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=1.462e^-12)
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	0.07545
In_3R_P	0.03591

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	5.9724	0.0505
In_2R_NS	7.0725	0.0291
In_3R_P	6.8247	0.033

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2475 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
3L	12710777	3L_12710777_SNP [dm3] 3L_12717677_SNP [dm6]	G	T	3.044e^-7	0.285	INTERGENIC
3L	12710782	3L_12710782_SNP [dm3] 3L_12717682_SNP [dm6]	G	A	3.044e^-7	0.285	INTERGENIC
2R	10532453	2R_10532453_SNP [dm3] 2R_14644948_SNP [dm6]	A	G	7.894e^-7	0.409	UPSTREAM CG10139 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10532472	2R_10532472_INS [dm3] 2R_14644967_INS [dm6]	A	AAA	9.648e^-7	0.409	UPSTREAM CG10139 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	8390049	2L_8390049_SNP [dm3] 2L_8390049_SNP [dm6]	C	T	2.250e^-6	0.409	UTR_3_PRIME CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3457477	2L_3457477_SNP [dm3] 2L_3457477_SNP [dm6]	C	T	2.256e^-6	0.409	SYNONYMOUS_CODING Sec5 UPSTREAM Cog3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2L	4717169	2L_4717169_INS [dm3] 2L_4717169_INS [dm6]	TT	AGAC	2.463e^-6	0.409	INTRON CG34351	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	1131908	3L_1131908_SNP [dm3] 3L_1131908_SNP [dm6]	T	C	2.597e^-6	0.409	INTERGENIC	regulatory region REDfly_CRMs
2R	9632088	2R_9632088_INS [dm3] 2R_13744583_INS [dm6]	T	TT	2.665e^-6	0.409	INTRON fas
2L	8390046	2L_8390046_SNP [dm3] 2L_8390046_SNP [dm6]	G	A	2.669e^-6	0.409	UTR_3_PRIME CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi
2L	5712219	2L_5712219_SNP [dm3] 2L_5712219_SNP [dm6]	C	T	2.733e^-6	0.409	INTRON CG7236
3L	1604325	3L_1604325_SNP [dm3] 3L_1604325_SNP [dm6]	A	C	2.764e^-6	0.409	NON_SYNONYMOUS_CODING CG18170 UTR_5_PRIME CG33791 UPSTREAM CG33791
2L	10643693	2L_10643693_SNP [dm3] 2L_10643693_SNP [dm6]	G	T	3.124e^-6	0.409	UPSTREAM CG18284 DOWNSTREAM CG31872 INTERGENIC
2R	12598741	2R_12598741_SNP [dm3] 2R_16711236_SNP [dm6]	A	G	3.359e^-6	0.409	INTRON CG30463
X	2823376	X_2823376_SNP [dm3] X_2929343_SNP [dm6]	G	C	3.537e^-6	0.409	UPSTREAM CG32793 INTRON kirre
2R	9253357	2R_9253357_SNP [dm3] 2R_13365852_SNP [dm6]	C	A	3.561e^-6	0.409	INTERGENIC	TF binding site mE1_TFBS_cad
X	2823428	X_2823428_SNP [dm3] X_2929395_SNP [dm6]	A	G	3.872e^-6	0.409	UPSTREAM CG32793 INTRON kirre
2R	9253351	2R_9253351_SNP [dm3] 2R_13365846_SNP [dm6]	A	T	4.088e^-6	0.409	INTERGENIC	TF binding site mE1_TFBS_cad
3L	10921255	3L_10921255_SNP [dm3] 3L_10928155_SNP [dm6]	T	C	4.292e^-6	0.409	INTERGENIC
X	9800486	X_9800486_SNP [dm3] X_9906453_SNP [dm6]	G	A	4.365e^-6	0.409	INTERGENIC
2L	5865178	2L_5865178_SNP [dm3] 2L_5865178_SNP [dm6]	G	A	5.033e^-6	0.426	INTRON rau	TF binding site BDTNP1_TFBS_twi
2L	9440069	2L_9440069_SNP [dm3] 2L_9440069_SNP [dm6]	T	C	5.246e^-6	0.426	NON_SYNONYMOUS_CODING CG33723 INTRON numb
2R	11704581	2R_11704581_SNP [dm3] 2R_15817076_SNP [dm6]	A	G	5.378e^-6	0.426	UPSTREAM Zasp52 INTRON tun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	5864670	2L_5864670_INS [dm3] 2L_5864670_INS [dm6]	CC	TGA	5.450e^-6	0.426	INTRON rau	TF binding site BDTNP1_TFBS_twi
X	12877933	X_12877933_SNP [dm3] X_12983900_SNP [dm6]	G	A	5.800e^-6	0.429	UPSTREAM CG32643 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12948734	3R_12948734_SNP [dm3] 3R_17123012_SNP [dm6]	G	T	5.946e^-6	0.429	UPSTREAM cher DOWNSTREAM CG42779 INTRON cher
2L	5864371	2L_5864371_SNP [dm3] 2L_5864371_SNP [dm6]	T	A	6.192e^-6	0.43	INTRON rau
2L	6398297	2L_6398297_DEL [dm3] 2L_6398297_DEL [dm6]	TCTGGAGGACGAAAG...	GT	6.824e^-6	0.434	INTRON CG42368
2R	9632106	2R_9632106_SNP [dm3] 2R_13744601_SNP [dm6]	A	T	6.853e^-6	0.434	INTRON fas
X	12877901	X_12877901_MNP [dm3] X_12983868_MNP [dm6]	TAT	ATA	6.935e^-6	0.434	UPSTREAM CG32643 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17342654	3L_17342654_SNP [dm3] 3L_17349554_SNP [dm6]	A	G	7.949e^-6	0.469	UTR_5_PRIME Mip	TF binding site BDTNP1_TFBS_dl
2L	3455416	2L_3455416_SNP [dm3] 2L_3455416_SNP [dm6]	C	T	8.219e^-6	0.469	SYNONYMOUS_CODING Cog3
3L	6518570	3L_6518570_DEL [dm3] 3L_6525470_DEL [dm6]	GCTGCCTG	G	8.691e^-6	0.469	INTRON sfl
2L	5865076	2L_5865076_SNP [dm3] 2L_5865076_SNP [dm6]	A	G	9.336e^-6	0.469	INTRON rau	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9631977	2R_9631977_SNP [dm3] 2R_13744472_SNP [dm6]	T	C	9.431e^-6	0.469	INTRON fas
2R	9632130	2R_9632130_SNP [dm3] 2R_13744625_SNP [dm6]	A	G	9.440e^-6	0.469	INTRON fas
X	2823447	X_2823447_SNP [dm3] X_2929414_SNP [dm6]	G	A	9.657e^-6	0.469	UPSTREAM CG32793 INTRON kirre
2L	7849716	2L_7849716_SNP [dm3] 2L_7849716_SNP [dm6]	G	T	9.741e^-6	0.469	INTRON CG14535
X	2823462	X_2823462_SNP [dm3] X_2929429_SNP [dm6]	A	G	9.966e^-6	0.469	UPSTREAM CG32793 INTRON kirre
2L	6001044	2L_6001044_SNP [dm3] 2L_6001044_SNP [dm6]	G	A	1.003e^-5	0.469	SYNONYMOUS_CODING Tsp26A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4717190	2L_4717190_SNP [dm3] 2L_4717190_SNP [dm6]	T	G	1.056e^-5	0.469	INTRON CG34351	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	15254400	2R_15254400_SNP [dm3] 2R_19366895_SNP [dm6]	T	C	1.120e^-5	0.469	SYNONYMOUS_CODING CG10051 DOWNSTREAM CG9416
2R	11711648	2R_11711648_SNP [dm3] 2R_15824143_SNP [dm6]	C	A	1.146e^-5	0.469	INTRON tun	TF binding site mE1_TFBS_cad
X	2823413	X_2823413_SNP [dm3] X_2929380_SNP [dm6]	A	G	1.187e^-5	0.469	UPSTREAM CG32793 INTRON kirre
2L	7849532	2L_7849532_SNP [dm3] 2L_7849532_SNP [dm6]	T	C	1.214e^-5	0.469	NON_SYNONYMOUS_CODING CG14535	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	17944451	2L_17944451_SNP [dm3] 2L_17944451_SNP [dm6]	G	T	1.241e^-5	0.469	INTERGENIC
2L	5866455	2L_5866455_SNP [dm3] 2L_5866455_SNP [dm6]	T	C	1.306e^-5	0.469	INTRON rau
3L	3528311	3L_3528311_SNP [dm3] 3L_3528311_SNP [dm6]	A	G	1.327e^-5	0.469	INTRON Eip63E
2L	5895083	2L_5895083_SNP [dm3] 2L_5895083_SNP [dm6]	C	G	1.328e^-5	0.469	INTERGENIC
2L	7847710	2L_7847710_SNP [dm3] 2L_7847710_SNP [dm6]	T	G	1.363e^-5	0.469	INTRON CG14535
2R	17180522	2R_17180522_SNP [dm3] 2R_21293017_SNP [dm6]	A	T	1.370e^-5	0.469	UPSTREAM CG30392 & 1 other INTRON Sgf29	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_sens
2R	17268226	2R_17268226_SNP [dm3] 2R_21380721_SNP [dm6]	G	T	1.386e^-5	0.469	INTERGENIC	TF binding site mE1_TFBS_sens
2R	17377458	2R_17377458_DEL [dm3] 2R_21489953_DEL [dm6]	TCCATTTCAT	T	1.386e^-5	0.469	INTRON Fkbp14
3L	6513749	3L_6513749_SNP [dm3] 3L_6520649_SNP [dm6]	G	A	1.393e^-5	0.469	INTRON sfl
X	9584882	X_9584882_SNP [dm3] X_9690849_SNP [dm6]	C	G	1.402e^-5	0.469	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	9261094	2L_9261094_SNP [dm3] 2L_9261094_SNP [dm6]	C	T	1.425e^-5	0.469	DOWNSTREAM CR45262 INTRON Ggamma30A
2L	9261095	2L_9261095_SNP [dm3] 2L_9261095_SNP [dm6]	C	T	1.425e^-5	0.469	DOWNSTREAM CR45262 INTRON Ggamma30A
2L	8390177	2L_8390177_SNP [dm3] 2L_8390177_SNP [dm6]	T	G	1.556e^-5	0.484	SYNONYMOUS_CODING CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17377431	2R_17377431_SNP [dm3] 2R_21489926_SNP [dm6]	G	A	1.562e^-5	0.484	INTRON Fkbp14
2L	8390546	2L_8390546_SNP [dm3] 2L_8390546_SNP [dm6]	T	C	1.572e^-5	0.484	NON_SYNONYMOUS_CODING CG42820 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	8464988	X_8464988_SNP [dm3] X_8570955_SNP [dm6]	C	T	1.624e^-5	0.484	UPSTREAM CG12111 DOWNSTREAM spirit & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	9025445	3L_9025445_INS [dm3] 3L_9032345_INS [dm6]	A	AA	1.627e^-5	0.484	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2R	10532301	2R_10532301_SNP [dm3] 2R_14644796_SNP [dm6]	T	A	1.662e^-5	0.484	UPSTREAM CG10139 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	1.667e^-5	0.484	INTERGENIC	TF binding site mE1_TFBS_inv
2L	9120540	2L_9120540_INS [dm3] 2L_9120540_INS [dm6]	C	CTC	1.678e^-5	0.484	DOWNSTREAM CR44617 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med
2L	9304036	2L_9304036_SNP [dm3] 2L_9304036_SNP [dm6]	C	T	1.719e^-5	0.489	DOWNSTREAM CR42844 INTERGENIC
2R	10692431	2R_10692431_SNP [dm3] 2R_14804926_SNP [dm6]	T	G	1.765e^-5	0.494	INTRON kn	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
2L	7681349	2L_7681349_SNP [dm3] 2L_7681349_SNP [dm6]	G	A	1.862e^-5	0.514	SYNONYMOUS_CODING Myo28B1	TF binding site mE1_TFBS_HSA
2R	10154275	2R_10154275_SNP [dm3] 2R_14266770_SNP [dm6]	A	G	2.005e^-5	0.539	INTRON CG8547
2L	9121247	2L_9121247_SNP [dm3] 2L_9121247_SNP [dm6]	T	C	2.011e^-5	0.539	DOWNSTREAM CR44616 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med
2L	10643716	2L_10643716_SNP [dm3] 2L_10643716_SNP [dm6]	T	C	2.071e^-5	0.543	UPSTREAM CG18284 DOWNSTREAM CG31872 INTERGENIC
3L	8718207	3L_8718207_SNP [dm3] 3L_8725107_SNP [dm6]	T	A	2.097e^-5	0.543	DOWNSTREAM CG43965 INTRON CG6511
2R	19047041	2R_19047041_SNP [dm3] 2R_23159518_SNP [dm6]	C	A	2.128e^-5	0.543	NON_SYNONYMOUS_CODING CG9899
2L	17054282	2L_17054282_SNP [dm3] 2L_17054282_SNP [dm6]	A	T	2.147e^-5	0.543	INTERGENIC
X	12877871	X_12877871_SNP [dm3] X_12983838_SNP [dm6]	T	G	2.172e^-5	0.543	UPSTREAM CG32643 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17268087	2R_17268087_SNP [dm3] 2R_21380582_SNP [dm6]	A	C	2.240e^-5	0.543	INTERGENIC
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	2.247e^-5	0.543	INTERGENIC	TF binding site mE1_TFBS_inv
2R	6599327	2R_6599327_SNP [dm3] 2R_10711822_SNP [dm6]	C	T	2.290e^-5	0.543	SYNONYMOUS_CODING stan
2R	10763630	2R_10763630_SNP [dm3] 2R_14876125_SNP [dm6]	G	C	2.295e^-5	0.543	NON_SYNONYMOUS_CODING Cyp6a23 DOWNSTREAM Cyp6a17
2R	9631995	2R_9631995_DEL [dm3] 2R_13744490_DEL [dm6]	GT	G	2.341e^-5	0.543	INTRON fas
2L	9303748	2L_9303748_INS [dm3] 2L_9303748_INS [dm6]	G	GTCGTGGCAATG...	2.425e^-5	0.543	DOWNSTREAM CR42844 INTERGENIC
X	6905965	X_6905965_SNP [dm3] X_7011932_SNP [dm6]	C	T	2.439e^-5	0.543	SYNONYMOUS_CODING CG42308 UTR_3_PRIME CG32736 UPSTREAM cm DOWNSTREAM CG3032	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8390166	2L_8390166_SNP [dm3] 2L_8390166_SNP [dm6]	A	G	2.473e^-5	0.543	SYNONYMOUS_CODING CG42820 UPSTREAM CG42819 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4376521	2L_4376521_SNP [dm3] 2L_4376521_SNP [dm6]	A	T	2.482e^-5	0.543	INTRON Traf4	TF binding site mE1_TFBS_cad
3R	22552060	3R_22552060_SNP [dm3] 3R_26726338_SNP [dm6]	G	A	2.488e^-5	0.543	SYNONYMOUS_CODING CG14244 UPSTREAM CG14246
3R	8071278	3R_8071278_SNP [dm3] 3R_12245556_SNP [dm6]	G	C	2.501e^-5	0.543	DOWNSTREAM CR45582 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
2L	19913184	2L_19913184_SNP [dm3] 2L_19913184_SNP [dm6]	A	G	2.525e^-5	0.543	SYNONYMOUS_CODING Victoria UPSTREAM TotF INTRON sick
2R	17378262	2R_17378262_SNP [dm3] 2R_21490757_SNP [dm6]	G	T	2.547e^-5	0.543	INTRON Fkbp14
2L	10643708	2L_10643708_SNP [dm3] 2L_10643708_SNP [dm6]	A	T	2.621e^-5	0.552	UPSTREAM CG18284 DOWNSTREAM CG31872 INTERGENIC
3L	6532545	3L_6532545_SNP [dm3] 3L_6539445_SNP [dm6]	A	G	2.659e^-5	0.554	INTRON sfl
X	18461540	X_18461540_SNP [dm3] X_18567507_SNP [dm6]	G	T	2.721e^-5	0.557	SPLICE_SITE_REGION Bx INTRON Bx
3L	2263668	3L_2263668_SNP [dm3] 3L_2263668_SNP [dm6]	T	A	2.758e^-5	0.557	NON_SYNONYMOUS_CODING ecd DOWNSTREAM CG13807	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	5615803	X_5615803_DEL [dm3] X_5721770_DEL [dm6]	ATTGTGCA	A	2.792e^-5	0.557	INTRON CG32758
X	5615812	X_5615812_SNP [dm3] X_5721779_SNP [dm6]	C	T	2.792e^-5	0.557	INTRON CG32758
2L	2844914	2L_2844914_SNP [dm3] 2L_2844914_SNP [dm6]	G	A	2.902e^-5	0.57	NON_SYNONYMOUS_CODING CG18557 UPSTREAM CG18558	TF binding site mE1_TFBS_cad
X	4548215	X_4548215_SNP [dm3] X_4654182_SNP [dm6]	T	C	2.916e^-5	0.57	SYNONYMOUS_CODING CG15473 INTRON Cbp80	TF binding site mE1_TFBS_chinmo
3L	4100722	3L_4100722_SNP [dm3] 3L_4100722_SNP [dm6]	C	T	3.044e^-5	0.583	INTRON CG14995
2L	7847730	2L_7847730_SNP [dm3] 2L_7847730_SNP [dm6]	T	G	3.046e^-5	0.583	INTRON CG14535	TF binding site mE1_TFBS_cad
2R	10673027	2R_10673027_SNP [dm3] 2R_14785522_SNP [dm6]	G	A	3.091e^-5	0.586	INTRON kn
2R	10151602	2R_10151602_SNP [dm3] 2R_14264097_SNP [dm6]	C	T	3.149e^-5	0.589	INTRON CG8547	TF binding site mE1_TFBS_cad

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By genomic position
Variant impact
Gene name

Delta_Alive.at.48h Experience 3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results