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=5.323e^-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

2001 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
2L	3790257	2L_3790257_SNP [dm3] 2L_3790257_SNP [dm6]	T	A	6.716e^-7	0.72	INTRON CG3921	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	3694940	3R_3694940_SNP [dm3] 3R_7869218_SNP [dm6]	A	G	1.073e^-6	0.72	INTRON CG17816
3R	12000816	3R_12000816_DEL [dm3] 3R_16175094_DEL [dm6]	TT	T	2.445e^-6	0.72	INTRON CG8925
2L	1962948	2L_1962948_SNP [dm3] 2L_1962948_SNP [dm6]	A	G	5.099e^-6	0.72	INTRON erm	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
4	1045077	4_1045077_SNP [dm3] 4_1024451_SNP [dm6]	T	A	5.252e^-6	0.72	INTRON PlexA	transposable element FlyBase
X	3339613	X_3339613_INS [dm3] X_3445580_INS [dm6]	T	TTTTT	5.414e^-6	0.72	UPSTREAM CG12535 INTRON CR44999 & 1 other
3L	14144017	3L_14144017_SNP [dm3] 3L_14150917_SNP [dm6]	T	A	5.962e^-6	0.72	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14551266	3L_14551266_SNP [dm3] 3L_14558166_SNP [dm6]	T	G	6.251e^-6	0.72	INTERGENIC
2L	1950162	2L_1950162_SNP [dm3] 2L_1950162_SNP [dm6]	T	C	6.915e^-6	0.72	DOWNSTREAM erm INTERGENIC
4	905876	4_905876_SNP [dm3] 4_885250_SNP [dm6]	A	G	8.288e^-6	0.72	DOWNSTREAM CR44029 INTRON unc-13
2R	18593318	2R_18593318_DEL [dm3] 2R_22705813_DEL [dm6]	TAAAA	C	8.773e^-6	0.72	DOWNSTREAM Obp58c & 1 other INTERGENIC
X	8401874	X_8401874_SNP [dm3] X_8507841_SNP [dm6]	A	G	8.841e^-6	0.72	INTRON CG33181
2R	18593336	2R_18593336_SNP [dm3] 2R_22705831_SNP [dm6]	A	T	8.961e^-6	0.72	DOWNSTREAM Obp58c & 1 other INTERGENIC
2L	2343535	2L_2343535_DEL [dm3] 2L_2343535_DEL [dm6]	AATTTAGCGCTTGAGCAA...	A	1.181e^-5	0.72	INTRON CG9967 & 1 other
4	949736	4_949736_SNP [dm3] 4_929110_SNP [dm6]	A	G	1.212e^-5	0.72	INTRON eIF4G
2L	12673778	2L_12673778_SNP [dm3] 2L_12673778_SNP [dm6]	C	T	1.351e^-5	0.72	INTRON pdm2
X	8401856	X_8401856_SNP [dm3] X_8507823_SNP [dm6]	A	G	1.360e^-5	0.72	INTRON CG33181
X	3339520	X_3339520_SNP [dm3] X_3445487_SNP [dm6]	G	A	1.406e^-5	0.72	UPSTREAM CG12535 INTRON CR44999 & 1 other
2L	4064484	2L_4064484_SNP [dm3] 2L_4064484_SNP [dm6]	C	G	1.409e^-5	0.72	INTRON ed
2R	4688447	2R_4688447_SNP [dm3] 2R_8800942_SNP [dm6]	A	C	1.436e^-5	0.72	INTRON sns	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
4	1014427	4_1014427_SNP [dm3] 4_993801_SNP [dm6]	A	C	1.583e^-5	0.72	INTRON toy	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
4	1107540	4_1107540_SNP [dm3] 4_1086914_SNP [dm6]	A	T	1.584e^-5	0.72	INTERGENIC	regulatory region REDfly_CRMs
4	983467	4_983467_SNP [dm3] 4_962841_SNP [dm6]	G	T	1.631e^-5	0.72	DOWNSTREAM CR44030 INTRON fuss
2L	15942867	2L_15942867_INS [dm3] 2L_15942867_INS [dm6]	C	CT	1.690e^-5	0.72	DOWNSTREAM CG12448 INTRON beat-Ib
2L	918534	2L_918534_SNP [dm3] 2L_918534_SNP [dm6]	C	G	1.726e^-5	0.72	DOWNSTREAM GluRIIC INTERGENIC	TF binding site mE1_TFBS_cad
4	943229	4_943229_SNP [dm3] 4_922603_SNP [dm6]	C	A	1.726e^-5	0.72	INTRON eIF4G	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
3L	15472633	3L_15472633_DEL [dm3] 3L_15479533_DEL [dm6]	AAAATCAGCAGCAGCA...	A	1.730e^-5	0.72	INTERGENIC
X	3339621	X_3339621_INS [dm3] X_3445588_INS [dm6]	C	CCATTGGGC	1.825e^-5	0.72	UPSTREAM CG12535 INTRON CR44999 & 1 other
3L	2347256	3L_2347256_SNP [dm3] 3L_2347256_SNP [dm6]	T	A	1.835e^-5	0.72	INTERGENIC
4	1131714	4_1131714_SNP [dm3] 4_1111088_SNP [dm6]	A	G	1.882e^-5	0.72	DOWNSTREAM sv INTRON sv
4	716979	4_716979_SNP [dm3] 4_696353_SNP [dm6]	T	A	1.887e^-5	0.72	UPSTREAM myo INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
4	1015402	4_1015402_SNP [dm3] 4_994776_SNP [dm6]	C	G	1.990e^-5	0.72	INTRON toy	TF binding site BDTNP1_TFBS_dl
4	954995	4_954995_SNP [dm3] 4_934369_SNP [dm6]	C	A	2.031e^-5	0.72	INTERGENIC	transposable element FlyBase
3R	10459335	3R_10459335_SNP [dm3] 3R_14633613_SNP [dm6]	G	T	2.135e^-5	0.72	INTRON CG7886 & 1 other
3L	5373766	3L_5373766_SNP [dm3] 3L_5380666_SNP [dm6]	C	T	2.242e^-5	0.72	INTRON Ir64a	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	12673826	2L_12673826_SNP [dm3] 2L_12673826_SNP [dm6]	A	G	2.246e^-5	0.72	INTRON pdm2
3R	14584366	3R_14584366_SNP [dm3] 3R_18758644_SNP [dm6]	C	T	2.268e^-5	0.72	NON_SYNONYMOUS_CODING CG14299 DOWNSTREAM CG7720	TF binding site mE1_TFBS_cad mE1_TFBS_run mE1_TFBS_Ubx
X	7894193	X_7894193_SNP [dm3] X_8000160_SNP [dm6]	G	A	2.287e^-5	0.72	INTRON Tbh	TF binding site BDTNP1_TFBS_dl
2L	16963878	2L_16963878_SNP [dm3] 2L_16963878_SNP [dm6]	A	T	2.303e^-5	0.72	INTERGENIC
X	9195898	X_9195898_SNP [dm3] X_9301865_SNP [dm6]	A	C	2.359e^-5	0.72	INTRON lz	TF binding site mE1_TFBS_chinmo
2L	870223	2L_870223_SNP [dm3] 2L_870223_SNP [dm6]	G	A	2.374e^-5	0.72	UPSTREAM PNUTS & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	16963918	2L_16963918_SNP [dm3] 2L_16963918_SNP [dm6]	C	T	2.387e^-5	0.72	INTERGENIC
4	898277	4_898277_SNP [dm3] 4_877651_SNP [dm6]	T	G	2.399e^-5	0.72	INTRON unc-13	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	15362472	X_15362472_SNP [dm3] X_15468439_SNP [dm6]	C	T	2.413e^-5	0.72	SYNONYMOUS_CODING Grip128 UPSTREAM CG15642 DOWNSTREAM CG15641	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	9018278	3L_9018278_SNP [dm3] 3L_9025178_SNP [dm6]	A	C	2.468e^-5	0.72	INTERGENIC
2L	12049436	2L_12049436_SNP [dm3] 2L_12049436_SNP [dm6]	A	C	2.558e^-5	0.72	UTR_5_PRIME CG14945 UPSTREAM CG14945 & 1 other	TF binding site mE1_TFBS_HSA
2L	5288399	2L_5288399_SNP [dm3] 2L_5288399_SNP [dm6]	C	T	2.587e^-5	0.72	UPSTREAM vri DOWNSTREAM CR44742 INTRON CR44743	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	5288434	2L_5288434_SNP [dm3] 2L_5288434_SNP [dm6]	A	T	2.587e^-5	0.72	UPSTREAM vri DOWNSTREAM CR44742 EXON CR44743	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
4	917516	4_917516_DEL [dm3] 4_896890_DEL [dm6]	TT	T	2.616e^-5	0.72	INTRON unc-13
2R	18593427	2R_18593427_DEL [dm3] 2R_22705922_DEL [dm6]	CAGAA	TT	2.627e^-5	0.72	UTR_3_PRIME Obp58c DOWNSTREAM Obp58b	TF binding site mE1_TFBS_inv
2L	4059848	2L_4059848_SNP [dm3] 2L_4059848_SNP [dm6]	G	A	2.681e^-5	0.72	INTRON ed
4	952085	4_952085_SNP [dm3] 4_931459_SNP [dm6]	A	G	2.728e^-5	0.72	UPSTREAM eIF4G INTERGENIC	transposable element FlyBase
2L	918563	2L_918563_SNP [dm3] 2L_918563_SNP [dm6]	T	C	2.738e^-5	0.72	DOWNSTREAM GluRIIC INTERGENIC	TF binding site mE1_TFBS_cad
2L	918574	2L_918574_SNP [dm3] 2L_918574_SNP [dm6]	T	C	2.738e^-5	0.72	DOWNSTREAM GluRIIC INTERGENIC	TF binding site mE1_TFBS_cad
3L	6762799	3L_6762799_SNP [dm3] 3L_6769699_SNP [dm6]	A	C	2.791e^-5	0.72	INTERGENIC
4	851780	4_851780_SNP [dm3] 4_831154_SNP [dm6]	T	G	2.795e^-5	0.72	INTRON Sox102F
3L	24393020	3L_24393020_SNP [dm3] 3L_24399920_SNP [dm6]	C	A	2.811e^-5	0.72	INTRON nvd
3L	9844799	3L_9844799_INS [dm3] 3L_9851699_INS [dm6]	C	CGTTCCC	2.830e^-5	0.72	INTRON RasGAP1	TF binding site mE1_TFBS_cad
4	965726	4_965726_SNP [dm3] 4_945100_SNP [dm6]	A	T	2.833e^-5	0.72	DOWNSTREAM mGluR INTRON mGluR	transposable element FlyBase
3L	15302659	3L_15302659_SNP [dm3] 3L_15309559_SNP [dm6]	G	C	2.849e^-5	0.72	NON_SYNONYMOUS_CODING CG7255 INTRON CG7255	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	7893966	X_7893966_SNP [dm3] X_7999933_SNP [dm6]	T	A	2.855e^-5	0.72	INTRON Tbh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2767279	2L_2767279_SNP [dm3] 2L_2767279_SNP [dm6]	A	T	2.878e^-5	0.72	UTR_3_PRIME aph-1 UPSTREAM Taf10 DOWNSTREAM Taf10b & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	6762877	3L_6762877_SNP [dm3] 3L_6769777_SNP [dm6]	G	T	2.918e^-5	0.72	INTERGENIC
4	912580	4_912580_SNP [dm3] 4_891954_SNP [dm6]	G	C	2.987e^-5	0.72	NON_SYNONYMOUS_CODING unc-13 INTRON unc-13
4	907416	4_907416_SNP [dm3] 4_886790_SNP [dm6]	T	C	2.992e^-5	0.72	INTRON unc-13
2L	877106	2L_877106_SNP [dm3] 2L_877106_SNP [dm6]	G	T	3.006e^-5	0.72	UPSTREAM ninaA DOWNSTREAM CG15824 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
4	960900	4_960900_SNP [dm3] 4_940274_SNP [dm6]	C	T	3.026e^-5	0.72	SYNONYMOUS_CODING mGluR INTRON mGluR
3R	15696484	3R_15696484_SNP [dm3] 3R_19870762_SNP [dm6]	A	G	3.067e^-5	0.72	SYNONYMOUS_CODING CG4562	TF binding site mE1_TFBS_cad
4	903318	4_903318_SNP [dm3] 4_882692_SNP [dm6]	C	T	3.106e^-5	0.72	NON_SYNONYMOUS_CODING unc-13 INTRON unc-13 EXON CR44029
3L	24393019	3L_24393019_SNP [dm3] 3L_24399919_SNP [dm6]	C	T	3.107e^-5	0.72	INTRON nvd
3R	20876412	3R_20876412_SNP [dm3] 3R_25050690_SNP [dm6]	C	G	3.157e^-5	0.72	UTR_5_PRIME CG11791 INTRON CG11791	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
4	1029121	4_1029121_SNP [dm3] 4_1008495_SNP [dm6]	G	A	3.252e^-5	0.72	DOWNSTREAM toy INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_Trl
3R	5129773	3R_5129773_SNP [dm3] 3R_9304051_SNP [dm6]	G	T	3.258e^-5	0.72	INTRON CG8861
4	1136217	4_1136217_SNP [dm3] 4_1115591_SNP [dm6]	A	G	3.297e^-5	0.72	UTR_3_PRIME Cals
3L	12039628	3L_12039628_SNP [dm3] 3L_12046528_SNP [dm6]	A	T	3.363e^-5	0.72	INTRON rols
3L	24392997	3L_24392997_DEL [dm3] 3L_24399897_DEL [dm6]	TTA	T	3.375e^-5	0.72	INTRON nvd
3L	24393004	3L_24393004_SNP [dm3] 3L_24399904_SNP [dm6]	C	T	3.375e^-5	0.72	INTRON nvd
3L	24393023	3L_24393023_SNP [dm3] 3L_24399923_SNP [dm6]	C	T	3.375e^-5	0.72	INTRON nvd
3L	24522577	3L_24522577_SNP [dm3] 3L_24529477_SNP [dm6]	C	T	3.375e^-5	0.72	INTERGENIC
4	641107	4_641107_SNP [dm3] 4_620481_SNP [dm6]	A	C	3.391e^-5	0.72	UTR_3_PRIME Eph DOWNSTREAM Eph
4	1191630	4_1191630_SNP [dm3] 4_1171004_SNP [dm6]	T	G	3.421e^-5	0.72	INTERGENIC
2L	14887090	2L_14887090_SNP [dm3] 2L_14887090_SNP [dm6]	A	G	3.477e^-5	0.72	INTERGENIC
2R	6680132	2R_6680132_SNP [dm3] 2R_10792627_SNP [dm6]	T	A	3.533e^-5	0.72	INTRON CG33144 & 1 other
3R	12035549	3R_12035549_SNP [dm3] 3R_16209827_SNP [dm6]	T	A	3.541e^-5	0.72	UPSTREAM CR45639 & 1 other DOWNSTREAM CR45640 EXON CR45637
2R	16406401	2R_16406401_SNP [dm3] 2R_20518896_SNP [dm6]	G	C	3.603e^-5	0.72	INTERGENIC
3R	13913767	3R_13913767_SNP [dm3] 3R_18088045_SNP [dm6]	T	C	3.638e^-5	0.72	INTERGENIC
4	759105	4_759105_SNP [dm3] 4_738479_SNP [dm6]	A	G	3.639e^-5	0.72	INTRON bt
2L	8252792	2L_8252792_SNP [dm3] 2L_8252792_SNP [dm6]	A	T	3.643e^-5	0.72	INTRON CG8086
4	747586	4_747586_SNP [dm3] 4_726960_SNP [dm6]	G	A	3.652e^-5	0.72	SPLICE_SITE_REGION bt SYNONYMOUS_CODING bt INTRON bt
2L	15942848	2L_15942848_SNP [dm3] 2L_15942848_SNP [dm6]	C	A	3.669e^-5	0.72	UTR_3_PRIME CG12448 INTRON beat-Ib
2R	18701551	2R_18701551_SNP [dm3] 2R_22814046_SNP [dm6]	A	T	3.684e^-5	0.72	INTRON stl	TF binding site mE1_TFBS_chinmo
4	851782	4_851782_SNP [dm3] 4_831156_SNP [dm6]	A	G	3.712e^-5	0.72	INTRON Sox102F
2L	12673815	2L_12673815_SNP [dm3] 2L_12673815_SNP [dm6]	G	A	3.736e^-5	0.72	INTRON pdm2
2R	19998330	2R_19998330_SNP [dm3] 2R_24110807_SNP [dm6]	T	A	3.828e^-5	0.72	INTRON CG4049
4	1122770	4_1122770_SNP [dm3] 4_1102144_SNP [dm6]	T	C	3.830e^-5	0.72	INTRON sv
3L	24393006	3L_24393006_DEL [dm3] 3L_24399906_DEL [dm6]	GCT	A	3.873e^-5	0.72	INTRON nvd
3L	24393029	3L_24393029_SNP [dm3] 3L_24399929_SNP [dm6]	G	T	3.891e^-5	0.72	INTRON nvd
2L	526695	2L_526695_SNP [dm3] 2L_526695_SNP [dm6]	T	G	3.966e^-5	0.72	INTRON ush	regulatory region REDfly_CRMs
3R	8132919	3R_8132919_SNP [dm3] 3R_12307197_SNP [dm6]	A	G	4.077e^-5	0.72	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	24501997	3L_24501997_SNP [dm3] 3L_24508897_SNP [dm6]	C	A	4.080e^-5	0.72	INTERGENIC

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mn_Protein phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results