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=1.789e^-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

Covariate	p-value	Significance
wolba	0.02533
In_2L_t	0.06862

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2158 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
3R	5366433	3R_5366433_SNP [dm3] 3R_9540711_SNP [dm6]	A	T	9.782e^-7	0.625	SYNONYMOUS_CODING mura	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	17618570	3R_17618570_SNP [dm3] 3R_21792848_SNP [dm6]	A	G	2.277e^-6	0.625	INTRON CASK	TF binding site mE1_TFBS_cad
3R	25210851	3R_25210851_SNP [dm3] 3R_29385129_SNP [dm6]	C	A	2.327e^-6	0.625	INTRON Ptp99A
3R	5443035	3R_5443035_SNP [dm3] 3R_9617313_SNP [dm6]	A	G	2.751e^-6	0.625	INTRON CG8312
X	13351507	X_13351507_SNP [dm3] X_13457474_SNP [dm6]	T	C	3.391e^-6	0.625	NON_SYNONYMOUS_CODING CG34324 INTRON Neto
3L	14212573	3L_14212573_SNP [dm3] 3L_14219473_SNP [dm6]	C	T	4.171e^-6	0.625	UPSTREAM nuf DOWNSTREAM CG7768 INTRON nuf	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	5523009	3L_5523009_SNP [dm3] 3L_5529909_SNP [dm6]	A	T	4.328e^-6	0.625	UPSTREAM Lkr INTERGENIC
3L	23141225	3L_23141225_SNP [dm3] 3L_23148125_SNP [dm6]	C	T	4.771e^-6	0.625	NON_SYNONYMOUS_CODING CG32350
3L	16012418	3L_16012418_SNP [dm3] 3L_16019318_SNP [dm6]	C	T	4.883e^-6	0.625	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	16233661	3R_16233661_SNP [dm3] 3R_20407939_SNP [dm6]	A	G	4.937e^-6	0.625	UPSTREAM CG10881 & 1 other INTRON Gfrl
3R	21681623	3R_21681623_SNP [dm3] 3R_25855901_SNP [dm6]	T	C	5.088e^-6	0.625	UPSTREAM CG5890 INTERGENIC
2R	12818569	2R_12818569_SNP [dm3] 2R_16931064_SNP [dm6]	T	C	5.169e^-6	0.625	INTRON Pkc53E
3R	25210781	3R_25210781_SNP [dm3] 3R_29385059_SNP [dm6]	C	T	5.263e^-6	0.625	INTRON Ptp99A
3R	25210808	3R_25210808_INS [dm3] 3R_29385086_INS [dm6]	C	CACC	5.276e^-6	0.625	INTRON Ptp99A
3R	21681629	3R_21681629_SNP [dm3] 3R_25855907_SNP [dm6]	C	G	5.276e^-6	0.625	UPSTREAM CG5890 INTERGENIC
3R	11543653	3R_11543653_SNP [dm3] 3R_15717931_SNP [dm6]	G	C	5.336e^-6	0.625	INTERGENIC
3R	21681620	3R_21681620_SNP [dm3] 3R_25855898_SNP [dm6]	A	G	6.260e^-6	0.664	UPSTREAM CG5890 INTERGENIC
3L	14079083	3L_14079083_SNP [dm3] 3L_14085983_SNP [dm6]	T	G	6.376e^-6	0.664	DOWNSTREAM CG8100 INTERGENIC
3R	17618547	3R_17618547_SNP [dm3] 3R_21792825_SNP [dm6]	C	A	6.904e^-6	0.681	INTRON CASK	TF binding site mE1_TFBS_cad
3L	14210678	3L_14210678_INS [dm3] 3L_14217578_INS [dm6]	T	TT	9.092e^-6	0.781	UPSTREAM CG7768 INTRON nuf
3L	4516597	3L_4516597_SNP [dm3] 3L_4516597_SNP [dm6]	G	C	9.490e^-6	0.781	INTRON Tie	TF binding site mE1_TFBS_inv
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	1.034e^-5	0.781	DOWNSTREAM nrm INTERGENIC
2R	8294112	2R_8294112_SNP [dm3] 2R_12406607_SNP [dm6]	T	C	1.084e^-5	0.781	UTR_3_PRIME Cpr49Af DOWNSTREAM Cpr49Af
3R	5393507	3R_5393507_SNP [dm3] 3R_9567785_SNP [dm6]	G	A	1.086e^-5	0.781	SYNONYMOUS_CODING CG16789	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15363310	3R_15363310_SNP [dm3] 3R_19537588_SNP [dm6]	G	A	1.104e^-5	0.781	INTRON Dys
3L	17027644	3L_17027644_SNP [dm3] 3L_17034544_SNP [dm6]	G	A	1.105e^-5	0.781	UPSTREAM CR43250 INTERGENIC
3L	4700971	3L_4700971_SNP [dm3] 3L_4700971_SNP [dm6]	C	A	1.167e^-5	0.781	INTRON RhoGEF64C
3R	10373679	3R_10373679_SNP [dm3] 3R_14547957_SNP [dm6]	C	G	1.171e^-5	0.781	INTRON Pde6
3L	14291438	3L_14291438_SNP [dm3] 3L_14298338_SNP [dm6]	C	T	1.208e^-5	0.781	INTRON fz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Trl
3L	14079086	3L_14079086_SNP [dm3] 3L_14085986_SNP [dm6]	A	C	1.314e^-5	0.821	DOWNSTREAM CG8100 INTERGENIC
3L	3726865	3L_3726865_SNP [dm3] 3L_3726865_SNP [dm6]	T	C	1.358e^-5	0.822	INTRON CG32264
3R	11543738	3R_11543738_SNP [dm3] 3R_15718016_SNP [dm6]	C	T	1.414e^-5	0.829	INTERGENIC
3L	15943355	3L_15943355_SNP [dm3] 3L_15950255_SNP [dm6]	G	A	1.587e^-5	0.849	INTRON Pka-C3
3L	15055734	3L_15055734_SNP [dm3] 3L_15062634_SNP [dm6]	T	C	1.645e^-5	0.849	UPSTREAM CG13460 & 1 other INTRON Sytbeta
3L	14210674	3L_14210674_SNP [dm3] 3L_14217574_SNP [dm6]	C	T	1.847e^-5	0.849	UPSTREAM CG7768 INTRON nuf
2L	7484924	2L_7484924_SNP [dm3] 2L_7484924_SNP [dm6]	G	C	1.857e^-5	0.849	INTRON Ziz
3R	5648003	3R_5648003_SNP [dm3] 3R_9822281_SNP [dm6]	A	G	1.894e^-5	0.849	DOWNSTREAM CG34302 INTERGENIC
3R	21311871	3R_21311871_SNP [dm3] 3R_25486149_SNP [dm6]	C	T	1.912e^-5	0.849	UTR_3_PRIME Dhap-at DOWNSTREAM CG42488 & 1 other	TF binding site mE1_TFBS_cad
3L	1414405	3L_1414405_SNP [dm3] 3L_1414405_SNP [dm6]	C	T	1.957e^-5	0.849	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	14210635	3L_14210635_DEL [dm3] 3L_14217535_DEL [dm6]	GTTCTCGGTTACTAG...	G	1.998e^-5	0.849	UPSTREAM CG7768 INTRON nuf
2L	16782112	2L_16782112_SNP [dm3] 2L_16782112_SNP [dm6]	T	C	2.009e^-5	0.849	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3L	13102906	3L_13102906_DEL [dm3] 3L_13109806_DEL [dm6]	ATGTCCGA	A	2.031e^-5	0.849	INTERGENIC
3L	23148368	3L_23148368_SNP [dm3] 3L_23155268_SNP [dm6]	A	C	2.033e^-5	0.849	INTERGENIC	transposable element FlyBase
X	8418184	X_8418184_SNP [dm3] X_8524151_SNP [dm6]	T	A	2.083e^-5	0.849	INTRON Nrg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12612853	3L_12612853_SNP [dm3] 3L_12619753_SNP [dm6]	A	C	2.097e^-5	0.849	SYNONYMOUS_CODING caup	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	18819641	3L_18819641_SNP [dm3] 3L_18826541_SNP [dm6]	T	C	2.153e^-5	0.849	SYNONYMOUS_CODING Cat	TF binding site mE1_TFBS_chinmo
3R	10249528	3R_10249528_SNP [dm3] 3R_14423806_SNP [dm6]	A	G	2.162e^-5	0.849	INTRON cv-c
2R	12830616	2R_12830616_SNP [dm3] 2R_16943111_SNP [dm6]	T	C	2.195e^-5	0.849	UTR_3_PRIME Pkc53E DOWNSTREAM Pkc53E	TF binding site mE1_TFBS_inv
2L	16782062	2L_16782062_SNP [dm3] 2L_16782062_SNP [dm6]	G	A	2.282e^-5	0.849	INTRON Mhc	TF binding site mE1_TFBS_chinmo
2R	6058050	2R_6058050_SNP [dm3] 2R_10170545_SNP [dm6]	C	T	2.386e^-5	0.849	INTRON KCNQ
2L	16781974	2L_16781974_DEL [dm3] 2L_16781974_DEL [dm6]	GG	A	2.434e^-5	0.849	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3R	21681335	3R_21681335_INS [dm3] 3R_25855613_INS [dm6]	G	GTGTGCGAGG	2.438e^-5	0.849	UPSTREAM CG5890 INTERGENIC
3R	21681337	3R_21681337_INS [dm3] 3R_25855615_INS [dm6]	A	ATAAAATTATTTTGCCTT...	2.438e^-5	0.849	UPSTREAM CG5890 INTERGENIC
3R	11006745	3R_11006745_SNP [dm3] 3R_15181023_SNP [dm6]	G	C	2.444e^-5	0.849	UPSTREAM Mf INTRON Gyc88E & 1 other
2L	8262214	2L_8262214_SNP [dm3] 2L_8262214_SNP [dm6]	G	A	2.550e^-5	0.856	SYNONYMOUS_CODING Btk29A
3L	5523021	3L_5523021_SNP [dm3] 3L_5529921_SNP [dm6]	C	T	2.659e^-5	0.856	UPSTREAM Lkr INTERGENIC
3L	4701038	3L_4701038_SNP [dm3] 3L_4701038_SNP [dm6]	C	A	2.732e^-5	0.856	INTRON RhoGEF64C
X	12088885	X_12088885_SNP [dm3] X_12194852_SNP [dm6]	T	C	2.745e^-5	0.856	INTRON Ten-a
2L	3388550	2L_3388550_SNP [dm3] 2L_3388550_SNP [dm6]	T	G	2.818e^-5	0.856	UPSTREAM Sfp23F & 2 others INTERGENIC
3R	5445890	3R_5445890_SNP [dm3] 3R_9620168_SNP [dm6]	A	G	2.856e^-5	0.856	INTRON CG8312
2R	10228102	2R_10228102_INS [dm3] 2R_14340597_INS [dm6]	A	ACCCCTGCGAA...	2.874e^-5	0.856	INTRON Shroom
3R	5727434	3R_5727434_DEL [dm3] 3R_9901712_DEL [dm6]	TGT	T	2.907e^-5	0.856	INTRON Glut4EF
2L	16782103	2L_16782103_SNP [dm3] 2L_16782103_SNP [dm6]	T	A	2.957e^-5	0.856	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3L	23048784	3L_23048784_SNP [dm3] 3L_23055684_SNP [dm6]	T	C	2.992e^-5	0.856	INTERGENIC
3R	21486240	3R_21486240_SNP [dm3] 3R_25660518_SNP [dm6]	G	A	3.120e^-5	0.856	INTRON Tnks	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4880023	2L_4880023_SNP [dm3] 2L_4880023_SNP [dm6]	G	A	3.122e^-5	0.856	INTRON Cf2
3L	5534674	3L_5534674_SNP [dm3] 3L_5541574_SNP [dm6]	T	G	3.206e^-5	0.856	INTRON CG10625
2R	16090909	2R_16090909_SNP [dm3] 2R_20203404_SNP [dm6]	C	A	3.249e^-5	0.856	INTERGENIC
2R	12968077	2R_12968077_SNP [dm3] 2R_17080572_SNP [dm6]	G	A	3.360e^-5	0.856	INTRON CG30460
3L	14210684	3L_14210684_SNP [dm3] 3L_14217584_SNP [dm6]	C	A	3.363e^-5	0.856	UPSTREAM CG7768 INTRON nuf
3L	4701154	3L_4701154_SNP [dm3] 3L_4701154_SNP [dm6]	C	A	3.501e^-5	0.856	INTRON RhoGEF64C
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	3.650e^-5	0.856	INTRON pHCl
X	15068918	X_15068918_SNP [dm3] X_15174885_SNP [dm6]	A	T	3.699e^-5	0.856	UPSTREAM CG43737 INTERGENIC
X	3142787	X_3142787_INS [dm3] X_3248754_INS [dm6]	G	GCTG	3.706e^-5	0.856	CODON_INSERTION Pig1 UPSTREAM Sgs4 INTRON dnc
3R	5727398	3R_5727398_SNP [dm3] 3R_9901676_SNP [dm6]	T	C	3.791e^-5	0.856	INTRON Glut4EF
3L	16723767	3L_16723767_SNP [dm3] 3L_16730667_SNP [dm6]	A	T	3.862e^-5	0.856	INTRON Dbp73D	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21751121	3R_21751121_SNP [dm3] 3R_25925399_SNP [dm6]	C	T	4.069e^-5	0.856	INTRON CCAP-R
2L	4341634	2L_4341634_SNP [dm3] 2L_4341634_SNP [dm6]	C	T	4.129e^-5	0.856	SYNONYMOUS_CODING Atet INTRON Atet	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	5502830	2L_5502830_SNP [dm3] 2L_5502830_SNP [dm6]	A	G	4.182e^-5	0.856	INTERGENIC
3L	2680513	3L_2680513_SNP [dm3] 3L_2680513_SNP [dm6]	A	C	4.205e^-5	0.856	INTRON Fife
2R	13093069	2R_13093069_SNP [dm3] 2R_17205564_SNP [dm6]	A	T	4.294e^-5	0.856	NON_SYNONYMOUS_CODING CG43237
2L	5891814	2L_5891814_SNP [dm3] 2L_5891814_SNP [dm6]	T	A	4.483e^-5	0.856	DOWNSTREAM Acp26Ab INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	11533149	3R_11533149_SNP [dm3] 3R_15707427_SNP [dm6]	T	C	4.526e^-5	0.856	SYNONYMOUS_CODING CG5404
3L	4377238	3L_4377238_SNP [dm3] 3L_4377238_SNP [dm6]	A	T	4.596e^-5	0.856	DOWNSTREAM CR44360 INTRON DopEcR
3R	9884122	3R_9884122_SNP [dm3] 3R_14058400_SNP [dm6]	A	C	4.762e^-5	0.856	INTRON foxo
X	8098093	X_8098093_SNP [dm3] X_8204060_SNP [dm6]	T	G	4.869e^-5	0.856	INTRON sdt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14866127	2L_14866127_SNP [dm3] 2L_14866127_SNP [dm6]	C	T	4.882e^-5	0.856	INTERGENIC
2L	10521858	2L_10521858_SNP [dm3] 2L_10521858_SNP [dm6]	T	C	5.045e^-5	0.856	INTERGENIC
3L	10930521	3L_10930521_DEL [dm3] 3L_10937421_DEL [dm6]	AAG	A	5.142e^-5	0.856	INTERGENIC
3L	10930525	3L_10930525_INS [dm3] 3L_10937425_INS [dm6]	T	TAATTAA	5.142e^-5	0.856	INTERGENIC
2R	19599322	2R_19599322_INS [dm3] 2R_23711799_INS [dm6]	T	TC	5.233e^-5	0.856	INTERGENIC
3L	23115613	3L_23115613_SNP [dm3] 3L_23122513_SNP [dm6]	G	A	5.317e^-5	0.856	INTERGENIC	transposable element FlyBase
3R	14093531	3R_14093531_SNP [dm3] 3R_18267809_SNP [dm6]	G	C	5.323e^-5	0.856	UTR_5_PRIME CG18599	TF binding site mE1_TFBS_run
3R	5942189	3R_5942189_SNP [dm3] 3R_10116467_SNP [dm6]	C	G	5.376e^-5	0.856	INTRON CG3940
2L	8263358	2L_8263358_DEL [dm3] 2L_8263358_DEL [dm6]	TT	T	5.391e^-5	0.856	INTRON Btk29A
3R	21751105	3R_21751105_INS [dm3] 3R_25925383_INS [dm6]	T	TATA	5.395e^-5	0.856	INTRON CCAP-R
X	4715234	X_4715234_SNP [dm3] X_4821201_SNP [dm6]	A	G	5.411e^-5	0.856	INTERGENIC
3L	4701112	3L_4701112_SNP [dm3] 3L_4701112_SNP [dm6]	T	C	5.440e^-5	0.856	INTRON RhoGEF64C
3L	9007740	3L_9007740_SNP [dm3] 3L_9014640_SNP [dm6]	G	A	5.477e^-5	0.856	INTRON Doc2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	5327683	3R_5327683_SNP [dm3] 3R_9501961_SNP [dm6]	A	G	5.527e^-5	0.856	INTRON RhoL	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

pc_Surv_MeHg_10_CAFF phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results