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=1.307e^-2)
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

1266 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	13588263	3R_13588263_INS [dm3] 3R_17762541_INS [dm6]	G	GTCG	1.161e^-6	0.919	UTR_5_PRIME TyrR UPSTREAM TyrR
3R	9196465	3R_9196465_SNP [dm3] 3R_13370743_SNP [dm6]	C	A	3.926e^-6	0.919	DOWNSTREAM CheA87a INTRON Lip3
3R	9196475	3R_9196475_SNP [dm3] 3R_13370753_SNP [dm6]	T	C	3.926e^-6	0.919	DOWNSTREAM CheA87a INTRON Lip3
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	5.383e^-6	0.919	INTRON Glut1
3R	9196104	3R_9196104_SNP [dm3] 3R_13370382_SNP [dm6]	G	A	5.408e^-6	0.919	SYNONYMOUS_CODING Lip3 DOWNSTREAM CheA87a
3R	26119375	3R_26119375_SNP [dm3] 3R_30293653_SNP [dm6]	T	A	8.757e^-6	0.919	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11361515	2L_11361515_SNP [dm3] 2L_11361515_SNP [dm6]	A	G	8.799e^-6	0.919	INTRON salr	regulatory region REDfly_CRMs
3L	17335883	3L_17335883_SNP [dm3] 3L_17342783_SNP [dm6]	G	A	1.081e^-5	0.919	INTRON brv2
2L	11360994	2L_11360994_SNP [dm3] 2L_11360994_SNP [dm6]	G	C	1.134e^-5	0.919	INTRON salr	regulatory region REDfly_CRMs
3R	16739456	3R_16739456_SNP [dm3] 3R_20913734_SNP [dm6]	C	T	1.142e^-5	0.919	UPSTREAM snoRNA:CG31191-a & 1 other DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8010191	2L_8010191_SNP [dm3] 2L_8010191_SNP [dm6]	G	A	1.170e^-5	0.919	SYNONYMOUS_CODING CG34010 UPSTREAM CG12560	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	13588248	3R_13588248_SNP [dm3] 3R_17762526_SNP [dm6]	G	A	1.372e^-5	0.919	UTR_5_PRIME TyrR UPSTREAM TyrR
3R	26119383	3R_26119383_SNP [dm3] 3R_30293661_SNP [dm6]	G	C	1.407e^-5	0.919	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	11139011	X_11139011_SNP [dm3] X_11244978_SNP [dm6]	C	G	1.422e^-5	0.919	INTRON CG44422
3R	24217371	3R_24217371_SNP [dm3] 3R_28391649_SNP [dm6]	C	A	1.438e^-5	0.919	INTERGENIC
3L	1383873	3L_1383873_SNP [dm3] 3L_1383873_SNP [dm6]	A	C	1.448e^-5	0.919	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
X	3911257	X_3911257_SNP [dm3] X_4017224_SNP [dm6]	G	A	1.597e^-5	0.919	INTERGENIC
3L	5376612	3L_5376612_DEL [dm3] 3L_5383512_DEL [dm6]	CTGT	A	1.619e^-5	0.919	UPSTREAM Ir64a INTERGENIC
3R	26119373	3R_26119373_SNP [dm3] 3R_30293651_SNP [dm6]	G	C	2.128e^-5	0.919	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	19282276	X_19282276_SNP [dm3] X_19388243_SNP [dm6]	A	C	2.194e^-5	0.919	INTRON kek5
X	3911217	X_3911217_SNP [dm3] X_4017184_SNP [dm6]	C	A	2.419e^-5	0.919	INTERGENIC
X	3911229	X_3911229_SNP [dm3] X_4017196_SNP [dm6]	T	G	2.419e^-5	0.919	INTERGENIC
X	11151575	X_11151575_SNP [dm3] X_11257542_SNP [dm6]	T	C	2.425e^-5	0.919	INTRON CG44422
3R	9151822	3R_9151822_SNP [dm3] 3R_13326100_SNP [dm6]	T	C	2.441e^-5	0.919	INTERGENIC
X	6537601	X_6537601_SNP [dm3] X_6643568_SNP [dm6]	G	A	2.822e^-5	0.919	INTRON pigs	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	1605240	3L_1605240_SNP [dm3] 3L_1605240_SNP [dm6]	A	C	2.924e^-5	0.919	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170
3L	2622009	3L_2622009_SNP [dm3] 3L_2622009_SNP [dm6]	A	T	2.982e^-5	0.919	INTRON Pxn
X	2794934	X_2794934_SNP [dm3] X_2900901_SNP [dm6]	A	C	3.018e^-5	0.919	INTRON kirre
X	3911242	X_3911242_DEL [dm3] X_4017209_DEL [dm6]	TAATATCAGT	T	3.061e^-5	0.919	INTERGENIC
3L	15737816	3L_15737816_SNP [dm3] 3L_15744716_SNP [dm6]	A	T	3.126e^-5	0.919	INTERGENIC
3R	17993103	3R_17993103_SNP [dm3] 3R_22167381_SNP [dm6]	G	C	3.277e^-5	0.919	INTRON SKIP	TF binding site mE1_TFBS_Kr
3L	16433813	3L_16433813_SNP [dm3] 3L_16440713_SNP [dm6]	G	A	3.659e^-5	0.919	INTRON CG33158 & 1 other
X	12940092	X_12940092_SNP [dm3] X_13046059_SNP [dm6]	T	G	3.726e^-5	0.919	INTRON rad
3L	12834135	3L_12834135_SNP [dm3] 3L_12841035_SNP [dm6]	G	T	3.968e^-5	0.919	INTRON CG10960	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	9088728	3L_9088728_SNP [dm3] 3L_9095628_SNP [dm6]	C	T	4.166e^-5	0.919	DOWNSTREAM CG32032 INTERGENIC
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	4.386e^-5	0.919	INTRON salr	regulatory region REDfly_CRMs
3R	24807557	3R_24807557_SNP [dm3] 3R_28981835_SNP [dm6]	C	T	4.541e^-5	0.919	INTERGENIC
3R	12384171	3R_12384171_SNP [dm3] 3R_16558449_SNP [dm6]	C	T	4.664e^-5	0.919	INTRON CG42342
X	3911227	X_3911227_SNP [dm3] X_4017194_SNP [dm6]	A	T	4.712e^-5	0.919	INTERGENIC
3L	7061417	3L_7061417_SNP [dm3] 3L_7068317_SNP [dm6]	G	A	4.776e^-5	0.919	SYNONYMOUS_CODING CG32391 DOWNSTREAM CG14823 INTRON CG8641
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	4.861e^-5	0.919	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	4.861e^-5	0.919	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	4.861e^-5	0.919	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	4.861e^-5	0.919	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	4.861e^-5	0.919	INTERGENIC
3R	9196495	3R_9196495_SNP [dm3] 3R_13370773_SNP [dm6]	A	G	4.936e^-5	0.919	DOWNSTREAM CheA87a INTRON Lip3
3R	24691184	3R_24691184_SNP [dm3] 3R_28865462_SNP [dm6]	G	T	4.957e^-5	0.919	SYNONYMOUS_CODING spg	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	14382716	X_14382716_SNP [dm3] X_14488683_SNP [dm6]	T	C	4.987e^-5	0.919	INTERGENIC
2L	4902338	2L_4902338_SNP [dm3] 2L_4902338_SNP [dm6]	T	C	5.075e^-5	0.919	SYNONYMOUS_CODING CG3036	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	5318902	2R_5318902_INS [dm3] 2R_9431397_INS [dm6]	A	ATACA	5.178e^-5	0.919	INTRON Pdk
3L	7904156	3L_7904156_SNP [dm3] 3L_7911056_SNP [dm6]	G	T	5.314e^-5	0.919	INTRON pbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	13591362	3R_13591362_SNP [dm3] 3R_17765640_SNP [dm6]	G	A	5.330e^-5	0.919	INTERGENIC
2R	7310122	2R_7310122_SNP [dm3] 2R_11422617_SNP [dm6]	G	C	5.369e^-5	0.919	INTRON Drip
2L	14352150	2L_14352150_SNP [dm3] 2L_14352150_SNP [dm6]	A	C	5.433e^-5	0.919	UTR_5_PRIME CG43052 UPSTREAM l_2_34Fc DOWNSTREAM l_2_34Fd
3L	1192482	3L_1192482_SNP [dm3] 3L_1192482_SNP [dm6]	T	A	5.484e^-5	0.919	INTRON Trh	TF binding site mE1_TFBS_chinmo
3L	1192494	3L_1192494_SNP [dm3] 3L_1192494_SNP [dm6]	C	T	5.484e^-5	0.919	INTRON Trh	TF binding site mE1_TFBS_chinmo
2L	5372497	2L_5372497_DEL [dm3] 2L_5372497_DEL [dm6]	CAGAGCCG	C	5.497e^-5	0.919	INTERGENIC
3R	12426591	3R_12426591_SNP [dm3] 3R_16600869_SNP [dm6]	C	A	5.519e^-5	0.919	INTRON CG10345
2R	6452247	2R_6452247_SNP [dm3] 2R_10564742_SNP [dm6]	C	T	5.539e^-5	0.919	INTRON psq	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	4587438	3L_4587438_SNP [dm3] 3L_4587438_SNP [dm6]	T	C	5.622e^-5	0.919	INTRON CG42540
2R	10687961	2R_10687961_DEL [dm3] 2R_14800456_DEL [dm6]	GG	G	5.676e^-5	0.919	INTRON kn	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
3R	24289988	3R_24289988_SNP [dm3] 3R_28464266_SNP [dm6]	C	T	5.736e^-5	0.919	INTRON beat-VI
3R	25114806	3R_25114806_SNP [dm3] 3R_29289084_SNP [dm6]	T	C	5.879e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	25834938	3R_25834938_SNP [dm3] 3R_30009216_SNP [dm6]	G	A	5.951e^-5	0.919	UPSTREAM CG7912 INTRON Nlp
3L	13541893	3L_13541893_INS [dm3] 3L_13548793_INS [dm6]	C	CGGACAC	6.059e^-5	0.919	INTRON bru-3
3R	15456508	3R_15456508_SNP [dm3] 3R_19630786_SNP [dm6]	T	C	6.143e^-5	0.919	INTRON CG6231
3R	9151242	3R_9151242_SNP [dm3] 3R_13325520_SNP [dm6]	T	A	6.210e^-5	0.919	INTERGENIC
3R	25365859	3R_25365859_SNP [dm3] 3R_29540137_SNP [dm6]	T	A	6.686e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	9088629	3L_9088629_SNP [dm3] 3L_9095529_SNP [dm6]	C	G	6.716e^-5	0.919	DOWNSTREAM CG32032 INTERGENIC
3L	16433911	3L_16433911_SNP [dm3] 3L_16440811_SNP [dm6]	A	T	6.842e^-5	0.919	INTRON CG33158 & 1 other
3R	25365840	3R_25365840_SNP [dm3] 3R_29540118_SNP [dm6]	T	C	7.131e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	19388879	3L_19388879_SNP [dm3] 3L_19395779_SNP [dm6]	G	C	7.293e^-5	0.919	INTRON CG32206
3L	1390461	3L_1390461_SNP [dm3] 3L_1390461_SNP [dm6]	A	T	7.382e^-5	0.919	INTRON Ptp61F	TF binding site mE1_TFBS_cad
3L	19388797	3L_19388797_SNP [dm3] 3L_19395697_SNP [dm6]	A	G	7.413e^-5	0.919	INTRON CG32206
3R	9193779	3R_9193779_SNP [dm3] 3R_13368057_SNP [dm6]	G	A	7.418e^-5	0.919	SYNONYMOUS_CODING Dic1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23922182	3R_23922182_SNP [dm3] 3R_28096460_SNP [dm6]	A	T	7.538e^-5	0.919	INTERGENIC
3L	9088625	3L_9088625_SNP [dm3] 3L_9095525_SNP [dm6]	C	T	7.571e^-5	0.919	DOWNSTREAM CG32032 INTERGENIC
3L	16433825	3L_16433825_SNP [dm3] 3L_16440725_SNP [dm6]	A	G	7.619e^-5	0.919	INTRON CG33158 & 1 other
3R	9385445	3R_9385445_SNP [dm3] 3R_13559723_SNP [dm6]	T	A	7.895e^-5	0.919	INTERGENIC
3R	9385447	3R_9385447_SNP [dm3] 3R_13559725_SNP [dm6]	C	T	7.895e^-5	0.919	INTERGENIC
3L	9081917	3L_9081917_SNP [dm3] 3L_9088817_SNP [dm6]	C	T	7.944e^-5	0.919	SYNONYMOUS_CODING Tequila INTRON Tequila
3L	9081928	3L_9081928_SNP [dm3] 3L_9088828_SNP [dm6]	A	C	7.944e^-5	0.919	SYNONYMOUS_CODING Tequila INTRON Tequila
3L	9082021	3L_9082021_SNP [dm3] 3L_9088921_SNP [dm6]	A	T	7.944e^-5	0.919	SYNONYMOUS_CODING Tequila INTRON Tequila	TF binding site mE1_TFBS_cad
2R	6379235	2R_6379235_SNP [dm3] 2R_10491730_SNP [dm6]	C	T	8.016e^-5	0.919	UTR_3_PRIME lola INTRON lola
2R	6508001	2R_6508001_SNP [dm3] 2R_10620496_SNP [dm6]	A	C	8.016e^-5	0.919	INTRON CG11883
3R	11618443	3R_11618443_SNP [dm3] 3R_15792721_SNP [dm6]	A	G	8.205e^-5	0.919	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx
2L	12135321	2L_12135321_SNP [dm3] 2L_12135321_SNP [dm6]	T	G	8.340e^-5	0.919	INTERGENIC
2R	12345223	2R_12345223_INS [dm3] 2R_16457718_INS [dm6]	G	GG	8.387e^-5	0.919	INTERGENIC
3R	24355427	3R_24355427_SNP [dm3] 3R_28529705_SNP [dm6]	A	G	8.394e^-5	0.919	INTRON Ppn	TF binding site mE1_TFBS_chinmo
3R	24359452	3R_24359452_SNP [dm3] 3R_28533730_SNP [dm6]	G	A	8.394e^-5	0.919	INTRON Ppn
3R	24360688	3R_24360688_SNP [dm3] 3R_28534966_SNP [dm6]	T	G	8.394e^-5	0.919	INTRON Ppn
3R	24362526	3R_24362526_SNP [dm3] 3R_28536804_SNP [dm6]	A	T	8.394e^-5	0.919	INTRON Ppn
2R	12366379	2R_12366379_SNP [dm3] 2R_16478874_SNP [dm6]	T	C	8.400e^-5	0.919	INTERGENIC
3R	14135128	3R_14135128_SNP [dm3] 3R_18309406_SNP [dm6]	T	A	9.182e^-5	0.919	START_GAINED PKD UTR_5_PRIME PKD
3L	3188583	3L_3188583_SNP [dm3] 3L_3188583_SNP [dm6]	A	G	9.207e^-5	0.919	SYNONYMOUS_CODING CG42525 DOWNSTREAM CG14957	TF binding site mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3R	24316014	3R_24316014_SNP [dm3] 3R_28490292_SNP [dm6]	T	A	9.310e^-5	0.919	INTRON Dhc98D
3L	16433660	3L_16433660_SNP [dm3] 3L_16440560_SNP [dm6]	A	C	9.586e^-5	0.919	INTRON CG33158 & 1 other
2R	9867005	2R_9867005_SNP [dm3] 2R_13979500_SNP [dm6]	A	C	9.615e^-5	0.919	START_GAINED CG6701 UTR_5_PRIME CG6701 DOWNSTREAM Ctf4 INTRON CG6701	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13837645	3L_13837645_SNP [dm3] 3L_13844545_SNP [dm6]	A	T	9.736e^-5	0.919	SYNONYMOUS_CODING Tsp68C	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	24327835	3R_24327835_SNP [dm3] 3R_28502113_SNP [dm6]	C	T	9.877e^-5	0.919	INTRON Dhc98D

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By genomic position
Variant impact
Gene name

sons1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results