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=8.753e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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
In_3R_K	0.09686

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	2.8182	0.0932

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1050 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
X	15404856	X_15404856_SNP [dm3] X_15510823_SNP [dm6]	G	A	2.860e^-6	0.964	UTR_3_PRIME Gmap DOWNSTREAM Ac13E & 1 other
3L	3094909	3L_3094909_SNP [dm3] 3L_3094909_SNP [dm6]	A	T	3.161e^-6	0.964	UPSTREAM tRNA:CR32288 INTRON Cht7	TF binding site mE1_TFBS_cad
2R	15713621	2R_15713621_SNP [dm3] 2R_19826116_SNP [dm6]	T	C	6.208e^-6	0.964	UPSTREAM Toll-7 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	12169048	2L_12169048_SNP [dm3] 2L_12169048_SNP [dm6]	A	G	1.399e^-5	0.964	SYNONYMOUS_CODING CG31760 UTR_3_PRIME CG31760
2R	687086	2R_687086_SNP [dm3] 2R_4799581_SNP [dm6]	T	C	1.402e^-5	0.964	INTERGENIC	transposable element FlyBase
2R	687102	2R_687102_SNP [dm3] 2R_4799597_SNP [dm6]	T	C	1.402e^-5	0.964	INTERGENIC	transposable element FlyBase
3R	20449977	3R_20449977_SNP [dm3] 3R_24624255_SNP [dm6]	G	T	1.663e^-5	0.964	DOWNSTREAM mld INTRON Syx18
3R	20449992	3R_20449992_SNP [dm3] 3R_24624270_SNP [dm6]	G	A	1.663e^-5	0.964	DOWNSTREAM mld INTRON Syx18
3R	20450093	3R_20450093_SNP [dm3] 3R_24624371_SNP [dm6]	T	C	1.663e^-5	0.964	DOWNSTREAM mld INTRON Syx18
2R	9251733	2R_9251733_SNP [dm3] 2R_13364228_SNP [dm6]	C	G	2.153e^-5	0.964	INTERGENIC
3L	3001348	3L_3001348_SNP [dm3] 3L_3001348_SNP [dm6]	C	T	2.248e^-5	0.964	UPSTREAM FMRFaR INTERGENIC
2L	4329992	2L_4329992_SNP [dm3] 2L_4329992_SNP [dm6]	T	C	2.369e^-5	0.964	INTRON CG16857
3R	20450085	3R_20450085_SNP [dm3] 3R_24624363_SNP [dm6]	C	T	2.535e^-5	0.964	DOWNSTREAM mld INTRON Syx18
3R	20450078	3R_20450078_SNP [dm3] 3R_24624356_SNP [dm6]	A	C	3.114e^-5	0.964	DOWNSTREAM mld INTRON Syx18
3R	20450074	3R_20450074_SNP [dm3] 3R_24624352_SNP [dm6]	A	T	3.178e^-5	0.964	DOWNSTREAM mld INTRON Syx18
2L	16388493	2L_16388493_SNP [dm3] 2L_16388493_SNP [dm6]	T	A	3.280e^-5	0.964	INTERGENIC
3R	18820617	3R_18820617_SNP [dm3] 3R_22994895_SNP [dm6]	A	G	3.923e^-5	0.964	INTRON Nha2
2L	7384771	2L_7384771_SNP [dm3] 2L_7384771_SNP [dm6]	T	C	3.989e^-5	0.964	UTR_3_PRIME CG5149 DOWNSTREAM ninaC
X	14776837	X_14776837_SNP [dm3] X_14882804_SNP [dm6]	A	C	4.010e^-5	0.964	UPSTREAM CG45065 & 1 other INTRON Flo2
2L	19584118	2L_19584118_SNP [dm3] 2L_19584118_SNP [dm6]	G	C	4.368e^-5	0.964	UPSTREAM CG10366 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	19584148	2L_19584148_SNP [dm3] 2L_19584148_SNP [dm6]	T	A	4.368e^-5	0.964	UPSTREAM CG10366 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
X	15404737	X_15404737_SNP [dm3] X_15510704_SNP [dm6]	T	C	4.372e^-5	0.964	UTR_3_PRIME Gmap DOWNSTREAM Ac13E
X	12940980	X_12940980_SNP [dm3] X_13046947_SNP [dm6]	C	T	4.725e^-5	0.964	SYNONYMOUS_CODING rad UTR_5_PRIME rad
2L	4325734	2L_4325734_SNP [dm3] 2L_4325734_SNP [dm6]	G	T	4.908e^-5	0.964	INTRON CG16857
2L	5555913	2L_5555913_SNP [dm3] 2L_5555913_SNP [dm6]	G	A	5.070e^-5	0.964	SYNONYMOUS_CODING GluRIIA DOWNSTREAM CG14017
2R	16620701	2R_16620701_SNP [dm3] 2R_20733196_SNP [dm6]	G	A	5.527e^-5	0.964	INTRON dpr
X	7364276	X_7364276_SNP [dm3] X_7470243_SNP [dm6]	G	T	5.653e^-5	0.964	INTERGENIC
2L	14534070	2L_14534070_SNP [dm3] 2L_14534070_SNP [dm6]	T	C	5.695e^-5	0.964	UPSTREAM CR44852 INTERGENIC
2L	9323557	2L_9323557_SNP [dm3] 2L_9323557_SNP [dm6]	A	T	5.707e^-5	0.964	INTERGENIC
2L	1446573	2L_1446573_SNP [dm3] 2L_1446573_SNP [dm6]	G	A	6.112e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	9305185	2L_9305185_SNP [dm3] 2L_9305185_SNP [dm6]	A	G	6.433e^-5	0.964	UPSTREAM CR42844 INTERGENIC
2R	17856409	2R_17856409_SNP [dm3] 2R_21968904_SNP [dm6]	G	A	6.556e^-5	0.964	INTRON ppk9
3L	3201257	3L_3201257_SNP [dm3] 3L_3201257_SNP [dm6]	G	A	6.720e^-5	0.964	SYNONYMOUS_CODING gry DOWNSTREAM CG32271	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	9958515	3R_9958515_SNP [dm3] 3R_14132793_SNP [dm6]	G	A	6.806e^-5	0.964	UPSTREAM CG14356 INTERGENIC
X	2772245	X_2772245_SNP [dm3] X_2878212_SNP [dm6]	C	T	6.972e^-5	0.964	INTRON kirre
3R	9958539	3R_9958539_SNP [dm3] 3R_14132817_SNP [dm6]	A	T	7.014e^-5	0.964	UPSTREAM CG14356 INTERGENIC
3L	11852039	3L_11852039_SNP [dm3] 3L_11858939_SNP [dm6]	C	G	7.021e^-5	0.964	INTRON CG44837
3L	11852114	3L_11852114_SNP [dm3] 3L_11859014_SNP [dm6]	C	T	7.021e^-5	0.964	INTRON CG44837
2R	9251683	2R_9251683_SNP [dm3] 2R_13364178_SNP [dm6]	C	G	7.172e^-5	0.964	INTERGENIC
2L	9305215	2L_9305215_SNP [dm3] 2L_9305215_SNP [dm6]	T	C	7.263e^-5	0.964	UPSTREAM CR42844 INTERGENIC
3L	4741339	3L_4741339_SNP [dm3] 3L_4741339_SNP [dm6]	A	G	7.329e^-5	0.964	INTRON RhoGEF64C
2L	5404538	2L_5404538_SNP [dm3] 2L_5404538_SNP [dm6]	C	T	7.352e^-5	0.964	UTR_5_PRIME H15 UPSTREAM H15	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
2L	4415803	2L_4415803_SNP [dm3] 2L_4415803_SNP [dm6]	G	A	7.648e^-5	0.964	INTRON CG15431
2L	19722149	2L_19722149_SNP [dm3] 2L_19722149_SNP [dm6]	A	C	7.816e^-5	0.964	INTRON Lar
3R	17015574	3R_17015574_SNP [dm3] 3R_21189852_SNP [dm6]	G	T	7.892e^-5	0.964	INTRON SNF4Agamma	TF binding site BDTNP1_TFBS_dl
2R	18545016	2R_18545016_SNP [dm3] 2R_22657511_SNP [dm6]	G	T	8.003e^-5	0.964	UPSTREAM CG13510 & 4 others INTERGENIC
X	4919549	X_4919549_SNP [dm3] X_5025516_SNP [dm6]	T	C	8.006e^-5	0.964	INTRON CR44833
X	3479817	X_3479817_SNP [dm3] X_3585784_SNP [dm6]	T	G	8.071e^-5	0.964	INTRON AstA-R1
2R	9251741	2R_9251741_SNP [dm3] 2R_13364236_SNP [dm6]	G	A	8.183e^-5	0.964	INTERGENIC
X	7364280	X_7364280_SNP [dm3] X_7470247_SNP [dm6]	C	T	8.285e^-5	0.964	INTERGENIC
2L	4415801	2L_4415801_SNP [dm3] 2L_4415801_SNP [dm6]	T	C	8.313e^-5	0.964	INTRON CG15431
2L	14531330	2L_14531330_SNP [dm3] 2L_14531330_SNP [dm6]	G	A	8.776e^-5	0.964	UPSTREAM tRNA:G3:35Bd & 1 other INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	15873047	X_15873047_SNP [dm3] X_15979014_SNP [dm6]	T	C	9.005e^-5	0.964	SYNONYMOUS_CODING CG9170	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	20449938	3R_20449938_SNP [dm3] 3R_24624216_SNP [dm6]	G	T	9.078e^-5	0.964	DOWNSTREAM mld INTRON Syx18
3L	20941290	3L_20941290_SNP [dm3] 3L_20948190_SNP [dm6]	T	C	9.156e^-5	0.964	INTRON fng
2R	704185	2R_704185_SNP [dm3] 2R_4816680_SNP [dm6]	G	A	9.168e^-5	0.964	UTR_3_PRIME CG17528 DOWNSTREAM CG17528	TF binding site mE1_TFBS_cad
3R	25287571	3R_25287571_SNP [dm3] 3R_29461849_SNP [dm6]	G	T	9.254e^-5	0.964	UTR_5_PRIME Ptp99A UPSTREAM Ptp99A INTRON Ptp99A	TF binding site BDTNP1_TFBS_twi
X	6005458	X_6005458_SNP [dm3] X_6111425_SNP [dm6]	A	G	9.601e^-5	0.964	INTRON Ca-alpha1T	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12354158	3R_12354158_SNP [dm3] 3R_16528436_SNP [dm6]	A	C	9.858e^-5	0.964	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
X	12769080	X_12769080_INS [dm3] X_12875047_INS [dm6]	C	CT	1.002e^-4	0.964	INTRON Pde9
2L	8010187	2L_8010187_SNP [dm3] 2L_8010187_SNP [dm6]	C	A	1.014e^-4	0.964	NON_SYNONYMOUS_CODING CG34010 UPSTREAM CG12560	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	4963071	2L_4963071_SNP [dm3] 2L_4963071_SNP [dm6]	T	A	1.050e^-4	0.964	SYNONYMOUS_CODING CG34124 DOWNSTREAM CR43824	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	15751352	2R_15751352_SNP [dm3] 2R_19863847_SNP [dm6]	A	C	1.054e^-4	0.964	UPSTREAM Obp56i INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	15751361	2R_15751361_SNP [dm3] 2R_19863856_SNP [dm6]	T	G	1.054e^-4	0.964	UPSTREAM Obp56i INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	2892875	3L_2892875_SNP [dm3] 3L_2892875_SNP [dm6]	A	G	1.069e^-4	0.964	UPSTREAM spz5 INTERGENIC
2L	7331995	2L_7331995_SNP [dm3] 2L_7331995_SNP [dm6]	C	G	1.095e^-4	0.964	INTERGENIC
2L	12445651	2L_12445651_SNP [dm3] 2L_12445651_SNP [dm6]	T	C	1.125e^-4	0.964	DOWNSTREAM CG5421 INTRON Oatp33Ea	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	20351462	2L_20351462_SNP [dm3] 2L_20351462_SNP [dm6]	G	A	1.129e^-4	0.964	INTRON RtGEF
3L	3094603	3L_3094603_SNP [dm3] 3L_3094603_SNP [dm6]	T	C	1.130e^-4	0.964	SYNONYMOUS_CODING Cht7	TF binding site mE1_TFBS_cad
X	14161154	X_14161154_INS [dm3] X_14267121_INS [dm6]	A	AAA	1.130e^-4	0.964	UPSTREAM CG13404 INTRON na
X	14161159	X_14161159_SNP [dm3] X_14267126_SNP [dm6]	G	T	1.130e^-4	0.964	UPSTREAM CG13404 INTRON na
X	14161165	X_14161165_SNP [dm3] X_14267132_SNP [dm6]	C	A	1.130e^-4	0.964	UPSTREAM CG13404 INTRON na
2L	12448794	2L_12448794_DEL [dm3] 2L_12448794_DEL [dm6]	CA	C	1.148e^-4	0.964	UPSTREAM CG5421 INTRON Oatp33Eb
3L	1412812	3L_1412812_SNP [dm3] 3L_1412812_SNP [dm6]	G	A	1.153e^-4	0.964	NON_SYNONYMOUS_CODING CG9168 INTRON Ptp61F
X	3481263	X_3481263_SNP [dm3] X_3587230_SNP [dm6]	T	G	1.161e^-4	0.964	INTRON AstA-R1
2R	12620293	2R_12620293_SNP [dm3] 2R_16732788_SNP [dm6]	T	C	1.187e^-4	0.964	UTR_5_PRIME CG30463	TF binding site BDTNP1_TFBS_sna
X	7130285	X_7130285_SNP [dm3] X_7236252_SNP [dm6]	G	A	1.193e^-4	0.964	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	19584045	2L_19584045_SNP [dm3] 2L_19584045_SNP [dm6]	T	C	1.197e^-4	0.964	UPSTREAM CG10366 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	12596799	3L_12596799_SNP [dm3] 3L_12603699_SNP [dm6]	T	C	1.213e^-4	0.964	INTERGENIC
2R	10584445	2R_10584445_SNP [dm3] 2R_14696940_SNP [dm6]	T	C	1.216e^-4	0.964	INTRON mspo
2R	10584452	2R_10584452_SNP [dm3] 2R_14696947_SNP [dm6]	T	C	1.216e^-4	0.964	INTRON mspo
3L	2416414	3L_2416414_SNP [dm3] 3L_2416414_SNP [dm6]	C	T	1.224e^-4	0.964	INTRON CG45186
2L	16371309	2L_16371309_SNP [dm3] 2L_16371309_SNP [dm6]	C	T	1.226e^-4	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_inv
X	11213837	X_11213837_SNP [dm3] X_11319804_SNP [dm6]	G	A	1.234e^-4	0.964	INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA
2R	16620703	2R_16620703_SNP [dm3] 2R_20733198_SNP [dm6]	T	C	1.238e^-4	0.964	INTRON dpr
X	1009875	X_1009875_SNP [dm3] X_1115842_SNP [dm6]	C	T	1.240e^-4	0.964	INTRON CG3655	TF binding site mE1_TFBS_HSA
3L	2568819	3L_2568819_SNP [dm3] 3L_2568819_SNP [dm6]	C	A	1.285e^-4	0.964	INTRON msn
3L	2568825	3L_2568825_SNP [dm3] 3L_2568825_SNP [dm6]	G	A	1.285e^-4	0.964	INTRON msn
2R	18538526	2R_18538526_SNP [dm3] 2R_22651021_SNP [dm6]	C	T	1.310e^-4	0.964	INTRON nsr	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	20399476	X_20399476_SNP [dm3] X_20528449_SNP [dm6]	G	T	1.318e^-4	0.964	DOWNSTREAM CG42579 INTERGENIC
2L	13804056	2L_13804056_SNP [dm3] 2L_13804056_SNP [dm6]	T	G	1.334e^-4	0.964	INTRON CAH1
3L	10900191	3L_10900191_SNP [dm3] 3L_10907091_SNP [dm6]	T	C	1.344e^-4	0.964	INTERGENIC
3L	10900198	3L_10900198_SNP [dm3] 3L_10907098_SNP [dm6]	T	A	1.344e^-4	0.964	INTERGENIC
3L	2409971	3L_2409971_SNP [dm3] 3L_2409971_SNP [dm6]	A	T	1.363e^-4	0.964	DOWNSTREAM CG45186 INTRON CG45186	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv
3L	2699584	3L_2699584_SNP [dm3] 3L_2699584_SNP [dm6]	A	C	1.384e^-4	0.964	INTRON Fife
2L	7341264	2L_7341264_SNP [dm3] 2L_7341264_SNP [dm6]	G	T	1.386e^-4	0.964	INTRON Wnt6	TF binding site mE1_TFBS_sbb
3L	18108932	3L_18108932_SNP [dm3] 3L_18115832_SNP [dm6]	A	T	1.390e^-4	0.964	UTR_3_PRIME CG32195 INTRON CG7341
X	12512200	X_12512200_SNP [dm3] X_12618167_SNP [dm6]	G	A	1.391e^-4	0.964	INTRON CG11085	TF binding site mE1_TFBS_inv
3L	7245077	3L_7245077_SNP [dm3] 3L_7251977_SNP [dm6]	T	C	1.396e^-4	0.964	NON_SYNONYMOUS_CODING CG14830 EXON CR43470	TF binding site mE1_TFBS_chinmo
2R	16620410	2R_16620410_SNP [dm3] 2R_20732905_SNP [dm6]	T	A	1.403e^-4	0.964	INTRON dpr

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By genomic position
Variant impact
Gene name

Mating phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results