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=7.930e^-7)
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

3093 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	25052715	3R_25052715_SNP [dm3] 3R_29226993_SNP [dm6]	C	T	4.004e^-8	0.074	DOWNSTREAM Brd8 INTRON CG14507	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10432228	2L_10432228_SNP [dm3] 2L_10432228_SNP [dm6]	A	G	2.755e^-7	0.111	DOWNSTREAM CG5337 INTRON TfIIB	TF binding site mE1_TFBS_sens
X	19001007	X_19001007_INS [dm3] X_19106974_INS [dm6]	C	CCATTTA	2.939e^-7	0.111	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	5974460	2R_5974460_SNP [dm3] 2R_10086955_SNP [dm6]	A	G	4.489e^-7	0.111	SYNONYMOUS_CODING sut4 UPSTREAM CG2269 INTRON CG2269
3R	25052675	3R_25052675_SNP [dm3] 3R_29226953_SNP [dm6]	G	A	4.489e^-7	0.111	DOWNSTREAM Brd8 INTRON CG14507	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	25052708	3R_25052708_INS [dm3] 3R_29226986_INS [dm6]	G	GTAGTTCTCGAG...	4.489e^-7	0.111	DOWNSTREAM Brd8 INTRON CG14507	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	14295019	3R_14295019_SNP [dm3] 3R_18469297_SNP [dm6]	C	G	4.596e^-7	0.111	INTRON fru
2L	10432123	2L_10432123_SNP [dm3] 2L_10432123_SNP [dm6]	A	C	5.027e^-7	0.111	SYNONYMOUS_CODING TfIIB DOWNSTREAM CG5337	TF binding site mE1_TFBS_sens
3R	14295058	3R_14295058_SNP [dm3] 3R_18469336_SNP [dm6]	G	A	5.402e^-7	0.111	INTRON fru
2L	13948339	2L_13948339_SNP [dm3] 2L_13948339_SNP [dm6]	G	C	6.143e^-7	0.111	UPSTREAM CG16884 INTRON Ance-3
2L	1243076	2L_1243076_SNP [dm3] 2L_1243076_SNP [dm6]	G	A	6.808e^-7	0.111	DOWNSTREAM CG5397 INTERGENIC
3R	22306257	3R_22306257_SNP [dm3] 3R_26480535_SNP [dm6]	T	C	7.236e^-7	0.111	INTRON plum
2R	12031180	2R_12031180_SNP [dm3] 2R_16143675_SNP [dm6]	G	A	1.282e^-6	0.182	NON_SYNONYMOUS_CODING Aats-cys DOWNSTREAM CG30094	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	24485992	3R_24485992_SNP [dm3] 3R_28660270_SNP [dm6]	G	T	1.528e^-6	0.195	INTERGENIC
3L	9337796	3L_9337796_SNP [dm3] 3L_9344696_SNP [dm6]	C	T	1.585e^-6	0.195	INTRON PGRP-LC
3R	22248763	3R_22248763_SNP [dm3] 3R_26423041_SNP [dm6]	C	T	1.696e^-6	0.196	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	11064771	2R_11064771_SNP [dm3] 2R_15177266_SNP [dm6]	T	C	1.982e^-6	0.215	INTRON igl
2R	17873569	2R_17873569_SNP [dm3] 2R_21986064_SNP [dm6]	G	A	2.826e^-6	0.285	SYNONYMOUS_CODING CG30401	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	25052694	3R_25052694_SNP [dm3] 3R_29226972_SNP [dm6]	C	T	2.932e^-6	0.285	DOWNSTREAM Brd8 INTRON CG14507	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	17120344	2R_17120344_SNP [dm3] 2R_21232839_SNP [dm6]	T	C	3.903e^-6	0.288	INTRON ASPP
3R	12114233	3R_12114233_SNP [dm3] 3R_16288511_SNP [dm6]	C	T	4.197e^-6	0.288	UPSTREAM gish INTRON gish	TF binding site mE1_TFBS_inv
3R	23449489	3R_23449489_SNP [dm3] 3R_27623767_SNP [dm6]	A	G	4.328e^-6	0.288	SYNONYMOUS_CODING CG5612 INTRON Tusp
3L	5357783	3L_5357783_SNP [dm3] 3L_5364683_SNP [dm6]	A	T	4.603e^-6	0.288	INTRON Uev1A	TF binding site mE1_TFBS_inv
X	14801187	X_14801187_SNP [dm3] X_14907154_SNP [dm6]	C	A	5.247e^-6	0.288	NON_SYNONYMOUS_CODING CG9509 INTRON Flo2
2L	9581440	2L_9581440_SNP [dm3] 2L_9581440_SNP [dm6]	A	G	5.293e^-6	0.288	SYNONYMOUS_CODING gcm	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	8784041	3R_8784041_SNP [dm3] 3R_12958319_SNP [dm6]	G	T	5.481e^-6	0.288	INTRON grsm	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	2689211	3R_2689211_SNP [dm3] 3R_6863489_SNP [dm6]	A	T	5.871e^-6	0.288	UPSTREAM ftz INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
X	10829665	X_10829665_SNP [dm3] X_10935632_SNP [dm6]	C	T	6.135e^-6	0.288	INTRON Myo10A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	8389705	2L_8389705_SNP [dm3] 2L_8389705_SNP [dm6]	A	G	6.440e^-6	0.288	UPSTREAM snRNA:U6atac:29B & 1 other DOWNSTREAM CG13384 & 1 other INTERGENIC
2L	12406591	2L_12406591_SNP [dm3] 2L_12406591_SNP [dm6]	G	A	6.450e^-6	0.288	DOWNSTREAM vir-1 INTRON vir-1
2L	12213802	2L_12213802_SNP [dm3] 2L_12213802_SNP [dm6]	T	C	6.458e^-6	0.288	INTRON aret	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	3692349	3L_3692349_SNP [dm3] 3L_3692349_SNP [dm6]	C	G	6.917e^-6	0.288	INTERGENIC
2L	13947108	2L_13947108_SNP [dm3] 2L_13947108_SNP [dm6]	T	A	7.085e^-6	0.288	UTR_5_PRIME CG16884 INTRON Ance-3
2L	13947278	2L_13947278_SNP [dm3] 2L_13947278_SNP [dm6]	G	T	7.085e^-6	0.288	INTRON Ance-3 & 1 other
2L	13947307	2L_13947307_SNP [dm3] 2L_13947307_SNP [dm6]	A	G	7.085e^-6	0.288	INTRON Ance-3 & 1 other
2L	13947316	2L_13947316_SNP [dm3] 2L_13947316_SNP [dm6]	C	T	7.085e^-6	0.288	INTRON Ance-3 & 1 other
2L	13947331	2L_13947331_SNP [dm3] 2L_13947331_SNP [dm6]	C	A	7.085e^-6	0.288	INTRON Ance-3 & 1 other
3R	19163087	3R_19163087_SNP [dm3] 3R_23337365_SNP [dm6]	T	C	7.323e^-6	0.288	INTRON pnt	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	4884999	2L_4884999_SNP [dm3] 2L_4884999_SNP [dm6]	G	A	7.916e^-6	0.288	SYNONYMOUS_CODING CG3008	TF binding site mE1_TFBS_sens
2L	14111845	2L_14111845_SNP [dm3] 2L_14111845_SNP [dm6]	T	A	8.161e^-6	0.288	INTERGENIC	TF binding site mE1_TFBS_cad
3R	19673290	3R_19673290_SNP [dm3] 3R_23847568_SNP [dm6]	C	A	8.181e^-6	0.288	INTRON CG34355	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	10894813	X_10894813_INS [dm3] X_11000780_INS [dm6]	T	TCCCTTTT	8.318e^-6	0.288	INTRON CG42339
X	9247617	X_9247617_SNP [dm3] X_9353584_SNP [dm6]	C	A	8.450e^-6	0.288	INTRON CG34449
3L	462588	3L_462588_DEL [dm3] 3L_462588_DEL [dm6]	AA	A	8.544e^-6	0.288	INTRON klar
3R	25844163	3R_25844163_SNP [dm3] 3R_30018441_SNP [dm6]	T	A	8.773e^-6	0.288	INTRON Mgat2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	3692530	3L_3692530_SNP [dm3] 3L_3692530_SNP [dm6]	A	C	9.076e^-6	0.288	INTERGENIC
3L	11120691	3L_11120691_SNP [dm3] 3L_11127591_SNP [dm6]	G	T	9.493e^-6	0.288	INTRON CG42575
3L	9339460	3L_9339460_SNP [dm3] 3L_9346360_SNP [dm6]	C	T	9.501e^-6	0.288	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2R	11067108	2R_11067108_SNP [dm3] 2R_15179603_SNP [dm6]	A	C	9.846e^-6	0.288	INTRON igl
3L	1591252	3L_1591252_SNP [dm3] 3L_1591252_SNP [dm6]	G	A	1.018e^-5	0.288	INTRON CG13917
3R	24871998	3R_24871998_SNP [dm3] 3R_29046276_SNP [dm6]	C	G	1.040e^-5	0.288	UTR_3_PRIME Pkc98E
3L	3692291	3L_3692291_SNP [dm3] 3L_3692291_SNP [dm6]	T	C	1.063e^-5	0.288	INTERGENIC
2R	1719588	2R_1719588_SNP [dm3] 2R_5832083_SNP [dm6]	G	A	1.096e^-5	0.288	INTRON dpr12
3R	6259016	3R_6259016_SNP [dm3] 3R_10433294_SNP [dm6]	G	C	1.104e^-5	0.288	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10218405	3L_10218405_SNP [dm3] 3L_10225305_SNP [dm6]	A	C	1.222e^-5	0.288	UPSTREAM scramb1 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	20436932	3R_20436932_SNP [dm3] 3R_24611210_SNP [dm6]	A	C	1.270e^-5	0.288	INTRON mld
3R	25845695	3R_25845695_SNP [dm3] 3R_30019973_SNP [dm6]	C	G	1.311e^-5	0.288	INTRON Mgat2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10418764	2L_10418764_DEL [dm3] 2L_10418764_DEL [dm6]	AAGAACAAAGTTCTTCA...	A	1.337e^-5	0.288	UTR_3_PRIME Klp31E UPSTREAM RfC3	TF binding site BDTNP1_TFBS_Med
2L	10432979	2L_10432979_SNP [dm3] 2L_10432979_SNP [dm6]	T	A	1.362e^-5	0.288	UTR_3_PRIME TfIIB & 1 other DOWNSTREAM TfIIB	TF binding site mE1_TFBS_cad
3R	23640170	3R_23640170_SNP [dm3] 3R_27814448_SNP [dm6]	C	A	1.371e^-5	0.288	INTRON CG34353
3L	13316069	3L_13316069_SNP [dm3] 3L_13322969_SNP [dm6]	C	A	1.374e^-5	0.288	INTERGENIC
3L	2852133	3L_2852133_SNP [dm3] 3L_2852133_SNP [dm6]	G	A	1.445e^-5	0.288	INTRON CG43444	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3R	24485568	3R_24485568_INS [dm3] 3R_28659846_INS [dm6]	C	CAGG	1.475e^-5	0.288	INTERGENIC
3L	8890464	3L_8890464_SNP [dm3] 3L_8897364_SNP [dm6]	A	G	1.506e^-5	0.288	SYNONYMOUS_CODING TrpA1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	12114289	3R_12114289_SNP [dm3] 3R_16288567_SNP [dm6]	C	A	1.520e^-5	0.288	UPSTREAM gish INTRON gish	TF binding site mE1_TFBS_inv
3R	12114921	3R_12114921_SNP [dm3] 3R_16289199_SNP [dm6]	C	A	1.520e^-5	0.288	UPSTREAM gish INTRON gish	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	25846749	3R_25846749_DEL [dm3] 3R_30021027_DEL [dm6]	TGACCCGGTCCCTTTATTAA...	T	1.527e^-5	0.288	INTRON Mgat2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3R	25246460	3R_25246460_SNP [dm3] 3R_29420738_SNP [dm6]	C	T	1.547e^-5	0.288	INTRON Ptp99A	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
X	11033732	X_11033732_SNP [dm3] X_11139699_SNP [dm6]	A	T	1.570e^-5	0.288	DOWNSTREAM CG32667 & 2 others EXON CR44054	TF binding site BDTNP1_TFBS_sna
2L	19263670	2L_19263670_SNP [dm3] 2L_19263670_SNP [dm6]	T	C	1.648e^-5	0.288	DOWNSTREAM CR44191 INTERGENIC
3R	7743523	3R_7743523_SNP [dm3] 3R_11917801_SNP [dm6]	G	A	1.648e^-5	0.288	INTRON Cad87A
3R	16486476	3R_16486476_INS [dm3] 3R_20660754_INS [dm6]	T	TT	1.705e^-5	0.288	UPSTREAM Nep4 INTERGENIC
2L	13946966	2L_13946966_SNP [dm3] 2L_13946966_SNP [dm6]	G	A	1.709e^-5	0.288	INTRON Ance-3 & 1 other
2L	19203907	2L_19203907_SNP [dm3] 2L_19203907_SNP [dm6]	A	T	1.714e^-5	0.288	INTRON drl	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2L	4287319	2L_4287319_SNP [dm3] 2L_4287319_SNP [dm6]	A	T	1.729e^-5	0.288	INTRON tutl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	8911665	2L_8911665_SNP [dm3] 2L_8911665_SNP [dm6]	G	A	1.747e^-5	0.288	INTRON CG34398	TF binding site mE1_TFBS_HSA
3R	12113150	3R_12113150_SNP [dm3] 3R_16287428_SNP [dm6]	C	A	1.767e^-5	0.288	INTRON gish
3R	12114335	3R_12114335_SNP [dm3] 3R_16288613_SNP [dm6]	G	C	1.767e^-5	0.288	UPSTREAM gish INTRON gish	TF binding site mE1_TFBS_inv
3R	20870160	3R_20870160_SNP [dm3] 3R_25044438_SNP [dm6]	A	T	1.851e^-5	0.288	INTRON 5PtaseI	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14598608	3L_14598608_SNP [dm3] 3L_14605508_SNP [dm6]	T	G	1.922e^-5	0.288	INTERGENIC
2L	19651301	2L_19651301_SNP [dm3] 2L_19651301_SNP [dm6]	C	T	1.931e^-5	0.288	INTRON Lar	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2R	18675282	2R_18675282_SNP [dm3] 2R_22787777_SNP [dm6]	A	G	1.937e^-5	0.288	INTRON CG42260
3R	24866068	3R_24866068_DEL [dm3] 3R_29040346_DEL [dm6]	CAATTAGAAAACGCG...	T	1.961e^-5	0.288	INTRON Pkc98E	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	24866540	3R_24866540_DEL [dm3] 3R_29040818_DEL [dm6]	ATAGTTAA	A	1.961e^-5	0.288	INTRON Pkc98E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna
3R	25807382	3R_25807382_SNP [dm3] 3R_29981660_SNP [dm6]	A	C	1.961e^-5	0.288	INTERGENIC
3R	25807414	3R_25807414_SNP [dm3] 3R_29981692_SNP [dm6]	A	G	1.961e^-5	0.288	INTERGENIC
2L	7631218	2L_7631218_SNP [dm3] 2L_7631218_SNP [dm6]	A	G	1.990e^-5	0.288	INTERGENIC
3R	20792648	3R_20792648_SNP [dm3] 3R_24966926_SNP [dm6]	T	G	2.013e^-5	0.288	INTERGENIC
X	19436957	X_19436957_SNP [dm3] X_19542924_SNP [dm6]	T	C	2.021e^-5	0.288	INTRON CG32532	TF binding site BDTNP1_TFBS_da
2R	11645713	2R_11645713_SNP [dm3] 2R_15758208_SNP [dm6]	T	A	2.025e^-5	0.288	INTRON CG30089	TF binding site mE1_TFBS_cad mE1_TFBS_Kr
3L	11085334	3L_11085334_SNP [dm3] 3L_11092234_SNP [dm6]	C	A	2.060e^-5	0.288	UPSTREAM JIL-1 INTRON JIL-1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	11086016	3L_11086016_SNP [dm3] 3L_11092916_SNP [dm6]	A	G	2.060e^-5	0.288	UTR_5_PRIME JIL-1 DOWNSTREAM CG6279	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	9733839	3R_9733839_SNP [dm3] 3R_13908117_SNP [dm6]	G	A	2.060e^-5	0.288	INTERGENIC
2L	11972194	2L_11972194_SNP [dm3] 2L_11972194_SNP [dm6]	T	A	2.081e^-5	0.288	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad
3R	4893792	3R_4893792_SNP [dm3] 3R_9068070_SNP [dm6]	C	T	2.119e^-5	0.288	UTR_3_PRIME pum
2L	9581479	2L_9581479_SNP [dm3] 2L_9581479_SNP [dm6]	A	G	2.175e^-5	0.288	SYNONYMOUS_CODING gcm	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	14090881	X_14090881_SNP [dm3] X_14196848_SNP [dm6]	T	C	2.181e^-5	0.288	SYNONYMOUS_CODING yl	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1121475	3L_1121475_SNP [dm3] 3L_1121475_SNP [dm6]	A	C	2.194e^-5	0.288	INTERGENIC
2L	19265570	2L_19265570_SNP [dm3] 2L_19265570_SNP [dm6]	C	T	2.211e^-5	0.288	INTERGENIC
3L	9146426	3L_9146426_SNP [dm3] 3L_9153326_SNP [dm6]	T	C	2.236e^-5	0.288	INTRON Rdl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_MB_Alpha_Missing phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results