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=3.844e^-8)
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

2807 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
2L	16995380	2L_16995380_SNP [dm3] 2L_16995380_SNP [dm6]	G	C	5.991e^-7	0.35	INTERGENIC
2L	9126793	2L_9126793_SNP [dm3] 2L_9126793_SNP [dm6]	C	T	1.082e^-6	0.35	UTR_5_PRIME CG32982 INTRON CG32982	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA
3R	4924608	3R_4924608_SNP [dm3] 3R_9098886_SNP [dm6]	T	C	1.148e^-6	0.35	INTRON pum
3L	6967601	3L_6967601_SNP [dm3] 3L_6974501_SNP [dm6]	T	A	1.260e^-6	0.35	INTRON Galphai
2L	14010458	2L_14010458_DEL [dm3] 2L_14010458_DEL [dm6]	AGCCGTTGCGGATTTGGTCG...	A	1.457e^-6	0.35	DOWNSTREAM tRNA:Q:34E INTERGENIC
3R	27465270	3R_27465270_SNP [dm3] 3R_31639548_SNP [dm6]	C	T	1.489e^-6	0.35	INTRON kek6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	12076080	2R_12076080_SNP [dm3] 2R_16188575_SNP [dm6]	T	C	1.889e^-6	0.35	SPLICE_SITE_REGION clu INTRON clu	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	10884870	3R_10884870_SNP [dm3] 3R_15059148_SNP [dm6]	A	G	2.128e^-6	0.35	INTRON dpr9
X	10864333	X_10864333_DEL [dm3] X_10970300_DEL [dm6]	TGCTGCT	T	2.772e^-6	0.35	INTRON CG42339
3R	23071265	3R_23071265_SNP [dm3] 3R_27245543_SNP [dm6]	C	G	2.806e^-6	0.35	UPSTREAM CG18766 DOWNSTREAM CG5984 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	14760371	2R_14760371_SNP [dm3] 2R_18872866_SNP [dm6]	G	A	2.911e^-6	0.35	INTERGENIC
3R	23071399	3R_23071399_SNP [dm3] 3R_27245677_SNP [dm6]	A	G	3.307e^-6	0.35	UPSTREAM CG18766 DOWNSTREAM CG5984 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3L	6967608	3L_6967608_SNP [dm3] 3L_6974508_SNP [dm6]	G	T	4.698e^-6	0.35	INTRON Galphai
3R	17952777	3R_17952777_SNP [dm3] 3R_22127055_SNP [dm6]	A	T	4.700e^-6	0.35	INTRON CG42390
3L	2997856	3L_2997856_SNP [dm3] 3L_2997856_SNP [dm6]	G	T	5.190e^-6	0.35	INTERGENIC
2L	7040005	2L_7040005_SNP [dm3] 2L_7040005_SNP [dm6]	A	T	5.271e^-6	0.35	INTRON milt	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23070775	3R_23070775_SNP [dm3] 3R_27245053_SNP [dm6]	T	C	5.693e^-6	0.35	UTR_5_PRIME CG18766 UPSTREAM CG18766 INTRON CG18766	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	23070937	3R_23070937_SNP [dm3] 3R_27245215_SNP [dm6]	G	A	5.693e^-6	0.35	UTR_5_PRIME CG18766 UPSTREAM CG18766	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	12076074	2R_12076074_SNP [dm3] 2R_16188569_SNP [dm6]	C	A	5.804e^-6	0.35	INTRON clu	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	17373688	2R_17373688_SNP [dm3] 2R_21486183_SNP [dm6]	T	C	6.040e^-6	0.35	SYNONYMOUS_CODING Sara DOWNSTREAM Fkbp14	TF binding site mE1_TFBS_HSA
X	7743135	X_7743135_SNP [dm3] X_7849102_SNP [dm6]	C	G	6.080e^-6	0.35	INTERGENIC
3L	15685324	3L_15685324_SNP [dm3] 3L_15692224_SNP [dm6]	G	C	6.397e^-6	0.35	UPSTREAM CG34451 INTERGENIC	TF binding site mE1_TFBS_sbb
3L	9358401	3L_9358401_SNP [dm3] 3L_9365301_SNP [dm6]	T	A	6.464e^-6	0.35	DOWNSTREAM CG4447 INTRON Klp67A	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	4954723	3R_4954723_SNP [dm3] 3R_9129001_SNP [dm6]	A	C	6.584e^-6	0.35	INTRON pum	TF binding site mE1_TFBS_Trl
2L	7824249	2L_7824249_SNP [dm3] 2L_7824249_SNP [dm6]	A	G	6.606e^-6	0.35	SYNONYMOUS_CODING CG7115	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	7824318	2L_7824318_SNP [dm3] 2L_7824318_SNP [dm6]	A	G	6.606e^-6	0.35	SYNONYMOUS_CODING CG7115	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	8128600	3R_8128600_SNP [dm3] 3R_12302878_SNP [dm6]	A	T	6.741e^-6	0.35	DOWNSTREAM svp INTERGENIC	TF binding site mE1_TFBS_inv
3R	10884948	3R_10884948_SNP [dm3] 3R_15059226_SNP [dm6]	T	G	6.767e^-6	0.35	INTRON dpr9
2L	7824403	2L_7824403_SNP [dm3] 2L_7824403_SNP [dm6]	A	T	6.770e^-6	0.35	DOWNSTREAM Rack1 INTRON CG7115	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	11176165	X_11176165_SNP [dm3] X_11282132_SNP [dm6]	C	A	6.931e^-6	0.35	INTRON CG44422
3R	23070485	3R_23070485_SNP [dm3] 3R_27244763_SNP [dm6]	T	A	6.940e^-6	0.35	START_GAINED CG18766 UTR_5_PRIME CG18766 INTRON CG18766	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	8887137	2R_8887137_SNP [dm3] 2R_12999632_SNP [dm6]	T	A	7.019e^-6	0.35	INTRON Su_z_2	TF binding site mE1_TFBS_HSA
3L	8873948	3L_8873948_DEL [dm3] 3L_8880848_DEL [dm6]	CTCTTGTTGATGTATC...	C	7.019e^-6	0.35	INTRON dally
3L	8873997	3L_8873997_SNP [dm3] 3L_8880897_SNP [dm6]	G	T	7.019e^-6	0.35	INTRON dally
3R	10885047	3R_10885047_SNP [dm3] 3R_15059325_SNP [dm6]	T	A	7.019e^-6	0.35	INTRON dpr9
3R	10885214	3R_10885214_SNP [dm3] 3R_15059492_SNP [dm6]	T	C	7.019e^-6	0.35	INTRON dpr9
3R	10885215	3R_10885215_SNP [dm3] 3R_15059493_SNP [dm6]	A	C	7.019e^-6	0.35	INTRON dpr9
3R	17952796	3R_17952796_SNP [dm3] 3R_22127074_SNP [dm6]	T	A	7.589e^-6	0.353	INTRON CG42390
2L	6789406	2L_6789406_SNP [dm3] 2L_6789406_SNP [dm6]	A	G	7.592e^-6	0.353	DOWNSTREAM nrv2 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
3R	10889899	3R_10889899_SNP [dm3] 3R_15064177_SNP [dm6]	G	C	7.681e^-6	0.353	INTRON dpr9
3L	3706189	3L_3706189_SNP [dm3] 3L_3706189_SNP [dm6]	T	C	7.844e^-6	0.353	INTERGENIC
3R	10884920	3R_10884920_SNP [dm3] 3R_15059198_SNP [dm6]	T	A	8.297e^-6	0.364	INTRON dpr9
3L	12680458	3L_12680458_SNP [dm3] 3L_12687358_SNP [dm6]	T	A	9.654e^-6	0.398	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3013935	3L_3013935_SNP [dm3] 3L_3013935_SNP [dm6]	A	G	1.030e^-5	0.398	DOWNSTREAM CG32488 INTERGENIC
3R	15314846	3R_15314846_SNP [dm3] 3R_19489124_SNP [dm6]	A	G	1.060e^-5	0.398	DOWNSTREAM CG15025 INTRON Dys
3R	15314912	3R_15314912_SNP [dm3] 3R_19489190_SNP [dm6]	T	G	1.060e^-5	0.398	DOWNSTREAM CG15025 INTRON Dys
2R	16529181	2R_16529181_DEL [dm3] 2R_20641676_DEL [dm6]	TCTGCATCGCCT...	T	1.086e^-5	0.398	UPSTREAM rig & 1 other DOWNSTREAM CG33785 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	4924610	3R_4924610_SNP [dm3] 3R_9098888_SNP [dm6]	T	A	1.133e^-5	0.398	INTRON pum
2R	19390961	2R_19390961_SNP [dm3] 2R_23503438_SNP [dm6]	A	G	1.147e^-5	0.398	NON_SYNONYMOUS_CODING CG13559
3R	10884539	3R_10884539_SNP [dm3] 3R_15058817_SNP [dm6]	T	C	1.169e^-5	0.398	INTRON dpr9
3R	4862576	3R_4862576_SNP [dm3] 3R_9036854_SNP [dm6]	A	C	1.184e^-5	0.398	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	4865238	3R_4865238_SNP [dm3] 3R_9039516_SNP [dm6]	C	T	1.184e^-5	0.398	UPSTREAM hyx & 1 other INTRON hyx	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Ubx
2L	15255073	2L_15255073_SNP [dm3] 2L_15255073_SNP [dm6]	A	T	1.275e^-5	0.398	SYNONYMOUS_CODING Pol32 DOWNSTREAM dao	TF binding site mE1_TFBS_HSA
3R	27465163	3R_27465163_SNP [dm3] 3R_31639441_SNP [dm6]	T	C	1.333e^-5	0.398	INTRON kek6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	10608411	2R_10608411_SNP [dm3] 2R_14720906_SNP [dm6]	A	G	1.336e^-5	0.398	INTERGENIC
3L	1414838	3L_1414838_SNP [dm3] 3L_1414838_SNP [dm6]	C	A	1.438e^-5	0.398	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da
2R	10941832	2R_10941832_SNP [dm3] 2R_15054327_SNP [dm6]	C	T	1.453e^-5	0.398	INTERGENIC
3R	24202072	3R_24202072_SNP [dm3] 3R_28376350_SNP [dm6]	C	A	1.458e^-5	0.398	INTERGENIC	TF binding site mE1_TFBS_sbb
3L	12194215	3L_12194215_SNP [dm3] 3L_12201115_SNP [dm6]	C	T	1.489e^-5	0.398	INTRON Adk1
3L	3706179	3L_3706179_SNP [dm3] 3L_3706179_SNP [dm6]	A	C	1.499e^-5	0.398	INTERGENIC
3L	3706229	3L_3706229_MNP [dm3] 3L_3706229_MNP [dm6]	AAA	GCC	1.499e^-5	0.398	INTERGENIC
3R	17952791	3R_17952791_SNP [dm3] 3R_22127069_SNP [dm6]	C	T	1.508e^-5	0.398	INTRON CG42390
3R	17952801	3R_17952801_SNP [dm3] 3R_22127079_SNP [dm6]	T	A	1.508e^-5	0.398	INTRON CG42390
3R	16553115	3R_16553115_DEL [dm3] 3R_20727393_DEL [dm6]	AATTAA	A	1.531e^-5	0.398	INTERGENIC
2R	17762037	2R_17762037_SNP [dm3] 2R_21874532_SNP [dm6]	A	C	1.566e^-5	0.398	INTRON Fili	TF binding site BDTNP1_TFBS_da
2R	17762038	2R_17762038_SNP [dm3] 2R_21874533_SNP [dm6]	T	A	1.566e^-5	0.398	INTRON Fili	TF binding site BDTNP1_TFBS_da
3R	4864146	3R_4864146_SNP [dm3] 3R_9038424_SNP [dm6]	G	T	1.644e^-5	0.398	UPSTREAM hyx INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	13822283	3L_13822283_SNP [dm3] 3L_13829183_SNP [dm6]	C	T	1.649e^-5	0.398	INTERGENIC
3L	13822291	3L_13822291_SNP [dm3] 3L_13829191_SNP [dm6]	G	A	1.649e^-5	0.398	INTERGENIC
3L	1557737	3L_1557737_SNP [dm3] 3L_1557737_SNP [dm6]	A	T	1.703e^-5	0.398	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
2R	8440230	2R_8440230_SNP [dm3] 2R_12552725_SNP [dm6]	C	T	1.712e^-5	0.398	INTRON fra
X	13822247	X_13822247_SNP [dm3] X_13928214_SNP [dm6]	C	T	1.740e^-5	0.398	INTRON mamo
3L	15681209	3L_15681209_DEL [dm3] 3L_15688109_DEL [dm6]	AAAATAACACCGCACGGTCA...	A	1.746e^-5	0.398	UPSTREAM CG34452 DOWNSTREAM CG34451 INTERGENIC	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3706223	3L_3706223_SNP [dm3] 3L_3706223_SNP [dm6]	T	C	1.805e^-5	0.398	INTERGENIC
3R	2801803	3R_2801803_SNP [dm3] 3R_6976081_SNP [dm6]	C	T	1.820e^-5	0.398	INTRON Antp	TF binding site BDTNP1_TFBS_dl
3L	11635359	3L_11635359_SNP [dm3] 3L_11642259_SNP [dm6]	A	G	1.875e^-5	0.398	SYNONYMOUS_CODING CG32091 DOWNSTREAM CG6071	TF binding site mE1_TFBS_HSA
3L	11638515	3L_11638515_SNP [dm3] 3L_11645415_SNP [dm6]	A	C	1.875e^-5	0.398	DOWNSTREAM RIOK1 INTRON CG6071
3L	11638533	3L_11638533_SNP [dm3] 3L_11645433_SNP [dm6]	A	G	1.875e^-5	0.398	DOWNSTREAM RIOK1 INTRON CG6071
3L	11638553	3L_11638553_SNP [dm3] 3L_11645453_SNP [dm6]	T	G	1.875e^-5	0.398	NON_SYNONYMOUS_CODING CG6071 DOWNSTREAM RIOK1
3L	11642854	3L_11642854_SNP [dm3] 3L_11649754_SNP [dm6]	C	T	1.875e^-5	0.398	UTR_3_PRIME CG7339 DOWNSTREAM CG32085
3L	911148	3L_911148_SNP [dm3] 3L_911148_SNP [dm6]	A	G	1.875e^-5	0.398	UTR_3_PRIME nerfin-1	regulatory region REDfly_CRMs
3R	17952751	3R_17952751_SNP [dm3] 3R_22127029_SNP [dm6]	T	A	1.875e^-5	0.398	INTRON CG42390
3L	7162672	3L_7162672_SNP [dm3] 3L_7169572_SNP [dm6]	T	C	1.916e^-5	0.398	INTRON Dscam2	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	12937534	X_12937534_SNP [dm3] X_13043501_SNP [dm6]	A	C	1.932e^-5	0.398	INTRON rad
3L	3706061	3L_3706061_SNP [dm3] 3L_3706061_SNP [dm6]	G	T	1.934e^-5	0.398	INTERGENIC
3L	3706185	3L_3706185_SNP [dm3] 3L_3706185_SNP [dm6]	T	A	1.934e^-5	0.398	INTERGENIC
3R	16223570	3R_16223570_SNP [dm3] 3R_20397848_SNP [dm6]	T	G	1.945e^-5	0.398	INTRON Gfrl
3R	17878847	3R_17878847_SNP [dm3] 3R_22053125_SNP [dm6]	A	G	1.996e^-5	0.398	INTRON how	TF binding site BDTNP1_TFBS_dl
3R	17879003	3R_17879003_SNP [dm3] 3R_22053281_SNP [dm6]	G	A	1.996e^-5	0.398	INTRON how	regulatory region REDfly_CRMs
3L	2997925	3L_2997925_SNP [dm3] 3L_2997925_SNP [dm6]	C	T	2.043e^-5	0.398	INTERGENIC
3L	13868345	3L_13868345_SNP [dm3] 3L_13875245_SNP [dm6]	C	T	2.046e^-5	0.398	INTRON dysc
2R	13690387	2R_13690387_SNP [dm3] 2R_17802882_SNP [dm6]	C	T	2.066e^-5	0.398	UTR_5_PRIME grh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	18428495	2R_18428495_SNP [dm3] 2R_22540990_SNP [dm6]	A	C	2.116e^-5	0.398	INTRON px
2L	9061993	2L_9061993_SNP [dm3] 2L_9061993_SNP [dm6]	T	C	2.192e^-5	0.398	INTRON CG31708	TF binding site BDTNP1_TFBS_twi
3R	4924604	3R_4924604_SNP [dm3] 3R_9098882_SNP [dm6]	T	G	2.192e^-5	0.398	INTRON pum
3R	4924611	3R_4924611_DEL [dm3] 3R_9098889_DEL [dm6]	TC	T	2.192e^-5	0.398	INTRON pum
X	17454352	X_17454352_SNP [dm3] X_17560319_SNP [dm6]	G	A	2.208e^-5	0.398	INTRON CG43658
X	17454561	X_17454561_INS [dm3] X_17560528_INS [dm6]	T	TA	2.208e^-5	0.398	INTRON CG43658
3R	7876536	3R_7876536_SNP [dm3] 3R_12050814_SNP [dm6]	A	G	2.222e^-5	0.398	INTERGENIC
3R	4341466	3R_4341466_INS [dm3] 3R_8515744_INS [dm6]	T	TT	2.267e^-5	0.398	INTERGENIC	TF binding site BDTNP1_TFBS_twi

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By genomic position
Variant impact
Gene name

pc_MB_Alpha_Normal phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results