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=2.100e^-7)
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

1865 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	8564892	2R_8564892_SNP [dm3] 2R_12677387_SNP [dm6]	G	C	1.308e^-7	0.243	UPSTREAM CG42708 INTRON CG42708
3R	16491259	3R_16491259_SNP [dm3] 3R_20665537_SNP [dm6]	G	A	4.070e^-7	0.349	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9829111	2L_9829111_SNP [dm3] 2L_9829111_SNP [dm6]	A	G	7.876e^-7	0.349	INTRON nAChRalpha6
X	11110019	X_11110019_SNP [dm3] X_11215986_SNP [dm6]	G	A	8.939e^-7	0.349	INTERGENIC
3L	10909326	3L_10909326_SNP [dm3] 3L_10916226_SNP [dm6]	A	C	1.028e^-6	0.349	INTERGENIC
3L	10909452	3L_10909452_SNP [dm3] 3L_10916352_SNP [dm6]	A	C	1.315e^-6	0.349	INTERGENIC
3L	10909465	3L_10909465_SNP [dm3] 3L_10916365_SNP [dm6]	A	G	1.315e^-6	0.349	INTERGENIC
X	11110017	X_11110017_SNP [dm3] X_11215984_SNP [dm6]	A	G	1.742e^-6	0.373	INTERGENIC
3L	10909368	3L_10909368_SNP [dm3] 3L_10916268_SNP [dm6]	T	C	1.803e^-6	0.373	INTERGENIC
3R	18955231	3R_18955231_SNP [dm3] 3R_23129509_SNP [dm6]	G	A	2.665e^-6	0.421	INTRON hh	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	8564808	2R_8564808_INS [dm3] 2R_12677303_INS [dm6]	T	TTTTTGTTTCATTTCTCAAA...	2.683e^-6	0.421	UPSTREAM CG42708 INTRON CG42708
3R	3964184	3R_3964184_SNP [dm3] 3R_8138462_SNP [dm6]	T	A	2.713e^-6	0.421	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	8564927	2R_8564927_SNP [dm3] 2R_12677422_SNP [dm6]	T	A	3.373e^-6	0.446	UPSTREAM CG42708 INTRON CG42708
2R	8564825	2R_8564825_SNP [dm3] 2R_12677320_SNP [dm6]	A	T	3.576e^-6	0.446	UPSTREAM CG42708 INTRON CG42708
2R	2817832	2R_2817832_SNP [dm3] 2R_6930327_SNP [dm6]	C	A	3.701e^-6	0.446	SYNONYMOUS_CODING mim	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	12597388	3R_12597388_DEL [dm3] 3R_16771666_DEL [dm6]	TCCAAGCCAATGCTTTTACA...	A	3.836e^-6	0.446	INTRON bxd	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	8564723	2R_8564723_SNP [dm3] 2R_12677218_SNP [dm6]	T	C	4.605e^-6	0.465	UPSTREAM CG42708 INTRON CG42708
2L	744124	2L_744124_DEL [dm3] 2L_744124_DEL [dm6]	TGCTCCTTAGCTT...	T	5.374e^-6	0.465	UTR_5_PRIME Eaat2 INTRON Eaat2
3R	20407172	3R_20407172_SNP [dm3] 3R_24581450_SNP [dm6]	C	T	5.455e^-6	0.465	INTRON CG13624	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	3872068	2L_3872068_SNP [dm3] 2L_3872068_SNP [dm6]	C	A	5.579e^-6	0.465	DOWNSTREAM Cep97 & 1 other INTRON CG31957	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
X	12207372	X_12207372_SNP [dm3] X_12313339_SNP [dm6]	C	T	5.603e^-6	0.465	INTRON Ten-a
2L	744069	2L_744069_SNP [dm3] 2L_744069_SNP [dm6]	G	C	5.735e^-6	0.465	INTRON Eaat2
2R	8564805	2R_8564805_SNP [dm3] 2R_12677300_SNP [dm6]	G	A	6.086e^-6	0.465	UPSTREAM CG42708 INTRON CG42708
2L	9459078	2L_9459078_SNP [dm3] 2L_9459078_SNP [dm6]	T	C	6.182e^-6	0.465	INTRON numb
2R	15514869	2R_15514869_INS [dm3] 2R_19627364_INS [dm6]	C	CC	6.248e^-6	0.465	INTRON sm
3L	1140656	3L_1140656_SNP [dm3] 3L_1140656_SNP [dm6]	A	G	7.238e^-6	0.491	UTR_3_PRIME bab2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	19204264	2L_19204264_SNP [dm3] 2L_19204264_SNP [dm6]	G	A	7.358e^-6	0.491	INTRON drl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_Kr
2R	15514830	2R_15514830_SNP [dm3] 2R_19627325_SNP [dm6]	T	C	7.848e^-6	0.491	INTRON sm
2R	15514786	2R_15514786_SNP [dm3] 2R_19627281_SNP [dm6]	A	G	7.849e^-6	0.491	INTRON sm
X	7732071	X_7732071_SNP [dm3] X_7838038_SNP [dm6]	C	T	7.978e^-6	0.491	INTRON CG1402
3L	9510270	3L_9510270_DEL [dm3] 3L_9517170_DEL [dm6]	TT	A	8.348e^-6	0.491	INTRON CG33700
3L	15012944	3L_15012944_SNP [dm3] 3L_15019844_SNP [dm6]	A	G	8.690e^-6	0.491	INTRON Sytbeta
2R	8564379	2R_8564379_SNP [dm3] 2R_12676874_SNP [dm6]	G	T	8.702e^-6	0.491	UPSTREAM CG42708 INTRON CG42708
X	11110031	X_11110031_SNP [dm3] X_11215998_SNP [dm6]	G	C	9.564e^-6	0.523	INTERGENIC
3L	17941952	3L_17941952_SNP [dm3] 3L_17948852_SNP [dm6]	T	A	1.048e^-5	0.557	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	10630733	2L_10630733_SNP [dm3] 2L_10630733_SNP [dm6]	A	C	1.176e^-5	0.59	SYNONYMOUS_CODING CG7329	TF binding site mE1_TFBS_sens
3R	9606843	3R_9606843_SNP [dm3] 3R_13781121_SNP [dm6]	C	T	1.195e^-5	0.59	NON_SYNONYMOUS_CODING CG9286 DOWNSTREAM CG9288 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
X	11110229	X_11110229_SNP [dm3] X_11216196_SNP [dm6]	C	T	1.241e^-5	0.59	INTERGENIC
2L	19121423	2L_19121423_SNP [dm3] 2L_19121423_SNP [dm6]	G	A	1.251e^-5	0.59	UTR_3_PRIME l_2_37Cc DOWNSTREAM l_2_37Cc	regulatory region REDfly_CRMs
3R	21365535	3R_21365535_SNP [dm3] 3R_25539813_SNP [dm6]	A	G	1.268e^-5	0.59	INTRON msi
2L	6617729	2L_6617729_SNP [dm3] 2L_6617729_SNP [dm6]	A	G	1.347e^-5	0.611	DOWNSTREAM CG11050 INTRON CG11320	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	12481458	3R_12481458_SNP [dm3] 3R_16655736_SNP [dm6]	G	A	1.431e^-5	0.621	UPSTREAM modSP DOWNSTREAM Ubx INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_zfh1
X	11110005	X_11110005_SNP [dm3] X_11215972_SNP [dm6]	C	G	1.434e^-5	0.621	INTERGENIC
3R	19235650	3R_19235650_SNP [dm3] 3R_23409928_SNP [dm6]	G	A	1.475e^-5	0.624	UTR_3_PRIME CG4374
2R	14681130	2R_14681130_SNP [dm3] 2R_18793625_SNP [dm6]	G	A	1.552e^-5	0.642	SYNONYMOUS_CODING CG15080 DOWNSTREAM MFS15	TF binding site mE1_TFBS_chinmo
3R	19153765	3R_19153765_SNP [dm3] 3R_23328043_SNP [dm6]	C	T	1.628e^-5	0.659	INTRON pnt
3R	26303197	3R_26303197_SNP [dm3] 3R_30477475_SNP [dm6]	C	T	1.676e^-5	0.664	SYNONYMOUS_CODING spdo INTRON PH4alphaEFB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	26177447	3R_26177447_DEL [dm3] 3R_30351725_DEL [dm6]	CA	C	1.823e^-5	0.707	INTRON hdc	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	18599257	3R_18599257_SNP [dm3] 3R_22773535_SNP [dm6]	G	A	2.016e^-5	0.727	UPSTREAM mir-4953 INTRON Usp12-46 & 1 other
3R	23968396	3R_23968396_SNP [dm3] 3R_28142674_SNP [dm6]	T	G	2.083e^-5	0.727	INTERGENIC
3R	5213803	3R_5213803_SNP [dm3] 3R_9388081_SNP [dm6]	G	C	2.124e^-5	0.727	INTRON FER
2R	14681136	2R_14681136_SNP [dm3] 2R_18793631_SNP [dm6]	C	A	2.158e^-5	0.727	SYNONYMOUS_CODING CG15080 DOWNSTREAM MFS15	TF binding site mE1_TFBS_chinmo
3R	14162854	3R_14162854_SNP [dm3] 3R_18337132_SNP [dm6]	G	T	2.177e^-5	0.727	INTRON CG15803
3L	5417994	3L_5417994_INS [dm3] 3L_5424894_INS [dm6]	G	GG	2.192e^-5	0.727	INTRON CG34391
3R	23901337	3R_23901337_SNP [dm3] 3R_28075615_SNP [dm6]	T	A	2.308e^-5	0.727	INTRON CG34362
3R	9609921	3R_9609921_SNP [dm3] 3R_13784199_SNP [dm6]	T	G	2.380e^-5	0.727	SYNONYMOUS_CODING Dip-B	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	4130323	2L_4130323_SNP [dm3] 2L_4130323_SNP [dm6]	G	A	2.414e^-5	0.727	INTERGENIC
2R	8564816	2R_8564816_SNP [dm3] 2R_12677311_SNP [dm6]	T	A	2.415e^-5	0.727	UPSTREAM CG42708 INTRON CG42708
2R	11460445	2R_11460445_SNP [dm3] 2R_15572940_SNP [dm6]	G	A	2.417e^-5	0.727	UTR_3_PRIME CG30466 DOWNSTREAM CG8204
3R	12578238	3R_12578238_SNP [dm3] 3R_16752516_SNP [dm6]	C	A	2.504e^-5	0.727	UPSTREAM bxd INTRON bxd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	12579190	3R_12579190_SNP [dm3] 3R_16753468_SNP [dm6]	G	A	2.504e^-5	0.727	INTRON bxd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	12590223	3R_12590223_SNP [dm3] 3R_16764501_SNP [dm6]	A	G	2.504e^-5	0.727	UPSTREAM tre-3 DOWNSTREAM tre-1 INTRON bxd EXON tre-2	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_Ubx
3R	12594930	3R_12594930_SNP [dm3] 3R_16769208_SNP [dm6]	A	C	2.504e^-5	0.727	INTRON bxd	TF binding site mE1_TFBS_HSA mE1_TFBS_Ubx
2L	1904112	2L_1904112_SNP [dm3] 2L_1904112_SNP [dm6]	C	A	2.516e^-5	0.727	INTRON CG7337
3R	26177446	3R_26177446_SNP [dm3] 3R_30351724_SNP [dm6]	C	G	2.563e^-5	0.727	INTRON hdc	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	15514901	2R_15514901_SNP [dm3] 2R_19627396_SNP [dm6]	G	A	2.743e^-5	0.727	INTRON sm
3R	16986024	3R_16986024_SNP [dm3] 3R_21160302_SNP [dm6]	C	A	2.745e^-5	0.727	NON_SYNONYMOUS_CODING CG10824 INTRON SNF4Agamma
2R	7359147	2R_7359147_SNP [dm3] 2R_11471642_SNP [dm6]	T	G	2.749e^-5	0.727	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	15514959	2R_15514959_SNP [dm3] 2R_19627454_SNP [dm6]	T	C	2.758e^-5	0.727	INTRON sm
3L	10909309	3L_10909309_SNP [dm3] 3L_10916209_SNP [dm6]	A	G	2.785e^-5	0.727	INTERGENIC
3R	18185951	3R_18185951_SNP [dm3] 3R_22360229_SNP [dm6]	G	A	2.827e^-5	0.727	UTR_3_PRIME Sar1 DOWNSTREAM PSR
3R	14896169	3R_14896169_SNP [dm3] 3R_19070447_SNP [dm6]	C	T	2.846e^-5	0.727	INTRON cdi
2L	5263639	2L_5263639_SNP [dm3] 2L_5263639_SNP [dm6]	C	T	2.853e^-5	0.727	UPSTREAM Cyp4ac1 INTRON tkv
3R	25602005	3R_25602005_DEL [dm3] 3R_29776283_DEL [dm6]	ACAAAACACAA...	A	2.931e^-5	0.737	INTRON kay
3R	5402887	3R_5402887_SNP [dm3] 3R_9577165_SNP [dm6]	A	G	3.017e^-5	0.748	UPSTREAM CG8273 INTRON Kap-alpha3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	17952227	3R_17952227_SNP [dm3] 3R_22126505_SNP [dm6]	T	C	3.126e^-5	0.76	INTRON CG42390	TF binding site mE1_TFBS_cad
X	13870282	X_13870282_SNP [dm3] X_13976249_SNP [dm6]	T	C	3.207e^-5	0.76	INTRON mamo
3R	17952195	3R_17952195_SNP [dm3] 3R_22126473_SNP [dm6]	T	G	3.216e^-5	0.76	SPLICE_SITE_REGION CG42390 INTRON CG42390	TF binding site mE1_TFBS_cad
3R	25601378	3R_25601378_INS [dm3] 3R_29775656_INS [dm6]	T	TCACT	3.244e^-5	0.76	INTRON kay	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
3R	26612711	3R_26612711_SNP [dm3] 3R_30786989_SNP [dm6]	A	G	3.268e^-5	0.76	UTR_3_PRIME zfh1
3R	9606400	3R_9606400_SNP [dm3] 3R_13780678_SNP [dm6]	T	A	3.339e^-5	0.764	UTR_3_PRIME CG42375 & 1 other UPSTREAM CG9286	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	13956798	2L_13956798_SNP [dm3] 2L_13956798_SNP [dm6]	T	C	3.428e^-5	0.764	UPSTREAM NimA DOWNSTREAM Ance-3 INTERGENIC
2R	13693286	2R_13693286_SNP [dm3] 2R_17805781_SNP [dm6]	C	T	3.438e^-5	0.764	INTRON grh	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sbb
3L	7812046	3L_7812046_SNP [dm3] 3L_7818946_SNP [dm6]	T	A	3.451e^-5	0.764	INTRON Pdp1	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	21365503	3R_21365503_SNP [dm3] 3R_25539781_SNP [dm6]	A	T	3.491e^-5	0.764	INTRON msi
X	9092643	X_9092643_SNP [dm3] X_9198610_SNP [dm6]	A	G	3.733e^-5	0.808	SYNONYMOUS_CODING su_r_	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	20289950	2L_20289950_SNP [dm3] 2L_20289950_SNP [dm6]	G	A	4.030e^-5	0.809	INTERGENIC
X	12206837	X_12206837_SNP [dm3] X_12312804_SNP [dm6]	A	G	4.040e^-5	0.809	SYNONYMOUS_CODING Ten-a
3R	3964138	3R_3964138_SNP [dm3] 3R_8138416_SNP [dm6]	A	G	4.128e^-5	0.809	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
X	945540	X_945540_SNP [dm3] X_1051507_SNP [dm6]	A	G	4.195e^-5	0.809	UPSTREAM CG14629 INTRON CR44779
2R	8564418	2R_8564418_SNP [dm3] 2R_12676913_SNP [dm6]	C	A	4.287e^-5	0.809	UPSTREAM CG42708 INTRON CG42708
3R	5175468	3R_5175468_SNP [dm3] 3R_9349746_SNP [dm6]	G	T	4.333e^-5	0.809	INTRON CG45050	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	15052893	2R_15052893_SNP [dm3] 2R_19165388_SNP [dm6]	A	G	4.336e^-5	0.809	START_GAINED CG10737 UTR_5_PRIME CG10737 INTRON CG10737
3R	11282175	3R_11282175_DEL [dm3] 3R_15456453_DEL [dm6]	ATTGTA	A	4.446e^-5	0.809	INTRON AdamTS-A
3L	3577024	3L_3577024_SNP [dm3] 3L_3577024_SNP [dm6]	C	G	4.465e^-5	0.809	INTRON Eip63E
2L	4157435	2L_4157435_SNP [dm3] 2L_4157435_SNP [dm6]	T	A	4.532e^-5	0.809	INTERGENIC
3L	13953197	3L_13953197_SNP [dm3] 3L_13960097_SNP [dm6]	G	A	4.554e^-5	0.809	INTRON CG32137
X	938024	X_938024_SNP [dm3] X_1043991_SNP [dm6]	T	G	4.643e^-5	0.809	SYNONYMOUS_CODING su_w[a]_ UTR_3_PRIME su_w[a]_
3R	26177428	3R_26177428_SNP [dm3] 3R_30351706_SNP [dm6]	A	G	4.649e^-5	0.809	INTRON hdc	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	23986512	3R_23986512_SNP [dm3] 3R_28160790_SNP [dm6]	C	G	4.681e^-5	0.809	INTRON CG34354

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By genomic position
Variant impact
Gene name

Microbiota_OTU172 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results