	C	A	5.532e^-5	1	INTRON syd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	21840772	3R_21840772_SNP [dm3] 3R_26015050_SNP [dm6]	G	C	5.597e^-5	1	UPSTREAM CR45040 INTRON Kaz-m1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
3R	20301342	3R_20301342_SNP [dm3] 3R_24475620_SNP [dm6]	G	A	5.721e^-5	1	INTERGENIC
2L	21014463	2L_21014463_SNP [dm3] 2L_21014463_SNP [dm6]	A	G	5.730e^-5	1	INTRON CG42238
2R	10864992	2R_10864992_SNP [dm3] 2R_14977487_SNP [dm6]	G	C	5.799e^-5	1	INTRON ckn
3L	18079470	3L_18079470_SNP [dm3] 3L_18086370_SNP [dm6]	G	C	5.801e^-5	1	DOWNSTREAM CG34253 EXON CR32194
3R	5290553	3R_5290553_SNP [dm3] 3R_9464831_SNP [dm6]	G	A	5.947e^-5	1	UTR_3_PRIME CG16779
3L	7434931	3L_7434931_SNP [dm3] 3L_7441831_SNP [dm6]	G	A	5.988e^-5	1	INTRON CG42458
3R	11060414	3R_11060414_SNP [dm3] 3R_15234692_SNP [dm6]	G	A	6.018e^-5	1	SYNONYMOUS_CODING tefu	TF binding site BDTNP1_TFBS_twi
3L	1513827	3L_1513827_SNP [dm3] 3L_1513827_SNP [dm6]	G	A	6.031e^-5	1	INTRON Psa & 1 other	TF binding site BDTNP1_TFBS_da
2R	18794015	2R_18794015_SNP [dm3] 2R_22906492_SNP [dm6]	T	G	6.200e^-5	1	INTRON nahoda
X	3316032	X_3316032_SNP [dm3] X_3421999_SNP [dm6]	C	T	6.398e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	19892506	2R_19892506_SNP [dm3] 2R_24004983_SNP [dm6]	C	T	6.409e^-5	1	INTRON Unc-89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	4312456	2R_4312456_SNP [dm3] 2R_8424951_SNP [dm6]	A	G	6.441e^-5	1	INTRON CSN7	TF binding site mE1_TFBS_chinmo
X	13434287	X_13434287_SNP [dm3] X_13540254_SNP [dm6]	T	C	6.499e^-5	1	INTERGENIC
2R	6451349	2R_6451349_SNP [dm3] 2R_10563844_SNP [dm6]	C	A	6.534e^-5	1	INTRON psq	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
3L	18079466	3L_18079466_SNP [dm3] 3L_18086366_SNP [dm6]	G	T	6.580e^-5	1	DOWNSTREAM CG34253 EXON CR32194
2L	756958	2L_756958_SNP [dm3] 2L_756958_SNP [dm6]	C	T	6.623e^-5	1	SYNONYMOUS_CODING GABA-B-R3 UTR_3_PRIME GABA-B-R3	TF binding site mE1_TFBS_chinmo mE1_TFBS_eve mE1_TFBS_HSA
X	3316089	X_3316089_SNP [dm3] X_3422056_SNP [dm6]	A	G	6.648e^-5	1	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10629782	2R_10629782_SNP [dm3] 2R_14742277_SNP [dm6]	C	T	6.668e^-5	1	SYNONYMOUS_CODING CG12858
3R	17909578	3R_17909578_SNP [dm3] 3R_22083856_SNP [dm6]	A	T	6.679e^-5	1	DOWNSTREAM CG13408 INTERGENIC
3R	11106929	3R_11106929_SNP [dm3] 3R_15281207_SNP [dm6]	G	A	6.686e^-5	1	UPSTREAM Tm1 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3R	11106930	3R_11106930_SNP [dm3] 3R_15281208_SNP [dm6]	T	A	6.686e^-5	1	UPSTREAM Tm1 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl

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Phenotype distribution and association to known covariates

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GWAS results