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=7.511e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2043 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	7806766	3R_7806766_SNP [dm3] 3R_11981044_SNP [dm6]	G	A	1.109e^-6	0.805	SYNONYMOUS_CODING CG12224 UPSTREAM CG18547	TF binding site mE1_TFBS_chinmo mE1_TFBS_Trl
3R	22549408	3R_22549408_SNP [dm3] 3R_26723686_SNP [dm6]	G	T	1.500e^-6	0.805	INTRON CG6420	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	22882499	3R_22882499_SNP [dm3] 3R_27056777_SNP [dm6]	G	A	1.761e^-6	0.805	SPLICE_SITE_REGION RYa-R INTRON RYa-R	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	7528497	2R_7528497_SNP [dm3] 2R_11640992_SNP [dm6]	C	T	2.517e^-6	0.805	UPSTREAM CG9005 DOWNSTREAM CG9003 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	4510450	3L_4510450_SNP [dm3] 3L_4510450_SNP [dm6]	T	C	2.847e^-6	0.805	DOWNSTREAM Tie INTERGENIC
3R	22882498	3R_22882498_SNP [dm3] 3R_27056776_SNP [dm6]	G	A	2.892e^-6	0.805	SPLICE_SITE_REGION RYa-R INTRON RYa-R	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	18722165	2L_18722165_SNP [dm3] 2L_18722165_SNP [dm6]	C	T	4.309e^-6	0.805	INTRON CG10348
3R	22882230	3R_22882230_SNP [dm3] 3R_27056508_SNP [dm6]	T	C	4.566e^-6	0.805	INTRON RYa-R	TF binding site mE1_TFBS_inv
2L	1844748	2L_1844748_SNP [dm3] 2L_1844748_SNP [dm6]	A	C	4.698e^-6	0.805	INTRON wry
2L	8737357	2L_8737357_SNP [dm3] 2L_8737357_SNP [dm6]	A	T	5.329e^-6	0.805	INTRON raw
3R	22549137	3R_22549137_SNP [dm3] 3R_26723415_SNP [dm6]	A	T	5.441e^-6	0.805	INTRON CG6420
3L	16235775	3L_16235775_SNP [dm3] 3L_16242675_SNP [dm6]	A	G	5.561e^-6	0.805	INTERGENIC
X	19259130	X_19259130_SNP [dm3] X_19365097_SNP [dm6]	A	G	5.582e^-6	0.805	INTRON kek5
2L	18722005	2L_18722005_SNP [dm3] 2L_18722005_SNP [dm6]	T	G	7.162e^-6	0.816	INTRON CG10348
3R	13196662	3R_13196662_SNP [dm3] 3R_17370940_SNP [dm6]	C	A	7.217e^-6	0.816	DOWNSTREAM CR44256 INTERGENIC
2L	6958889	2L_6958889_SNP [dm3] 2L_6958889_SNP [dm6]	T	C	7.980e^-6	0.816	SYNONYMOUS_CODING CG3430 DOWNSTREAM Atac1
X	19259131	X_19259131_SNP [dm3] X_19365098_SNP [dm6]	C	T	8.303e^-6	0.816	INTRON kek5
X	13199667	X_13199667_SNP [dm3] X_13305634_SNP [dm6]	G	A	8.967e^-6	0.816	UTR_5_PRIME IP3K2 INTRON IP3K2 EXON CR45018	TF binding site mE1_TFBS_cad
3R	16799089	3R_16799089_SNP [dm3] 3R_20973367_SNP [dm6]	C	G	9.160e^-6	0.816	INTRON Atpalpha
3L	17911017	3L_17911017_SNP [dm3] 3L_17917917_SNP [dm6]	C	T	9.671e^-6	0.816	INTERGENIC
3R	22548961	3R_22548961_DEL [dm3] 3R_26723239_DEL [dm6]	TG	T	1.038e^-5	0.816	INTRON CG6420
3L	4510169	3L_4510169_SNP [dm3] 3L_4510169_SNP [dm6]	A	T	1.077e^-5	0.816	DOWNSTREAM Tie INTERGENIC
3R	16616922	3R_16616922_SNP [dm3] 3R_20791200_SNP [dm6]	C	T	1.151e^-5	0.816	INTRON Syp
3R	22549045	3R_22549045_SNP [dm3] 3R_26723323_SNP [dm6]	G	A	1.179e^-5	0.816	INTRON CG6420
2R	15525692	2R_15525692_SNP [dm3] 2R_19638187_SNP [dm6]	T	C	1.185e^-5	0.816	DOWNSTREAM CG18367 & 2 others INTERGENIC
2L	18761721	2L_18761721_DEL [dm3] 2L_18761721_DEL [dm6]	CAAAATGA	C	1.332e^-5	0.816	INTERGENIC
3R	22549199	3R_22549199_SNP [dm3] 3R_26723477_SNP [dm6]	A	T	1.338e^-5	0.816	INTRON CG6420
3L	16235807	3L_16235807_INS [dm3] 3L_16242707_INS [dm6]	A	GCTGTCGC	1.420e^-5	0.816	INTERGENIC
2R	16512063	2R_16512063_SNP [dm3] 2R_20624558_SNP [dm6]	A	G	1.448e^-5	0.816	NON_SYNONYMOUS_CODING CG16742	TF binding site mE1_TFBS_sens
2L	18718835	2L_18718835_SNP [dm3] 2L_18718835_SNP [dm6]	C	A	1.456e^-5	0.816	INTRON CG10348
2R	11416864	2R_11416864_SNP [dm3] 2R_15529359_SNP [dm6]	A	T	1.507e^-5	0.816	INTRON Khc-73	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	18716591	2L_18716591_SNP [dm3] 2L_18716591_SNP [dm6]	C	T	1.517e^-5	0.816	UTR_5_PRIME CG10348	TF binding site mE1_TFBS_cad
2R	4192850	2R_4192850_SNP [dm3] 2R_8305345_SNP [dm6]	T	G	1.520e^-5	0.816	DOWNSTREAM CR44447 INTERGENIC
3R	26611553	3R_26611553_SNP [dm3] 3R_30785831_SNP [dm6]	C	T	1.594e^-5	0.816	NON_SYNONYMOUS_CODING zfh1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2L	8737415	2L_8737415_SNP [dm3] 2L_8737415_SNP [dm6]	G	A	1.658e^-5	0.816	INTRON raw
2L	18716916	2L_18716916_DEL [dm3] 2L_18716916_DEL [dm6]	GG	G	1.660e^-5	0.816	INTRON CG10348
3R	9631414	3R_9631414_SNP [dm3] 3R_13805692_SNP [dm6]	G	T	1.661e^-5	0.816	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	22548932	3R_22548932_SNP [dm3] 3R_26723210_SNP [dm6]	C	A	1.679e^-5	0.816	INTRON CG6420
3L	3521221	3L_3521221_SNP [dm3] 3L_3521221_SNP [dm6]	C	G	1.790e^-5	0.816	INTRON Eip63E
3L	17911036	3L_17911036_SNP [dm3] 3L_17917936_SNP [dm6]	G	A	1.841e^-5	0.816	INTERGENIC
2L	18760825	2L_18760825_SNP [dm3] 2L_18760825_SNP [dm6]	C	T	1.846e^-5	0.816	INTERGENIC
3L	8574359	3L_8574359_SNP [dm3] 3L_8581259_SNP [dm6]	C	T	2.088e^-5	0.816	INTRON CG43078
3R	25810464	3R_25810464_SNP [dm3] 3R_29984742_SNP [dm6]	T	C	2.097e^-5	0.816	INTRON CG7896
2L	5906941	2L_5906941_SNP [dm3] 2L_5906941_SNP [dm6]	A	T	2.122e^-5	0.816	UPSTREAM bchs & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	8574361	3L_8574361_SNP [dm3] 3L_8581261_SNP [dm6]	C	T	2.158e^-5	0.816	INTRON CG43078
2L	20943731	2L_20943731_SNP [dm3] 2L_20943731_SNP [dm6]	T	A	2.179e^-5	0.816	INTERGENIC
3L	17911035	3L_17911035_SNP [dm3] 3L_17917935_SNP [dm6]	G	A	2.194e^-5	0.816	INTERGENIC
3R	19358394	3R_19358394_SNP [dm3] 3R_23532672_SNP [dm6]	A	T	2.239e^-5	0.816	DOWNSTREAM CG10170 INTERGENIC
2L	1783680	2L_1783680_SNP [dm3] 2L_1783680_SNP [dm6]	A	C	2.253e^-5	0.816	UPSTREAM Gr22e INTERGENIC	regulatory region REDfly_CRMs
3R	25163603	3R_25163603_SNP [dm3] 3R_29337881_SNP [dm6]	A	G	2.258e^-5	0.816	INTERGENIC
2L	15342125	2L_15342125_SNP [dm3] 2L_15342125_SNP [dm6]	G	T	2.266e^-5	0.816	INTERGENIC
3L	17911038	3L_17911038_SNP [dm3] 3L_17917938_SNP [dm6]	A	C	2.289e^-5	0.816	INTERGENIC
3L	4510654	3L_4510654_SNP [dm3] 3L_4510654_SNP [dm6]	T	A	2.307e^-5	0.816	DOWNSTREAM Tie INTERGENIC
X	4750219	X_4750219_DEL [dm3] X_4856186_DEL [dm6]	TGGGGCTGGCTGGCTGGTTG...	T	2.378e^-5	0.826	INTRON CG42594
2L	19120026	2L_19120026_SNP [dm3] 2L_19120026_SNP [dm6]	C	A	2.439e^-5	0.832	UTR_5_PRIME Ddc INTRON Ddc	regulatory region REDfly_CRMs
2R	15171691	2R_15171691_SNP [dm3] 2R_19284186_SNP [dm6]	T	G	2.493e^-5	0.835	UPSTREAM CG11906 DOWNSTREAM CG10476 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_GATAe mE1_TFBS_HSA
2L	1844384	2L_1844384_SNP [dm3] 2L_1844384_SNP [dm6]	A	C	2.571e^-5	0.836	SYNONYMOUS_CODING wry	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	17911039	3L_17911039_SNP [dm3] 3L_17917939_SNP [dm6]	T	C	2.586e^-5	0.836	INTERGENIC
2L	5906976	2L_5906976_SNP [dm3] 2L_5906976_SNP [dm6]	C	T	2.679e^-5	0.852	UPSTREAM bchs & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	8598288	3L_8598288_SNP [dm3] 3L_8605188_SNP [dm6]	A	G	2.769e^-5	0.855	INTRON CG6282	TF binding site BDTNP1_TFBS_dl
2L	9776217	2L_9776217_SNP [dm3] 2L_9776217_SNP [dm6]	C	T	2.782e^-5	0.855	INTERGENIC
2R	15525732	2R_15525732_SNP [dm3] 2R_19638227_SNP [dm6]	C	T	2.837e^-5	0.858	DOWNSTREAM CG18367 & 2 others INTERGENIC
3R	7160937	3R_7160937_SNP [dm3] 3R_11335215_SNP [dm6]	G	T	2.960e^-5	0.863	UTR_5_PRIME pros INTRON pros
2R	15525709	2R_15525709_SNP [dm3] 2R_19638204_SNP [dm6]	T	C	3.049e^-5	0.863	DOWNSTREAM CG18367 & 2 others INTERGENIC
2L	8507662	2L_8507662_SNP [dm3] 2L_8507662_SNP [dm6]	A	T	3.049e^-5	0.863	UPSTREAM Dh31 INTERGENIC
X	5593237	X_5593237_INS [dm3] X_5699204_INS [dm6]	T	TGTAT	3.081e^-5	0.863	UTR_5_PRIME CG4096 INTRON CG4096	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	12268816	3R_12268816_SNP [dm3] 3R_16443094_SNP [dm6]	A	G	3.110e^-5	0.863	UPSTREAM CG14882 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
3L	3395070	3L_3395070_DEL [dm3] 3L_3395070_DEL [dm6]	TTTCT	T	3.161e^-5	0.863	DOWNSTREAM CR45737 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	7537717	2R_7537717_SNP [dm3] 2R_11650212_SNP [dm6]	T	A	3.246e^-5	0.863	INTRON CG9003	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	3397412	3L_3397412_SNP [dm3] 3L_3397412_SNP [dm6]	A	T	3.461e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3L	3197577	3L_3197577_SNP [dm3] 3L_3197577_SNP [dm6]	A	G	3.539e^-5	0.863	START_GAINED CG14966 UTR_5_PRIME CG14966 DOWNSTREAM CG32276 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Ubx
2L	18731200	2L_18731200_SNP [dm3] 2L_18731200_SNP [dm6]	G	T	3.561e^-5	0.863	UTR_5_PRIME CG10348
2L	15342117	2L_15342117_SNP [dm3] 2L_15342117_SNP [dm6]	A	G	3.587e^-5	0.863	INTERGENIC
X	20431379	X_20431379_SNP [dm3] X_20560352_SNP [dm6]	A	C	3.601e^-5	0.863	INTRON RunxB
2L	1844376	2L_1844376_SNP [dm3] 2L_1844376_SNP [dm6]	G	A	3.615e^-5	0.863	NON_SYNONYMOUS_CODING wry	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22814753	3R_22814753_SNP [dm3] 3R_26989031_SNP [dm6]	A	T	3.633e^-5	0.863	UPSTREAM CG31075 DOWNSTREAM CG31076 INTERGENIC
3L	8574346	3L_8574346_SNP [dm3] 3L_8581246_SNP [dm6]	A	G	3.720e^-5	0.863	INTRON CG43078
3R	18825230	3R_18825230_DEL [dm3] 3R_22999508_DEL [dm6]	GATGATGATGACT...	G	3.730e^-5	0.863	UPSTREAM Nha2 DOWNSTREAM CG34375 INTERGENIC
2L	5826686	2L_5826686_SNP [dm3] 2L_5826686_SNP [dm6]	T	G	3.731e^-5	0.863	INTRON TrissinR
3R	16799706	3R_16799706_SNP [dm3] 3R_20973984_SNP [dm6]	G	A	3.870e^-5	0.863	UTR_3_PRIME Atpalpha
2R	15525812	2R_15525812_SNP [dm3] 2R_19638307_SNP [dm6]	G	A	3.895e^-5	0.863	DOWNSTREAM CG18367 & 2 others INTERGENIC
X	17940298	X_17940298_DEL [dm3] X_18046265_DEL [dm6]	AT	A	3.977e^-5	0.863	INTRON Sh & 1 other	TF binding site mE1_TFBS_chinmo
2L	6187849	2L_6187849_SNP [dm3] 2L_6187849_SNP [dm6]	C	A	4.037e^-5	0.863	INTRON CG34380	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	19098023	2L_19098023_SNP [dm3] 2L_19098023_SNP [dm6]	A	T	4.042e^-5	0.863	INTRON Lim3	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	19099542	2L_19099542_SNP [dm3] 2L_19099542_SNP [dm6]	C	T	4.088e^-5	0.863	INTRON Lim3
3R	12260571	3R_12260571_SNP [dm3] 3R_16434849_SNP [dm6]	T	C	4.174e^-5	0.863	UPSTREAM CG14881 DOWNSTREAM CG17565 INTERGENIC
3R	18824405	3R_18824405_SNP [dm3] 3R_22998683_SNP [dm6]	T	A	4.221e^-5	0.863	UPSTREAM Nha2 DOWNSTREAM CR43454 INTERGENIC
3L	7905741	3L_7905741_SNP [dm3] 3L_7912641_SNP [dm6]	T	C	4.227e^-5	0.863	NON_SYNONYMOUS_CODING CG8281 UPSTREAM pbl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	1843778	2L_1843778_SNP [dm3] 2L_1843778_SNP [dm6]	T	C	4.261e^-5	0.863	SYNONYMOUS_CODING wry	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	2493902	X_2493902_SNP [dm3] X_2599869_SNP [dm6]	G	T	4.289e^-5	0.863	NON_SYNONYMOUS_CODING Klp3A DOWNSTREAM egh	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	19835961	3R_19835961_SNP [dm3] 3R_24010239_SNP [dm6]	G	A	4.337e^-5	0.863	INTRON KrT95D
3R	19836085	3R_19836085_DEL [dm3] 3R_24010363_DEL [dm6]	TTGTTAAACAAT...	T	4.337e^-5	0.863	INTRON KrT95D
3R	22882264	3R_22882264_SNP [dm3] 3R_27056542_SNP [dm6]	T	C	4.340e^-5	0.863	INTRON RYa-R	TF binding site mE1_TFBS_inv
2L	6762979	2L_6762979_DEL [dm3] 2L_6762979_DEL [dm6]	TTGCAGGGTTCGGCAA...	T	4.380e^-5	0.863	CODON_DELETION CG11321	TF binding site mE1_TFBS_sens
3R	19835957	3R_19835957_SNP [dm3] 3R_24010235_SNP [dm6]	G	C	4.463e^-5	0.863	INTRON KrT95D
3R	26611380	3R_26611380_SNP [dm3] 3R_30785658_SNP [dm6]	C	T	4.563e^-5	0.863	SYNONYMOUS_CODING zfh1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	18722792	2L_18722792_INS [dm3] 2L_18722792_INS [dm6]	T	TGT	4.716e^-5	0.863	INTRON CG10348
3L	4509894	3L_4509894_SNP [dm3] 3L_4509894_SNP [dm6]	T	G	4.845e^-5	0.863	DOWNSTREAM Tie INTERGENIC
2L	19138987	2L_19138987_SNP [dm3] 2L_19138987_SNP [dm6]	G	A	4.878e^-5	0.863	INTRON brat	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_inv
3R	22814903	3R_22814903_SNP [dm3] 3R_26989181_SNP [dm6]	G	A	4.930e^-5	0.863	UPSTREAM CG31075 INTRON CG31076

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By genomic position
Variant impact
Gene name

Week 6 mean ascension (cm) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results