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=2.673e^-4)
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

1356 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	5000122	3L_5000122_SNP [dm3] 3L_5000122_SNP [dm6]	A	T	2.050e^-6	0.932	INTRON Con	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2R	13336270	2R_13336270_SNP [dm3] 2R_17448765_SNP [dm6]	C	T	3.731e^-6	0.932	UTR_3_PRIME mthl3
3L	3582380	3L_3582380_SNP [dm3] 3L_3582380_SNP [dm6]	G	A	4.465e^-6	0.932	INTRON Eip63E
3L	3582551	3L_3582551_SNP [dm3] 3L_3582551_SNP [dm6]	A	T	4.465e^-6	0.932	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3582607	3L_3582607_SNP [dm3] 3L_3582607_SNP [dm6]	T	A	4.465e^-6	0.932	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3582616	3L_3582616_SNP [dm3] 3L_3582616_SNP [dm6]	C	T	4.465e^-6	0.932	INTRON Eip63E	TF binding site mE1_TFBS_inv
3L	3693654	3L_3693654_SNP [dm3] 3L_3693654_SNP [dm6]	G	T	4.465e^-6	0.932	DOWNSTREAM CR43485 INTERGENIC
3L	3803698	3L_3803698_SNP [dm3] 3L_3803698_SNP [dm6]	C	T	4.465e^-6	0.932	DOWNSTREAM ntc INTRON CG32264
2R	17956194	2R_17956194_SNP [dm3] 2R_22068689_SNP [dm6]	C	A	5.154e^-6	0.932	DOWNSTREAM CG44249 INTRON Snp
2L	17209930	2L_17209930_SNP [dm3] 2L_17209930_SNP [dm6]	A	G	5.829e^-6	0.932	INTRON beat-IIIc
3L	3536372	3L_3536372_SNP [dm3] 3L_3536372_SNP [dm6]	C	A	6.479e^-6	0.932	INTRON Eip63E
2L	9735452	2L_9735452_SNP [dm3] 2L_9735452_SNP [dm6]	T	A	7.560e^-6	0.932	INTRON Nckx30C
2R	9683515	2R_9683515_SNP [dm3] 2R_13796010_SNP [dm6]	A	G	8.734e^-6	0.932	INTRON Cpr50Cb
2R	15152982	2R_15152982_SNP [dm3] 2R_19265477_SNP [dm6]	T	C	8.886e^-6	0.932	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3R	14362935	3R_14362935_SNP [dm3] 3R_18537213_SNP [dm6]	G	A	9.186e^-6	0.932	INTRON fru
3L	13289655	3L_13289655_SNP [dm3] 3L_13296555_SNP [dm6]	T	A	9.735e^-6	0.932	UTR_3_PRIME Sfp70A4 UPSTREAM CR45253 DOWNSTREAM Sfp70A4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13289669	3L_13289669_DEL [dm3] 3L_13296569_DEL [dm6]	TTTGTGAATTTATGAACCA...	T	9.735e^-6	0.932	UTR_3_PRIME Sfp70A4 UPSTREAM CR45253 DOWNSTREAM Sfp70A4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13289690	3L_13289690_DEL [dm3] 3L_13296590_DEL [dm6]	TAGAGTTCTGTAAATTTGGA...	T	9.735e^-6	0.932	UTR_3_PRIME Sfp70A4 UPSTREAM CR45253 DOWNSTREAM Sfp70A4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19403640	2R_19403640_SNP [dm3] 2R_23516117_SNP [dm6]	A	G	9.750e^-6	0.932	INTERGENIC
3R	17673248	3R_17673248_SNP [dm3] 3R_21847526_SNP [dm6]	T	G	1.044e^-5	0.948	UPSTREAM Gr93d DOWNSTREAM CR44087 INTERGENIC
3L	12847405	3L_12847405_SNP [dm3] 3L_12854305_SNP [dm6]	T	A	1.098e^-5	0.95	INTRON Ent3
3R	14363052	3R_14363052_SNP [dm3] 3R_18537330_SNP [dm6]	C	A	1.270e^-5	0.99	INTRON fru
2L	19494519	2L_19494519_SNP [dm3] 2L_19494519_SNP [dm6]	C	G	1.348e^-5	0.99	INTRON swm	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	3693713	3L_3693713_INS [dm3] 3L_3693713_INS [dm6]	C	TT	1.375e^-5	0.99	DOWNSTREAM CR43485 INTERGENIC
2R	13336250	2R_13336250_DEL [dm3] 2R_17448745_DEL [dm6]	ATA	A	1.394e^-5	0.99	UTR_3_PRIME mthl3
2R	19403638	2R_19403638_SNP [dm3] 2R_23516115_SNP [dm6]	C	G	1.418e^-5	0.99	INTERGENIC
3R	17785987	3R_17785987_SNP [dm3] 3R_21960265_SNP [dm6]	T	C	1.574e^-5	1	INTRON Eip93F
X	17735318	X_17735318_SNP [dm3] X_17841285_SNP [dm6]	A	T	1.622e^-5	1	UTR_3_PRIME CG6398 UPSTREAM e_y_1
3L	12847395	3L_12847395_SNP [dm3] 3L_12854295_SNP [dm6]	C	A	1.659e^-5	1	INTRON Ent3
2R	14893018	2R_14893018_SNP [dm3] 2R_19005513_SNP [dm6]	T	A	2.055e^-5	1	INTRON tn
X	18644040	X_18644040_SNP [dm3] X_18750007_SNP [dm6]	G	C	2.287e^-5	1	INTERGENIC
X	18273658	X_18273658_SNP [dm3] X_18379625_SNP [dm6]	A	G	2.457e^-5	1	SYNONYMOUS_CODING por UPSTREAM CG6179	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	11428439	2R_11428439_SNP [dm3] 2R_15540934_SNP [dm6]	G	A	2.894e^-5	1	SYNONYMOUS_CODING CG8187 UPSTREAM Vha36-1 DOWNSTREAM CG30467	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	3577251	3L_3577251_SNP [dm3] 3L_3577251_SNP [dm6]	C	T	2.965e^-5	1	INTRON Eip63E
3L	13294528	3L_13294528_SNP [dm3] 3L_13301428_SNP [dm6]	A	C	2.977e^-5	1	UPSTREAM SP & 1 other INTERGENIC
2R	13015014	2R_13015014_SNP [dm3] 2R_17127509_SNP [dm6]	C	G	3.090e^-5	1	UPSTREAM CG15605 & 1 other INTERGENIC
2R	17956198	2R_17956198_SNP [dm3] 2R_22068693_SNP [dm6]	A	C	3.145e^-5	1	DOWNSTREAM CG44249 INTRON Snp
2L	885686	2L_885686_SNP [dm3] 2L_885686_SNP [dm6]	T	G	3.377e^-5	1	UPSTREAM CG15824 INTERGENIC
2L	17209772	2L_17209772_SNP [dm3] 2L_17209772_SNP [dm6]	C	T	3.501e^-5	1	INTRON beat-IIIc
2L	17209775	2L_17209775_SNP [dm3] 2L_17209775_SNP [dm6]	A	G	3.743e^-5	1	INTRON beat-IIIc
3L	8684653	3L_8684653_SNP [dm3] 3L_8691553_SNP [dm6]	C	G	3.851e^-5	1	INTERGENIC
3L	3499025	3L_3499025_SNP [dm3] 3L_3499025_SNP [dm6]	C	T	3.895e^-5	1	INTRON CG42324
3L	4138335	3L_4138335_SNP [dm3] 3L_4138335_SNP [dm6]	C	T	3.907e^-5	1	SYNONYMOUS_CODING Rop UPSTREAM Ras64B	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	5860824	2L_5860824_SNP [dm3] 2L_5860824_SNP [dm6]	A	G	3.955e^-5	1	SYNONYMOUS_CODING rau	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	15292394	X_15292394_SNP [dm3] X_15398361_SNP [dm6]	C	T	4.042e^-5	1	INTRON Cngl
X	15292396	X_15292396_SNP [dm3] X_15398363_SNP [dm6]	T	G	4.042e^-5	1	INTRON Cngl
3R	10429876	3R_10429876_SNP [dm3] 3R_14604154_SNP [dm6]	G	A	4.216e^-5	1	INTRON stumps
3L	17789957	3L_17789957_SNP [dm3] 3L_17796857_SNP [dm6]	T	A	4.313e^-5	1	DOWNSTREAM NUCB1 INTRON CG42816
3L	17789958	3L_17789958_SNP [dm3] 3L_17796858_SNP [dm6]	A	T	4.313e^-5	1	DOWNSTREAM NUCB1 INTRON CG42816
3L	409947	3L_409947_SNP [dm3] 3L_409947_SNP [dm6]	C	T	4.770e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	19644919	2R_19644919_DEL [dm3] 2R_23757396_DEL [dm6]	CCCATTTTAC	C	4.792e^-5	1	INTRON CG9850
2R	10470081	2R_10470081_SNP [dm3] 2R_14582576_SNP [dm6]	C	T	4.999e^-5	1	INTRON ttv
3L	12364346	3L_12364346_SNP [dm3] 3L_12371246_SNP [dm6]	A	T	5.083e^-5	1	INTRON Ncc69
3L	12364372	3L_12364372_INS [dm3] 3L_12371272_INS [dm6]	G	ATCCATTA	5.083e^-5	1	INTRON Ncc69
3L	12364378	3L_12364378_INS [dm3] 3L_12371278_INS [dm6]	A	GCCGC	5.083e^-5	1	INTRON Ncc69
3L	12364403	3L_12364403_SNP [dm3] 3L_12371303_SNP [dm6]	A	G	5.083e^-5	1	INTRON Ncc69
3L	3755412	3L_3755412_SNP [dm3] 3L_3755412_SNP [dm6]	T	A	5.134e^-5	1	UPSTREAM ppk27 INTRON CG32264
2R	14347505	2R_14347505_SNP [dm3] 2R_18460000_SNP [dm6]	A	T	5.243e^-5	1	NON_SYNONYMOUS_CODING CG30116 INTRON CG30116	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	3805190	3L_3805190_SNP [dm3] 3L_3805190_SNP [dm6]	C	A	5.345e^-5	1	INTRON CG32264 & 1 other
3L	3805192	3L_3805192_SNP [dm3] 3L_3805192_SNP [dm6]	A	T	5.345e^-5	1	INTRON CG32264 & 1 other
3L	3805194	3L_3805194_DEL [dm3] 3L_3805194_DEL [dm6]	GTTA	G	5.345e^-5	1	INTRON CG32264 & 1 other
3L	3805203	3L_3805203_SNP [dm3] 3L_3805203_SNP [dm6]	G	A	5.345e^-5	1	INTRON CG32264 & 1 other
2L	21633588	2L_21633588_SNP [dm3] 2L_21633588_SNP [dm6]	C	T	5.415e^-5	1	UTR_5_PRIME Ac3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	19644659	2R_19644659_SNP [dm3] 2R_23757136_SNP [dm6]	C	A	5.501e^-5	1	NON_SYNONYMOUS_CODING CG9850 INTRON CG9850
2R	18945359	2R_18945359_SNP [dm3] 2R_23057836_SNP [dm6]	A	G	5.614e^-5	1	UPSTREAM CG44252 & 1 other INTRON CG44252
3L	12363850	3L_12363850_SNP [dm3] 3L_12370750_SNP [dm6]	G	A	5.756e^-5	1	INTRON Ncc69	TF binding site mE1_TFBS_HSA
3R	19015104	3R_19015104_SNP [dm3] 3R_23189382_SNP [dm6]	T	A	5.929e^-5	1	UPSTREAM cnc INTRON cnc	TF binding site mE1_TFBS_cad mE1_TFBS_cnc
2R	14914506	2R_14914506_SNP [dm3] 2R_19027001_SNP [dm6]	A	G	6.420e^-5	1	INTRON 5-HT1B
2L	14299006	2L_14299006_SNP [dm3] 2L_14299006_SNP [dm6]	T	G	6.741e^-5	1	INTRON wb
2L	13339247	2L_13339247_SNP [dm3] 2L_13339247_SNP [dm6]	A	C	6.831e^-5	1	INTERGENIC
3L	9563296	3L_9563296_INS [dm3] 3L_9570196_INS [dm6]	C	CC	6.976e^-5	1	INTRON CG42673
2L	14144004	2L_14144004_SNP [dm3] 2L_14144004_SNP [dm6]	C	G	7.300e^-5	1	INTRON CG17341
3R	22552277	3R_22552277_SNP [dm3] 3R_26726555_SNP [dm6]	C	T	7.465e^-5	1	UTR_3_PRIME CG14244 UPSTREAM CG14246
2L	9405653	2L_9405653_SNP [dm3] 2L_9405653_SNP [dm6]	T	A	7.614e^-5	1	INTRON Shawl
X	18273988	X_18273988_SNP [dm3] X_18379955_SNP [dm6]	G	T	7.735e^-5	1	UPSTREAM CG6179 & 1 other INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens
2L	1329847	2L_1329847_SNP [dm3] 2L_1329847_SNP [dm6]	C	T	7.745e^-5	1	SYNONYMOUS_CODING a5
X	8328996	X_8328996_SNP [dm3] X_8434963_SNP [dm6]	A	G	7.806e^-5	1	INTRON CG12125	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	18908882	2L_18908882_SNP [dm3] 2L_18908882_SNP [dm6]	G	A	8.000e^-5	1	INTERGENIC
2L	9744355	2L_9744355_INS [dm3] 2L_9744355_INS [dm6]	A	AAA	8.387e^-5	1	INTRON Nckx30C
2L	9744422	2L_9744422_DEL [dm3] 2L_9744422_DEL [dm6]	TGGCTT	T	8.387e^-5	1	INTRON Nckx30C
3L	11434359	3L_11434359_DEL [dm3] 3L_11441259_DEL [dm6]	AGGTTTTGCAAA...	A	8.420e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12411561	3L_12411561_SNP [dm3] 3L_12418461_SNP [dm6]	C	T	8.572e^-5	1	UPSTREAM ArfGAP1 INTERGENIC	TF binding site mE1_TFBS_cnc
3L	8684668	3L_8684668_SNP [dm3] 3L_8691568_SNP [dm6]	G	T	8.619e^-5	1	INTERGENIC
3L	11373916	3L_11373916_SNP [dm3] 3L_11380816_SNP [dm6]	A	T	8.896e^-5	1	INTERGENIC
3L	5000115	3L_5000115_SNP [dm3] 3L_5000115_SNP [dm6]	G	A	8.925e^-5	1	INTRON Con	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	9463583	2L_9463583_SNP [dm3] 2L_9463583_SNP [dm6]	G	A	8.932e^-5	1	UTR_3_PRIME numb DOWNSTREAM numb	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3L	13294182	3L_13294182_SNP [dm3] 3L_13301082_SNP [dm6]	G	A	9.142e^-5	1	UPSTREAM CG43147 & 1 other INTERGENIC
3R	24731874	3R_24731874_SNP [dm3] 3R_28906152_SNP [dm6]	G	A	9.190e^-5	1	SYNONYMOUS_CODING Doa INTRON Doa	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11085349	2R_11085349_SNP [dm3] 2R_15197844_SNP [dm6]	T	A	9.217e^-5	1	INTERGENIC
2R	2619007	2R_2619007_DEL [dm3] 2R_6731502_DEL [dm6]	AATAC	A	9.458e^-5	1	INTRON l_2_01289
X	4472906	X_4472906_SNP [dm3] X_4578873_SNP [dm6]	T	A	9.755e^-5	1	INTRON CR32773
3R	10878027	3R_10878027_SNP [dm3] 3R_15052305_SNP [dm6]	T	G	9.799e^-5	1	INTERGENIC
2L	9646973	2L_9646973_SNP [dm3] 2L_9646973_SNP [dm6]	T	A	9.810e^-5	1	SYNONYMOUS_CODING Apoltp
2L	16436133	2L_16436133_SNP [dm3] 2L_16436133_SNP [dm6]	A	T	9.865e^-5	1	INTRON CG5888
3R	19015451	3R_19015451_SNP [dm3] 3R_23189729_SNP [dm6]	T	C	1.018e^-4	1	UPSTREAM cnc INTRON cnc	TF binding site mE1_TFBS_cad mE1_TFBS_cnc
3L	13294600	3L_13294600_SNP [dm3] 3L_13301500_SNP [dm6]	C	A	1.025e^-4	1	UPSTREAM SP & 1 other INTERGENIC
2R	18875695	2R_18875695_SNP [dm3] 2R_22988172_SNP [dm6]	C	T	1.030e^-4	1	INTRON twi
3L	7449595	3L_7449595_SNP [dm3] 3L_7456495_SNP [dm6]	C	T	1.038e^-4	1	SYNONYMOUS_CODING ppk26	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	17831038	3R_17831038_SNP [dm3] 3R_22005316_SNP [dm6]	T	C	1.044e^-4	1	SYNONYMOUS_CODING Eip93F	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15153185	2R_15153185_SNP [dm3] 2R_19265680_SNP [dm6]	A	G	1.049e^-4	1	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens

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Missing results

By genomic position
Variant impact
Gene name

pc_KP_PElem_SC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results