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=5.151e^-3)
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

1276 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	8709413	X_8709413_SNP [dm3] X_8815380_SNP [dm6]	C	T	1.099e^-6	0.989	INTERGENIC
3L	2105320	3L_2105320_SNP [dm3] 3L_2105320_SNP [dm6]	T	C	5.250e^-6	0.989	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2L	5966209	2L_5966209_SNP [dm3] 2L_5966209_SNP [dm6]	T	G	6.891e^-6	0.989	SYNONYMOUS_CODING CG13992	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11473802	3L_11473802_SNP [dm3] 3L_11480702_SNP [dm6]	T	C	6.922e^-6	0.989	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	6953244	2L_6953244_SNP [dm3] 2L_6953244_SNP [dm6]	T	C	9.164e^-6	0.989	SYNONYMOUS_CODING SA	TF binding site mE1_TFBS_sens
2L	6953271	2L_6953271_SNP [dm3] 2L_6953271_SNP [dm6]	T	C	9.164e^-6	0.989	SYNONYMOUS_CODING SA	TF binding site mE1_TFBS_sens
3L	2105215	3L_2105215_SNP [dm3] 3L_2105215_SNP [dm6]	T	C	9.295e^-6	0.989	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3L	2105126	3L_2105126_SNP [dm3] 3L_2105126_SNP [dm6]	T	C	9.393e^-6	0.989	INTRON sls	TF binding site mE1_TFBS_chinmo
X	6448698	X_6448698_SNP [dm3] X_6554665_SNP [dm6]	C	T	9.452e^-6	0.989	SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_chinmo
X	6448651	X_6448651_SNP [dm3] X_6554618_SNP [dm6]	G	C	1.061e^-5	0.989	NON_SYNONYMOUS_CODING CG34417 INTRON CG34417	TF binding site mE1_TFBS_chinmo
2R	6949292	2R_6949292_DEL [dm3] 2R_11061787_DEL [dm6]	TA	G	1.128e^-5	0.989	INTRON luna
X	8708920	X_8708920_SNP [dm3] X_8814887_SNP [dm6]	A	T	1.144e^-5	0.989	INTERGENIC
2L	4196788	2L_4196788_SNP [dm3] 2L_4196788_SNP [dm6]	G	T	1.337e^-5	0.989	UTR_5_PRIME CG3714 INTRON CG3714	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb
3L	11852655	3L_11852655_SNP [dm3] 3L_11859555_SNP [dm6]	A	G	1.355e^-5	0.989	INTRON CG44837
2L	5966175	2L_5966175_SNP [dm3] 2L_5966175_SNP [dm6]	C	G	1.473e^-5	0.989	NON_SYNONYMOUS_CODING CG13992	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	8077363	3L_8077363_SNP [dm3] 3L_8084263_SNP [dm6]	C	G	1.579e^-5	0.989	INTRON Ect4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	1679433	3L_1679433_SNP [dm3] 3L_1679433_SNP [dm6]	T	G	1.648e^-5	0.989	INTRON CG7991
3L	16987512	3L_16987512_SNP [dm3] 3L_16994412_SNP [dm6]	T	G	1.778e^-5	0.989	DOWNSTREAM CG3764 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	16987692	3L_16987692_SNP [dm3] 3L_16994592_SNP [dm6]	G	A	1.778e^-5	0.989	DOWNSTREAM CG3764 & 1 other INTERGENIC
3R	13789150	3R_13789150_SNP [dm3] 3R_17963428_SNP [dm6]	G	T	1.823e^-5	0.989	INTRON cpo
2L	10096460	2L_10096460_SNP [dm3] 2L_10096460_SNP [dm6]	C	T	2.029e^-5	0.989	INTRON CG44153 & 1 other
2L	5966176	2L_5966176_SNP [dm3] 2L_5966176_SNP [dm6]	T	A	2.082e^-5	0.989	SYNONYMOUS_CODING CG13992	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	2105098	3L_2105098_SNP [dm3] 3L_2105098_SNP [dm6]	G	C	2.112e^-5	0.989	INTRON sls	TF binding site mE1_TFBS_chinmo
3L	2105272	3L_2105272_SNP [dm3] 3L_2105272_SNP [dm6]	G	T	2.138e^-5	0.989	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2L	4196823	2L_4196823_SNP [dm3] 2L_4196823_SNP [dm6]	G	T	2.223e^-5	0.989	INTRON CG3714	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb
X	11843367	X_11843367_SNP [dm3] X_11949334_SNP [dm6]	A	T	2.395e^-5	0.989	INTRON cac	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	1999806	2L_1999806_SNP [dm3] 2L_1999806_SNP [dm6]	G	T	2.418e^-5	0.989	UPSTREAM CR43464 INTRON CG33543
3R	25444559	3R_25444559_SNP [dm3] 3R_29618837_SNP [dm6]	G	T	2.434e^-5	0.989	UPSTREAM CG1907 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	3151597	3L_3151597_SNP [dm3] 3L_3151597_SNP [dm6]	C	T	2.529e^-5	0.989	INTRON BtbVII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	5182286	3L_5182286_SNP [dm3] 3L_5189186_SNP [dm6]	C	T	2.607e^-5	0.989	INTRON shep
3L	5182353	3L_5182353_SNP [dm3] 3L_5189253_SNP [dm6]	C	G	2.607e^-5	0.989	INTRON shep
2L	13729664	2L_13729664_SNP [dm3] 2L_13729664_SNP [dm6]	T	C	2.895e^-5	0.989	INTERGENIC
3R	25125892	3R_25125892_SNP [dm3] 3R_29300170_SNP [dm6]	A	T	2.988e^-5	0.989	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	11344665	2L_11344665_SNP [dm3] 2L_11344665_SNP [dm6]	C	G	3.051e^-5	0.989	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
X	15531943	X_15531943_INS [dm3] X_15637910_INS [dm6]	C	CTATATGCTATAC...	3.122e^-5	0.989	DOWNSTREAM CR44423 INTERGENIC
3L	2105204	3L_2105204_SNP [dm3] 3L_2105204_SNP [dm6]	T	C	3.319e^-5	0.989	NON_SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3L	1557781	3L_1557781_SNP [dm3] 3L_1557781_SNP [dm6]	G	A	3.588e^-5	0.989	SPLICE_SITE_REGION CG12099 UPSTREAM Pex10 INTRON CG12099	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	2105093	3L_2105093_SNP [dm3] 3L_2105093_SNP [dm6]	G	C	3.720e^-5	0.989	INTRON sls	TF binding site mE1_TFBS_chinmo
2L	4009682	2L_4009682_SNP [dm3] 2L_4009682_SNP [dm6]	G	A	3.842e^-5	0.989	DOWNSTREAM CG43774 INTERGENIC
3L	8830916	3L_8830916_SNP [dm3] 3L_8837816_SNP [dm6]	G	A	4.133e^-5	0.989	SYNONYMOUS_CODING CG32026 INTRON dally	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
2L	4629433	2L_4629433_SNP [dm3] 2L_4629433_SNP [dm6]	C	T	4.334e^-5	0.989	INTERGENIC
X	4467817	X_4467817_SNP [dm3] X_4573784_SNP [dm6]	T	A	4.471e^-5	0.989	INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	13795325	3R_13795325_SNP [dm3] 3R_17969603_SNP [dm6]	C	G	4.586e^-5	0.989	INTRON cpo
X	8709324	X_8709324_SNP [dm3] X_8815291_SNP [dm6]	T	A	4.598e^-5	0.989	INTERGENIC
2R	8609411	2R_8609411_SNP [dm3] 2R_12721906_SNP [dm6]	A	G	4.708e^-5	0.989	INTRON CG42663
X	11843369	X_11843369_SNP [dm3] X_11949336_SNP [dm6]	A	G	4.730e^-5	0.989	INTRON cac	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	14992711	2R_14992711_SNP [dm3] 2R_19105206_SNP [dm6]	C	G	4.737e^-5	0.989	INTRON 5-HT1A
3L	19046709	3L_19046709_INS [dm3] 3L_19053609_INS [dm6]	A	AGAAAAC	4.847e^-5	0.989	UPSTREAM CG43407 DOWNSTREAM CR44675 INTERGENIC
3L	19046711	3L_19046711_DEL [dm3] 3L_19053611_DEL [dm6]	AG	A	4.847e^-5	0.989	UPSTREAM CG43407 DOWNSTREAM CR44675 INTERGENIC
3R	10172088	3R_10172088_SNP [dm3] 3R_14346366_SNP [dm6]	A	C	4.944e^-5	0.989	INTRON NK7.1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	8323688	X_8323688_SNP [dm3] X_8429655_SNP [dm6]	A	G	5.122e^-5	0.989	UTR_3_PRIME Trf2 INTRON Trf2
3R	22100006	3R_22100006_SNP [dm3] 3R_26274284_SNP [dm6]	G	C	5.175e^-5	0.989	INTRON CG6154
2R	8360544	2R_8360544_SNP [dm3] 2R_12473039_SNP [dm6]	T	C	5.197e^-5	0.989	SYNONYMOUS_CODING CG8550
3R	19277538	3R_19277538_SNP [dm3] 3R_23451816_SNP [dm6]	T	C	5.254e^-5	0.989	INTRON CG4374	TF binding site BDTNP1_TFBS_dl
2R	12381432	2R_12381432_DEL [dm3] 2R_16493927_DEL [dm6]	TCT	T	5.344e^-5	0.989	DOWNSTREAM S-Lap8 INTERGENIC	TF binding site mE1_TFBS_HSA
3L	1557752	3L_1557752_SNP [dm3] 3L_1557752_SNP [dm6]	T	C	5.489e^-5	0.989	UPSTREAM Pex10 INTRON CG12099	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	1557758	3L_1557758_SNP [dm3] 3L_1557758_SNP [dm6]	T	A	5.489e^-5	0.989	UPSTREAM Pex10 INTRON CG12099	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	2105103	3L_2105103_SNP [dm3] 3L_2105103_SNP [dm6]	A	C	5.629e^-5	0.989	INTRON sls	TF binding site mE1_TFBS_chinmo
2R	2962650	2R_2962650_SNP [dm3] 2R_7075145_SNP [dm6]	G	A	5.752e^-5	0.989	UPSTREAM CG12831 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	10102232	2L_10102232_SNP [dm3] 2L_10102232_SNP [dm6]	G	C	5.854e^-5	0.989	INTRON CG44153 & 1 other
2L	6495166	2L_6495166_SNP [dm3] 2L_6495166_SNP [dm6]	A	T	5.980e^-5	0.989	UPSTREAM CG9547 INTRON CG31638	TF binding site mE1_TFBS_cad
3L	3303694	3L_3303694_SNP [dm3] 3L_3303694_SNP [dm6]	C	T	6.008e^-5	0.989	UPSTREAM ZnT63C & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
2R	14512976	2R_14512976_SNP [dm3] 2R_18625471_SNP [dm6]	A	C	6.045e^-5	0.989	SYNONYMOUS_CODING Sec6 UPSTREAM Atg7	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11852579	3L_11852579_DEL [dm3] 3L_11859479_DEL [dm6]	CGTAATCAGC	C	6.158e^-5	0.989	INTRON CG44837
X	4285620	X_4285620_SNP [dm3] X_4391587_SNP [dm6]	C	T	6.176e^-5	0.989	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	5853949	3R_5853949_SNP [dm3] 3R_10028227_SNP [dm6]	G	A	6.321e^-5	0.989	INTRON Mical
2R	13042332	2R_13042332_DEL [dm3] 2R_17154827_DEL [dm6]	TT	T	6.332e^-5	0.989	INTRON CG17290
2L	5456110	2L_5456110_SNP [dm3] 2L_5456110_SNP [dm6]	T	A	6.350e^-5	0.989	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3127227	3L_3127227_SNP [dm3] 3L_3127227_SNP [dm6]	T	G	6.391e^-5	0.989	UPSTREAM prominin-like DOWNSTREAM CG11537 INTRON prominin-like	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	8027606	2L_8027606_SNP [dm3] 2L_8027606_SNP [dm6]	C	T	6.438e^-5	0.989	SYNONYMOUS_CODING CG7367 DOWNSTREAM Tg
2L	11344575	2L_11344575_SNP [dm3] 2L_11344575_SNP [dm6]	A	G	6.486e^-5	0.989	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	1560016	3L_1560016_SNP [dm3] 3L_1560016_SNP [dm6]	C	T	6.604e^-5	0.989	UTR_3_PRIME CG7879 DOWNSTREAM Pex10	TF binding site mE1_TFBS_inv mE1_TFBS_sbb
3R	11302374	3R_11302374_SNP [dm3] 3R_15476652_SNP [dm6]	G	A	6.624e^-5	0.989	UPSTREAM AdamTS-A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	16373794	2L_16373794_SNP [dm3] 2L_16373794_SNP [dm6]	A	G	6.730e^-5	0.989	INTERGENIC
X	4467089	X_4467089_SNP [dm3] X_4573056_SNP [dm6]	T	A	6.735e^-5	0.989	INTRON CR32773
3L	1119065	3L_1119065_SNP [dm3] 3L_1119065_SNP [dm6]	G	A	6.799e^-5	0.989	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	2925476	2R_2925476_SNP [dm3] 2R_7037971_SNP [dm6]	C	T	6.843e^-5	0.989	UTR_5_PRIME CG33914 UPSTREAM CG33914
2R	14992596	2R_14992596_SNP [dm3] 2R_19105091_SNP [dm6]	C	T	6.933e^-5	0.989	INTRON 5-HT1A
X	4467772	X_4467772_SNP [dm3] X_4573739_SNP [dm6]	T	A	6.991e^-5	0.989	INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	9727916	2L_9727916_SNP [dm3] 2L_9727916_SNP [dm6]	T	A	6.998e^-5	0.989	INTRON Nckx30C
2L	9728018	2L_9728018_SNP [dm3] 2L_9728018_SNP [dm6]	C	T	6.998e^-5	0.989	INTRON Nckx30C
3L	3303590	3L_3303590_SNP [dm3] 3L_3303590_SNP [dm6]	C	T	7.044e^-5	0.989	UPSTREAM ZnT63C & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
2R	13760427	2R_13760427_SNP [dm3] 2R_17872922_SNP [dm6]	A	T	7.062e^-5	0.989	UPSTREAM Mapmodulin INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	1020220	2L_1020220_SNP [dm3] 2L_1020220_SNP [dm6]	G	A	7.088e^-5	0.989	INTRON IA-2
3L	9716343	3L_9716343_SNP [dm3] 3L_9723243_SNP [dm6]	A	C	7.264e^-5	0.989	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2R	13042287	2R_13042287_SNP [dm3] 2R_17154782_SNP [dm6]	T	G	7.287e^-5	0.989	INTRON CG17290
2R	2925460	2R_2925460_SNP [dm3] 2R_7037955_SNP [dm6]	C	G	7.456e^-5	0.989	UTR_5_PRIME CG33914 UPSTREAM CG33914
2R	16455993	2R_16455993_SNP [dm3] 2R_20568488_SNP [dm6]	T	C	7.484e^-5	0.989	INTRON qsm	TF binding site mE1_TFBS_chinmo
2R	15273213	2R_15273213_SNP [dm3] 2R_19385708_SNP [dm6]	T	A	7.520e^-5	0.989	UPSTREAM CG10081 DOWNSTREAM CG10073 INTERGENIC
X	19611014	X_19611014_SNP [dm3] X_19716981_SNP [dm6]	C	T	7.619e^-5	0.989	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	8184942	3L_8184942_SNP [dm3] 3L_8191842_SNP [dm6]	A	G	7.917e^-5	0.989	SYNONYMOUS_CODING CG7387 DOWNSTREAM Atg18a INTRON MED24	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	11844237	3R_11844237_SNP [dm3] 3R_16018515_SNP [dm6]	T	G	8.122e^-5	0.989	SYNONYMOUS_CODING GATAe	TF binding site mE1_TFBS_inv
3L	1559937	3L_1559937_DEL [dm3] 3L_1559937_DEL [dm6]	GAA	G	8.134e^-5	0.989	UTR_3_PRIME CG7879 DOWNSTREAM Pex10	TF binding site mE1_TFBS_sbb
X	9444430	X_9444430_SNP [dm3] X_9550397_SNP [dm6]	A	G	8.172e^-5	0.989	DOWNSTREAM l_1_G0320 INTRON CG32700
3L	5183348	3L_5183348_SNP [dm3] 3L_5190248_SNP [dm6]	A	T	8.278e^-5	0.989	INTRON shep
2R	8625628	2R_8625628_SNP [dm3] 2R_12738123_SNP [dm6]	G	A	8.299e^-5	0.989	INTRON CG42663
2L	3388388	2L_3388388_SNP [dm3] 2L_3388388_SNP [dm6]	A	G	8.471e^-5	0.989	NON_SYNONYMOUS_CODING CG42460 UPSTREAM Sfp23F & 1 other
X	4467787	X_4467787_SNP [dm3] X_4573754_SNP [dm6]	T	C	8.672e^-5	0.989	INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	18570111	2R_18570111_SNP [dm3] 2R_22682606_SNP [dm6]	A	G	8.695e^-5	0.989	INTERGENIC	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	10972634	3L_10972634_SNP [dm3] 3L_10979534_SNP [dm6]	A	C	8.776e^-5	0.989	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Hobo_Relative_Cov phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results