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=2.862e^-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

1990 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	16960128	2R_16960128_SNP [dm3] 2R_21072623_SNP [dm6]	A	G	3.932e^-7	0.402	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
2R	16959828	2R_16959828_SNP [dm3] 2R_21072323_SNP [dm6]	C	G	4.596e^-7	0.402	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
2R	16959829	2R_16959829_SNP [dm3] 2R_21072324_SNP [dm6]	T	G	8.214e^-7	0.402	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
X	20434979	X_20434979_SNP [dm3] X_20563952_SNP [dm6]	C	A	1.100e^-6	0.402	INTRON RunxB
3R	8400796	3R_8400796_SNP [dm3] 3R_12575074_SNP [dm6]	A	G	1.106e^-6	0.402	INTRON Octbeta2R
3L	11050564	3L_11050564_SNP [dm3] 3L_11057464_SNP [dm6]	A	G	1.991e^-6	0.603	INTRON CG7888
2L	7644136	2L_7644136_SNP [dm3] 2L_7644136_SNP [dm6]	T	A	3.484e^-6	0.704	SYNONYMOUS_CODING Slob UTR_3_PRIME Slob
2R	16959715	2R_16959715_SNP [dm3] 2R_21072210_SNP [dm6]	C	T	3.530e^-6	0.704	DOWNSTREAM CR44704 INTRON CG10527
2R	16959744	2R_16959744_SNP [dm3] 2R_21072239_SNP [dm6]	A	G	3.530e^-6	0.704	DOWNSTREAM CR44704 INTRON CG10527
3L	21968433	3L_21968433_SNP [dm3] 3L_21975333_SNP [dm6]	A	G	3.875e^-6	0.704	INTRON CG7470
2R	16959726	2R_16959726_SNP [dm3] 2R_21072221_SNP [dm6]	G	A	4.300e^-6	0.71	DOWNSTREAM CR44704 INTRON CG10527
2R	19341961	2R_19341961_SNP [dm3] 2R_23454438_SNP [dm6]	T	C	4.853e^-6	0.735	INTRON CG43795
X	8151464	X_8151464_SNP [dm3] X_8257431_SNP [dm6]	G	T	6.215e^-6	0.761	INTRON CG1632
3L	10396532	3L_10396532_SNP [dm3] 3L_10403432_SNP [dm6]	C	A	6.344e^-6	0.761	INTERGENIC
2R	16959837	2R_16959837_SNP [dm3] 2R_21072332_SNP [dm6]	A	C	6.696e^-6	0.761	DOWNSTREAM CR44704 INTRON CG10527	TF binding site mE1_TFBS_Trl
3L	14244718	3L_14244718_SNP [dm3] 3L_14251618_SNP [dm6]	T	G	7.298e^-6	0.761	INTERGENIC
2R	14346359	2R_14346359_SNP [dm3] 2R_18458854_SNP [dm6]	A	C	7.677e^-6	0.761	DOWNSTREAM CG30116 INTRON CG30116
3L	7628925	3L_7628925_SNP [dm3] 3L_7635825_SNP [dm6]	G	A	8.039e^-6	0.761	INTRON CG33275	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11122657	3L_11122657_SNP [dm3] 3L_11129557_SNP [dm6]	A	G	8.178e^-6	0.761	UTR_5_PRIME CG42575
X	20434973	X_20434973_SNP [dm3] X_20563946_SNP [dm6]	C	T	8.449e^-6	0.761	INTRON RunxB
3R	15301280	3R_15301280_SNP [dm3] 3R_19475558_SNP [dm6]	G	C	8.911e^-6	0.761	INTRON Dys	TF binding site mE1_TFBS_inv
3L	14068289	3L_14068289_SNP [dm3] 3L_14075189_SNP [dm6]	G	T	9.554e^-6	0.761	SYNONYMOUS_CODING Pex1 UPSTREAM btl
3L	13277233	3L_13277233_SNP [dm3] 3L_13284133_SNP [dm6]	T	G	1.037e^-5	0.761	DOWNSTREAM CR43146 INTRON CR43913 EXON CR43913
X	4884063	X_4884063_SNP [dm3] X_4990030_SNP [dm6]	C	T	1.192e^-5	0.761	INTRON CR44833
2L	3985015	2L_3985015_SNP [dm3] 2L_3985015_SNP [dm6]	C	A	1.398e^-5	0.761	INTRON fred
3L	21968126	3L_21968126_SNP [dm3] 3L_21975026_SNP [dm6]	T	A	1.464e^-5	0.761	INTRON CG7470
3L	21968129	3L_21968129_SNP [dm3] 3L_21975029_SNP [dm6]	T	C	1.464e^-5	0.761	INTRON CG7470
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	1.464e^-5	0.761	INTRON CG7470
3L	2353118	3L_2353118_SNP [dm3] 3L_2353118_SNP [dm6]	T	A	1.495e^-5	0.761	INTERGENIC
X	18639411	X_18639411_SNP [dm3] X_18745378_SNP [dm6]	C	A	1.539e^-5	0.761	DOWNSTREAM CG12609 INTERGENIC
2L	15325079	2L_15325079_SNP [dm3] 2L_15325079_SNP [dm6]	A	G	1.601e^-5	0.761	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
X	18639467	X_18639467_SNP [dm3] X_18745434_SNP [dm6]	T	A	1.626e^-5	0.761	DOWNSTREAM CG12609 INTERGENIC
3R	23749487	3R_23749487_SNP [dm3] 3R_27923765_SNP [dm6]	A	G	1.633e^-5	0.761	UPSTREAM snoRNA:Or-aca3 INTRON RpL4	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4659210	3L_4659210_SNP [dm3] 3L_4659210_SNP [dm6]	G	T	1.682e^-5	0.761	INTRON axo
X	20434955	X_20434955_SNP [dm3] X_20563928_SNP [dm6]	C	T	1.766e^-5	0.761	INTRON RunxB
X	8151420	X_8151420_SNP [dm3] X_8257387_SNP [dm6]	A	T	1.841e^-5	0.761	INTRON CG1632
3L	8958470	3L_8958470_SNP [dm3] 3L_8965370_SNP [dm6]	G	A	1.853e^-5	0.761	SYNONYMOUS_CODING CG5653 UPSTREAM CG5660	TF binding site mE1_TFBS_chinmo
3L	4659222	3L_4659222_SNP [dm3] 3L_4659222_SNP [dm6]	T	G	1.897e^-5	0.761	INTRON axo
2R	17132293	2R_17132293_INS [dm3] 2R_21244788_INS [dm6]	C	CC	2.048e^-5	0.761	INTRON ASPP	TF binding site BDTNP1_TFBS_prd
2L	2079325	2L_2079325_SNP [dm3] 2L_2079325_SNP [dm6]	A	G	2.057e^-5	0.761	UPSTREAM CG12674 INTRON dpr3
2L	5885421	2L_5885421_SNP [dm3] 2L_5885421_SNP [dm6]	T	C	2.085e^-5	0.761	UTR_3_PRIME CG43185 UPSTREAM Sfp26Ac & 1 other
2L	5466268	2L_5466268_SNP [dm3] 2L_5466268_SNP [dm6]	C	T	2.114e^-5	0.761	SYNONYMOUS_CODING mid	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26240869	3R_26240869_SNP [dm3] 3R_30415147_SNP [dm6]	T	C	2.126e^-5	0.761	INTERGENIC
2R	16959766	2R_16959766_SNP [dm3] 2R_21072261_SNP [dm6]	G	T	2.136e^-5	0.761	DOWNSTREAM CR44704 INTRON CG10527
3L	11132689	3L_11132689_SNP [dm3] 3L_11139589_SNP [dm6]	A	C	2.208e^-5	0.761	INTRON CG32082
3L	11132693	3L_11132693_SNP [dm3] 3L_11139593_SNP [dm6]	T	C	2.208e^-5	0.761	INTRON CG32082
3L	11132756	3L_11132756_SNP [dm3] 3L_11139656_SNP [dm6]	C	G	2.208e^-5	0.761	INTRON CG32082
3R	23613233	3R_23613233_SNP [dm3] 3R_27787511_SNP [dm6]	C	A	2.228e^-5	0.761	INTRON CG34353
3L	13060245	3L_13060245_SNP [dm3] 3L_13067145_SNP [dm6]	C	T	2.236e^-5	0.761	INTERGENIC
3L	11126371	3L_11126371_SNP [dm3] 3L_11133271_SNP [dm6]	G	T	2.281e^-5	0.761	NON_SYNONYMOUS_CODING CG42575 UPSTREAM CG32074	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	2079327	2L_2079327_SNP [dm3] 2L_2079327_SNP [dm6]	G	A	2.285e^-5	0.761	UPSTREAM CG12674 INTRON dpr3
3L	11125617	3L_11125617_SNP [dm3] 3L_11132517_SNP [dm6]	A	G	2.349e^-5	0.761	UPSTREAM CG32074 INTRON CG42575
3L	9525641	3L_9525641_SNP [dm3] 3L_9532541_SNP [dm6]	C	T	2.364e^-5	0.761	INTERGENIC
3L	9525659	3L_9525659_SNP [dm3] 3L_9532559_SNP [dm6]	C	T	2.364e^-5	0.761	INTERGENIC
3R	10249102	3R_10249102_SNP [dm3] 3R_14423380_SNP [dm6]	T	C	2.377e^-5	0.761	UPSTREAM CR44176 INTRON cv-c
2R	12342554	2R_12342554_SNP [dm3] 2R_16455049_SNP [dm6]	T	C	2.461e^-5	0.761	INTERGENIC
3R	11539917	3R_11539917_DEL [dm3] 3R_15714195_DEL [dm6]	GCGTTGAGTTG...	G	2.524e^-5	0.761	INTERGENIC
2R	13357309	2R_13357309_SNP [dm3] 2R_17469804_SNP [dm6]	A	G	2.534e^-5	0.761	UTR_5_PRIME qkr54B UPSTREAM Tes INTRON qkr54B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	5885453	2L_5885453_SNP [dm3] 2L_5885453_SNP [dm6]	A	G	2.612e^-5	0.761	UTR_3_PRIME CG43185 UPSTREAM Sfp26Ac & 1 other
3L	4659254	3L_4659254_SNP [dm3] 3L_4659254_SNP [dm6]	A	T	2.648e^-5	0.761	INTRON axo
3L	4659205	3L_4659205_SNP [dm3] 3L_4659205_SNP [dm6]	G	T	2.654e^-5	0.761	INTRON axo
3L	4659225	3L_4659225_SNP [dm3] 3L_4659225_SNP [dm6]	G	C	2.654e^-5	0.761	INTRON axo
3L	4659235	3L_4659235_SNP [dm3] 3L_4659235_SNP [dm6]	T	C	2.654e^-5	0.761	INTRON axo
2L	13328028	2L_13328028_DEL [dm3] 2L_13328028_DEL [dm6]	GCTATG	A	2.738e^-5	0.761	INTRON CG43778
2R	18942398	2R_18942398_SNP [dm3] 2R_23054875_SNP [dm6]	G	A	2.749e^-5	0.761	UPSTREAM CG44252 INTERGENIC
3R	6315006	3R_6315006_SNP [dm3] 3R_10489284_SNP [dm6]	T	A	2.766e^-5	0.761	EXON CR45576
3R	3867858	3R_3867858_SNP [dm3] 3R_8042136_SNP [dm6]	A	G	2.839e^-5	0.765	DOWNSTREAM CG43060 INTRON CG43060
3L	15793827	3L_15793827_SNP [dm3] 3L_15800727_SNP [dm6]	T	A	2.903e^-5	0.765	INTERGENIC
3R	14622504	3R_14622504_SNP [dm3] 3R_18796782_SNP [dm6]	T	G	2.975e^-5	0.765	INTERGENIC
3R	18768619	3R_18768619_SNP [dm3] 3R_22942897_SNP [dm6]	G	C	3.069e^-5	0.765	INTRON klg
2R	10612922	2R_10612922_SNP [dm3] 2R_14725417_SNP [dm6]	G	A	3.086e^-5	0.765	INTERGENIC
2L	9152379	2L_9152379_SNP [dm3] 2L_9152379_SNP [dm6]	A	G	3.098e^-5	0.765	INTRON CG32982
3L	4483604	3L_4483604_SNP [dm3] 3L_4483604_SNP [dm6]	T	C	3.113e^-5	0.765	SYNONYMOUS_CODING CG11350
3L	1585022	3L_1585022_SNP [dm3] 3L_1585022_SNP [dm6]	C	G	3.193e^-5	0.765	INTRON CG13917
2L	12211482	2L_12211482_SNP [dm3] 2L_12211482_SNP [dm6]	A	C	3.298e^-5	0.765	INTRON aret
3R	24466682	3R_24466682_SNP [dm3] 3R_28640960_SNP [dm6]	G	A	3.394e^-5	0.765	DOWNSTREAM CG14062 INTERGENIC	TF binding site mE1_TFBS_cad
3R	23749545	3R_23749545_SNP [dm3] 3R_27923823_SNP [dm6]	A	T	3.431e^-5	0.765	UPSTREAM snoRNA:Or-aca3 INTRON RpL4	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11044181	3L_11044181_INS [dm3] 3L_11051081_INS [dm6]	T	TGCAAT	3.459e^-5	0.765	UPSTREAM CG43693 DOWNSTREAM CR45119 INTRON CG43693
3L	17628889	3L_17628889_SNP [dm3] 3L_17635789_SNP [dm6]	T	C	3.505e^-5	0.765	INTRON CG7497
3L	11119866	3L_11119866_SNP [dm3] 3L_11126766_SNP [dm6]	G	T	3.580e^-5	0.765	INTRON CG42575	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	17628896	3L_17628896_SNP [dm3] 3L_17635796_SNP [dm6]	T	C	3.622e^-5	0.765	INTRON CG7497
X	8151496	X_8151496_SNP [dm3] X_8257463_SNP [dm6]	T	G	3.672e^-5	0.765	INTRON CG1632
2L	2068780	2L_2068780_SNP [dm3] 2L_2068780_SNP [dm6]	A	G	3.684e^-5	0.765	INTRON dpr3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	4771674	X_4771674_SNP [dm3] X_4877641_SNP [dm6]	C	T	3.713e^-5	0.765	DOWNSTREAM CG12681 INTRON CG42594
3R	5867251	3R_5867251_SNP [dm3] 3R_10041529_SNP [dm6]	A	G	3.733e^-5	0.765	INTRON Mical
X	8151421	X_8151421_SNP [dm3] X_8257388_SNP [dm6]	A	T	3.845e^-5	0.765	INTRON CG1632
3L	10699681	3L_10699681_SNP [dm3] 3L_10706581_SNP [dm6]	A	G	3.911e^-5	0.765	INTERGENIC
3L	4659296	3L_4659296_SNP [dm3] 3L_4659296_SNP [dm6]	T	C	3.919e^-5	0.765	INTRON axo
3L	4659302	3L_4659302_SNP [dm3] 3L_4659302_SNP [dm6]	A	G	3.919e^-5	0.765	INTRON axo
3L	4659304	3L_4659304_SNP [dm3] 3L_4659304_SNP [dm6]	A	T	3.919e^-5	0.765	INTRON axo
X	8151481	X_8151481_SNP [dm3] X_8257448_SNP [dm6]	A	T	3.939e^-5	0.765	INTRON CG1632
3L	4659310	3L_4659310_SNP [dm3] 3L_4659310_SNP [dm6]	G	A	4.044e^-5	0.765	INTRON axo
3R	27189997	3R_27189997_SNP [dm3] 3R_31364275_SNP [dm6]	C	A	4.092e^-5	0.765	INTRON CG34347
3L	11124419	3L_11124419_SNP [dm3] 3L_11131319_SNP [dm6]	G	T	4.112e^-5	0.765	UTR_3_PRIME nol DOWNSTREAM CG32074 INTRON CG42575
3L	11124420	3L_11124420_SNP [dm3] 3L_11131320_SNP [dm6]	G	A	4.112e^-5	0.765	UTR_3_PRIME nol DOWNSTREAM CG32074 INTRON CG42575
3R	5575562	3R_5575562_SNP [dm3] 3R_9749840_SNP [dm6]	C	T	4.116e^-5	0.765	SYNONYMOUS_CODING PpD3
X	18866809	X_18866809_INS [dm3] X_18972776_INS [dm6]	T	TT	4.175e^-5	0.765	INTRON CG43759
3L	22840756	3L_22840756_DEL [dm3] 3L_22847656_DEL [dm6]	GCCTTTGCTTGAAG...	G	4.422e^-5	0.765	DOWNSTREAM tRNA:CR32460 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	6977078	3L_6977078_SNP [dm3] 3L_6983978_SNP [dm6]	C	T	4.522e^-5	0.765	SYNONYMOUS_CODING CG43439 UTR_3_PRIME CG32388	TF binding site mE1_TFBS_sens
3L	11111607	3L_11111607_SNP [dm3] 3L_11118507_SNP [dm6]	C	T	4.576e^-5	0.765	UPSTREAM fd68A INTRON fd68A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_PElem_SS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results