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=2.024e^-23)
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_2R_NS	<

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	25.3783	3.0845e-06
In_2R_NS	28.2369	7.3865e-07

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3790 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
X	19496052	X_19496052_INS [dm3] X_19602019_INS [dm6]	T	TTT	6.904e^-9	0.013	UPSTREAM CG14220 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	4134760	3R_4134760_SNP [dm3] 3R_8309038_SNP [dm6]	A	G	8.354e^-7	0.235	SYNONYMOUS_CODING CG11693 UPSTREAM mir-4918 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	17619907	2L_17619907_SNP [dm3] 2L_17619907_SNP [dm6]	C	T	8.529e^-7	0.235	INTERGENIC	TF binding site mE1_TFBS_inv
2L	14846877	2L_14846877_SNP [dm3] 2L_14846877_SNP [dm6]	T	C	8.970e^-7	0.235	NON_SYNONYMOUS_CODING CG15279 INTRON CG15279
2L	19715057	2L_19715057_DEL [dm3] 2L_19715057_DEL [dm6]	CACCGGGC	C	1.034e^-6	0.235	INTRON Lar	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2R	16762358	2R_16762358_SNP [dm3] 2R_20874853_SNP [dm6]	C	T	1.183e^-6	0.235	NON_SYNONYMOUS_CODING Ipk1 INTRON Ipk1
3R	22520225	3R_22520225_INS [dm3] 3R_26694503_INS [dm6]	G	GTTGG	1.191e^-6	0.235	UPSTREAM TwdlQ INTERGENIC
2L	21064263	2L_21064263_SNP [dm3] 2L_21064263_SNP [dm6]	T	C	1.343e^-6	0.235	INTRON CG9265	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
2L	3405028	2L_3405028_SNP [dm3] 2L_3405028_SNP [dm6]	A	G	1.346e^-6	0.235	UTR_3_PRIME pgant2
3R	25222566	3R_25222566_SNP [dm3] 3R_29396844_SNP [dm6]	C	T	1.414e^-6	0.235	INTRON Ptp99A
2R	7280573	2R_7280573_DEL [dm3] 2R_11393068_DEL [dm6]	CAAGTGATC	C	1.505e^-6	0.235	INTRON sprt
3R	1206780	3R_1206780_DEL [dm3] 3R_5381058_DEL [dm6]	AA	A	2.053e^-6	0.235	INTRON kkv
2L	12289242	2L_12289242_SNP [dm3] 2L_12289242_SNP [dm6]	T	C	2.065e^-6	0.235	UTR_5_PRIME aret INTRON aret	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	12279048	2L_12279048_SNP [dm3] 2L_12279048_SNP [dm6]	G	A	2.197e^-6	0.235	INTRON aret
2L	13975947	2L_13975947_DEL [dm3] 2L_13975947_DEL [dm6]	ATAA	A	2.225e^-6	0.235	INTRON NimC1
3R	25222382	3R_25222382_DEL [dm3] 3R_29396660_DEL [dm6]	AG	A	2.295e^-6	0.235	INTRON Ptp99A
2L	21050757	2L_21050757_DEL [dm3] 2L_21050757_DEL [dm6]	TTATAGAT	T	2.698e^-6	0.235	INTRON CG42238	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	25222390	3R_25222390_SNP [dm3] 3R_29396668_SNP [dm6]	A	T	2.703e^-6	0.235	INTRON Ptp99A
X	4472554	X_4472554_INS [dm3] X_4578521_INS [dm6]	C	CA	2.740e^-6	0.235	INTRON CR32773	TF binding site BDTNP1_TFBS_da
3R	26709662	3R_26709662_SNP [dm3] 3R_30883940_SNP [dm6]	A	G	2.847e^-6	0.235	UPSTREAM CG15547 INTRON Sap-r	TF binding site mE1_TFBS_cad
3R	25222387	3R_25222387_INS [dm3] 3R_29396665_INS [dm6]	GC	AGATA	2.879e^-6	0.235	INTRON Ptp99A
2L	18587275	2L_18587275_SNP [dm3] 2L_18587275_SNP [dm6]	T	G	2.910e^-6	0.235	INTRON Pde11
2L	4819399	2L_4819399_DEL [dm3] 2L_4819399_DEL [dm6]	AA	A	3.083e^-6	0.235	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	15241503	3R_15241503_SNP [dm3] 3R_19415781_SNP [dm6]	T	C	3.170e^-6	0.235	UTR_5_PRIME CG31221
2L	5074858	2L_5074858_DEL [dm3] 2L_5074858_DEL [dm6]	AA	A	3.276e^-6	0.235	INTRON pgant5
3R	25222291	3R_25222291_SNP [dm3] 3R_29396569_SNP [dm6]	C	A	3.311e^-6	0.235	INTRON Ptp99A
3R	25222391	3R_25222391_SNP [dm3] 3R_29396669_SNP [dm6]	C	G	3.376e^-6	0.235	INTRON Ptp99A
X	16519235	X_16519235_DEL [dm3] X_16625202_DEL [dm6]	AA	A	3.925e^-6	0.257	UTR_3_PRIME Rok INTRON Rok
2L	21944642	2L_21944642_INS [dm3] 2L_21944642_INS [dm6]	C	CTTAAGCT	4.114e^-6	0.257	INTERGENIC
2L	21944643	2L_21944643_DEL [dm3] 2L_21944643_DEL [dm6]	AC	A	4.114e^-6	0.257	INTERGENIC
2L	12209977	2L_12209977_SNP [dm3] 2L_12209977_SNP [dm6]	G	C	4.418e^-6	0.263	UTR_3_PRIME CG31759 INTRON aret
2R	16707647	2R_16707647_DEL [dm3] 2R_20820142_DEL [dm6]	ACGCGCACCATA...	A	4.983e^-6	0.263	INTERGENIC
2L	12552342	2L_12552342_SNP [dm3] 2L_12552342_SNP [dm6]	T	A	5.052e^-6	0.263	INTERGENIC
2L	8854866	2L_8854866_SNP [dm3] 2L_8854866_SNP [dm6]	A	C	5.117e^-6	0.263	INTERGENIC
2L	19004441	2L_19004441_SNP [dm3] 2L_19004441_SNP [dm6]	T	A	5.144e^-6	0.263	INTRON CG31793	TF binding site mE1_TFBS_chinmo
2L	4059197	2L_4059197_SNP [dm3] 2L_4059197_SNP [dm6]	C	T	5.326e^-6	0.263	INTRON ed
3R	26710866	3R_26710866_SNP [dm3] 3R_30885144_SNP [dm6]	G	C	5.410e^-6	0.263	SYNONYMOUS_CODING Sap-r	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8854896	2L_8854896_INS [dm3] 2L_8854896_INS [dm6]	A	CCCCAACTTAT...	5.423e^-6	0.263	INTERGENIC
2L	4679653	2L_4679653_SNP [dm3] 2L_4679653_SNP [dm6]	G	A	5.471e^-6	0.263	INTERGENIC
2R	19616121	2R_19616121_DEL [dm3] 2R_23728598_DEL [dm6]	GG	A	5.676e^-6	0.266	INTRON Sesn
3R	20661039	3R_20661039_SNP [dm3] 3R_24835317_SNP [dm6]	T	C	5.930e^-6	0.271	UPSTREAM CR45216 & 1 other INTRON sosie	TF binding site BDTNP1_TFBS_dl
3R	13270270	3R_13270270_DEL [dm3] 3R_17444548_DEL [dm6]	TGT	T	6.073e^-6	0.271	INTRON CG5873
2L	19806150	2L_19806150_SNP [dm3] 2L_19806150_SNP [dm6]	A	G	6.804e^-6	0.297	INTRON sick
2L	4820028	2L_4820028_DEL [dm3] 2L_4820028_DEL [dm6]	CATTGTC	C	7.416e^-6	0.302	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	4679586	2L_4679586_SNP [dm3] 2L_4679586_SNP [dm6]	G	C	7.493e^-6	0.302	INTERGENIC
2L	12210043	2L_12210043_DEL [dm3] 2L_12210043_DEL [dm6]	AATTCG	A	7.495e^-6	0.302	UTR_3_PRIME CG31759 DOWNSTREAM CG31759 INTRON aret
2R	16762359	2R_16762359_SNP [dm3] 2R_20874854_SNP [dm6]	C	T	7.627e^-6	0.302	NON_SYNONYMOUS_CODING Ipk1 INTRON Ipk1
2L	21933009	2L_21933009_DEL [dm3] 2L_21933009_DEL [dm6]	CC	C	7.719e^-6	0.302	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	17809045	2R_17809045_SNP [dm3] 2R_21921540_SNP [dm6]	G	A	8.084e^-6	0.303	UTR_5_PRIME Fili	TF binding site mE1_TFBS_inv
3L	975783	3L_975783_SNP [dm3] 3L_975783_SNP [dm6]	A	G	8.158e^-6	0.303	INTRON Glut1
2R	19358438	2R_19358438_INS [dm3] 2R_23470915_INS [dm6]	T	TAGAT	8.237e^-6	0.303	INTRON CG43795 & 1 other
3R	19750711	3R_19750711_INS [dm3] 3R_23924989_INS [dm6]	C	CC	8.613e^-6	0.309	DOWNSTREAM CG31141 INTRON Ndc1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	19011676	2L_19011676_INS [dm3] 2L_19011676_INS [dm6]	T	TT	8.827e^-6	0.309	UPSTREAM CR45292 DOWNSTREAM robl37BC INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	9629705	3R_9629705_DEL [dm3] 3R_13803983_DEL [dm6]	TAAATCTACCATTATCACTA...	T	8.885e^-6	0.309	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4679336	2L_4679336_SNP [dm3] 2L_4679336_SNP [dm6]	A	G	9.133e^-6	0.311	INTERGENIC
2R	17998499	2R_17998499_SNP [dm3] 2R_22110994_SNP [dm6]	C	G	9.291e^-6	0.311	INTRON Vrp1	TF binding site mE1_TFBS_cad
3L	12107226	3L_12107226_SNP [dm3] 3L_12114126_SNP [dm6]	T	A	1.009e^-5	0.319	INTERGENIC
3R	22741710	3R_22741710_SNP [dm3] 3R_26915988_SNP [dm6]	C	T	1.023e^-5	0.319	INTRON sda	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
3R	24741850	3R_24741850_SNP [dm3] 3R_28916128_SNP [dm6]	G	T	1.028e^-5	0.319	INTRON Doa
3R	26709682	3R_26709682_SNP [dm3] 3R_30883960_SNP [dm6]	T	A	1.034e^-5	0.319	UPSTREAM CG15547 INTRON Sap-r	TF binding site mE1_TFBS_cad
2R	1329977	2R_1329977_SNP [dm3] 2R_5442472_SNP [dm6]	T	A	1.045e^-5	0.319	INTRON laccase2	transposable element FlyBase
2L	12552355	2L_12552355_SNP [dm3] 2L_12552355_SNP [dm6]	T	C	1.061e^-5	0.319	INTERGENIC
X	12624080	X_12624080_DEL [dm3] X_12730047_DEL [dm6]	AA	A	1.081e^-5	0.319	INTRON Smr & 1 other	TF binding site mE1_TFBS_GATAe
2L	3217742	2L_3217742_DEL [dm3] 2L_3217742_DEL [dm6]	TA	T	1.088e^-5	0.319	INTERGENIC
2L	1711319	2L_1711319_SNP [dm3] 2L_1711319_SNP [dm6]	T	A	1.130e^-5	0.325	UTR_3_PRIME mRpL48 & 1 other UPSTREAM CG17660 DOWNSTREAM frtz	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	650344	2L_650344_DEL [dm3] 2L_650344_DEL [dm6]	TT	T	1.150e^-5	0.325	INTRON ds
3R	25979460	3R_25979460_INS [dm3] 3R_30153738_INS [dm6]	A	AATTGATGGTA...	1.186e^-5	0.325	DOWNSTREAM CG15529 INTRON CG11498	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
2R	1127765	2R_1127765_DEL [dm3] 2R_5240260_DEL [dm6]	TGTTTCGATCTAATGGGGAG...	T	1.201e^-5	0.325	INTRON Nipped-A	TF binding site BDTNP1_TFBS_dl
2R	8268259	2R_8268259_DEL [dm3] 2R_12380754_DEL [dm6]	ATC	A	1.201e^-5	0.325	UPSTREAM CG13155 INTERGENIC
2L	7898797	2L_7898797_INS [dm3] 2L_7898797_INS [dm6]	T	TAT	1.219e^-5	0.325	INTRON Snoo	TF binding site mE1_TFBS_cad
2L	20960756	2L_20960756_INS [dm3] 2L_20960756_INS [dm6]	C	CAGTGC	1.246e^-5	0.325	INTERGENIC
2L	12552322	2L_12552322_SNP [dm3] 2L_12552322_SNP [dm6]	C	T	1.292e^-5	0.325	INTERGENIC
2R	18122805	2R_18122805_SNP [dm3] 2R_22235300_SNP [dm6]	G	T	1.305e^-5	0.325	DOWNSTREAM CR44755 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	3217451	2L_3217451_SNP [dm3] 2L_3217451_SNP [dm6]	G	C	1.306e^-5	0.325	INTERGENIC
2L	12309657	2L_12309657_SNP [dm3] 2L_12309657_SNP [dm6]	G	T	1.309e^-5	0.325	INTRON aret	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14675527	3L_14675527_DEL [dm3] 3L_14682427_DEL [dm6]	ATTTTTCA	A	1.316e^-5	0.325	INTRON ome
2L	12552395	2L_12552395_SNP [dm3] 2L_12552395_SNP [dm6]	G	C	1.366e^-5	0.333	INTERGENIC
2L	12552359	2L_12552359_SNP [dm3] 2L_12552359_SNP [dm6]	G	A	1.402e^-5	0.333	INTERGENIC
2L	13108034	2L_13108034_SNP [dm3] 2L_13108034_SNP [dm6]	T	A	1.442e^-5	0.333	SYNONYMOUS_CODING CG5142	TF binding site mE1_TFBS_chinmo
3L	12336855	3L_12336855_SNP [dm3] 3L_12343755_SNP [dm6]	A	G	1.445e^-5	0.333	INTRON CrzR
3L	21861112	3L_21861112_SNP [dm3] 3L_21868012_SNP [dm6]	A	C	1.500e^-5	0.333	INTRON mub	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	21291021	2L_21291021_SNP [dm3] 2L_21291021_SNP [dm6]	T	C	1.546e^-5	0.333	SYNONYMOUS_CODING Gr39a UPSTREAM Gr39a INTRON Mio	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	13807712	3R_13807712_INS [dm3] 3R_17981990_INS [dm6]	C	CC	1.560e^-5	0.333	INTRON cpo
3L	11652581	3L_11652581_SNP [dm3] 3L_11659481_SNP [dm6]	G	A	1.571e^-5	0.333	INTRON CG32085
3L	3867643	3L_3867643_SNP [dm3] 3L_3867643_SNP [dm6]	G	C	1.597e^-5	0.333	INTERGENIC
2L	21935017	2L_21935017_SNP [dm3] 2L_21935017_SNP [dm6]	A	C	1.600e^-5	0.333	INTERGENIC
3R	25496952	3R_25496952_SNP [dm3] 3R_29671230_SNP [dm6]	T	C	1.669e^-5	0.333	UTR_3_PRIME ppk30 UPSTREAM Obp99a	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18284264	2R_18284264_SNP [dm3] 2R_22396759_SNP [dm6]	A	G	1.679e^-5	0.333	INTRON babos	TF binding site BDTNP1_TFBS_dl
X	7997438	X_7997438_DEL [dm3] X_8103405_DEL [dm6]	CTTCGCC	C	1.700e^-5	0.333	UTR_3_PRIME Gclc
2L	12289447	2L_12289447_SNP [dm3] 2L_12289447_SNP [dm6]	T	G	1.731e^-5	0.333	INTRON aret
2L	2625695	2L_2625695_SNP [dm3] 2L_2625695_SNP [dm6]	C	A	1.741e^-5	0.333	EXON CR45705
2R	18127876	2R_18127876_SNP [dm3] 2R_22240371_SNP [dm6]	G	A	1.783e^-5	0.333	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	16780106	2R_16780106_SNP [dm3] 2R_20892601_SNP [dm6]	C	G	1.790e^-5	0.333	INTRON otp
2L	16877705	2L_16877705_SNP [dm3] 2L_16877705_SNP [dm6]	C	T	1.887e^-5	0.333	DOWNSTREAM CG32832 EXON CR31781	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	6779679	2L_6779679_INS [dm3] 2L_6779679_INS [dm6]	C	TCG	1.890e^-5	0.333	INTRON nrv1
2L	12210129	2L_12210129_SNP [dm3] 2L_12210129_SNP [dm6]	T	G	1.930e^-5	0.333	DOWNSTREAM CG31759 INTRON aret
X	16679364	X_16679364_DEL [dm3] X_16785331_DEL [dm6]	CGGATGTTTCTGAACGCAAA...	C	1.937e^-5	0.333	UTR_3_PRIME CG9609 DOWNSTREAM mRpL22
2L	2443910	2L_2443910_DEL [dm3] 2L_2443910_DEL [dm6]	TATAAATGCAAGTGA...	T	1.939e^-5	0.333	INTRON dpp	enhancer FlyBase regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
2L	6631112	2L_6631112_SNP [dm3] 2L_6631112_SNP [dm6]	G	A	1.944e^-5	0.333	INTRON Oatp26F
X	7293956	X_7293956_DEL [dm3] X_7399923_DEL [dm6]	TTTT	G	2.001e^-5	0.333	INTRON CG1677 & 1 other	TF binding site BDTNP1_TFBS_prd mE1_TFBS_sbb

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_2R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results