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=1.042e^-19)
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

Covariate	p-value	Significance
In_2R_NS	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	28.1445	7.7357e-07

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4193 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	21747097	2L_21747097_SNP [dm3] 2L_21747097_SNP [dm6]	C	A	3.502e^-8	0.045	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	9396551	2L_9396551_SNP [dm3] 2L_9396551_SNP [dm6]	G	A	5.072e^-8	0.045	DOWNSTREAM CG4438 INTRON Shawl
2L	9396702	2L_9396702_SNP [dm3] 2L_9396702_SNP [dm6]	C	T	7.217e^-8	0.045	DOWNSTREAM CG4438 INTRON Shawl
2L	21746983	2L_21746983_SNP [dm3] 2L_21746983_SNP [dm6]	A	T	1.042e^-7	0.049	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	5505861	2R_5505861_SNP [dm3] 2R_9618356_SNP [dm6]	A	G	2.358e^-7	0.088	INTRON Mmp2
2L	21748252	2L_21748252_SNP [dm3] 2L_21748252_SNP [dm6]	C	T	3.770e^-7	0.113	INTRON step	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12324182	2R_12324182_SNP [dm3] 2R_16436677_SNP [dm6]	G	A	4.213e^-7	0.113	UPSTREAM CG7848 INTERGENIC
2R	5505915	2R_5505915_SNP [dm3] 2R_9618410_SNP [dm6]	T	A	5.009e^-7	0.117	INTRON Mmp2
3L	12638578	3L_12638578_SNP [dm3] 3L_12645478_SNP [dm6]	A	T	8.281e^-7	0.128	EXON CR32111
2L	21747859	2L_21747859_SNP [dm3] 2L_21747859_SNP [dm6]	C	G	8.510e^-7	0.128	INTRON step	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	12315728	2R_12315728_SNP [dm3] 2R_16428223_SNP [dm6]	T	C	9.567e^-7	0.128	INTRON Sema-2b
3L	8033392	3L_8033392_SNP [dm3] 3L_8040292_SNP [dm6]	T	C	9.922e^-7	0.128	INTRON nmo
2L	22339456	2L_22339456_SNP [dm3] 2L_22339456_SNP [dm6]	G	C	1.040e^-6	0.128	INTRON CG17018	transposable element FlyBase
2L	9839544	2L_9839544_SNP [dm3] 2L_9839544_SNP [dm6]	T	G	1.247e^-6	0.128	INTRON nAChRalpha6	TF binding site mE1_TFBS_chinmo
X	8622823	X_8622823_SNP [dm3] X_8728790_SNP [dm6]	T	C	1.287e^-6	0.128	INTERGENIC
2L	21854007	2L_21854007_SNP [dm3] 2L_21854007_SNP [dm6]	G	T	1.371e^-6	0.128	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12638199	3L_12638199_SNP [dm3] 3L_12645099_SNP [dm6]	C	A	1.372e^-6	0.128	INTRON CR32111	regulatory region REDfly_CRMs
2L	21855509	2L_21855509_SNP [dm3] 2L_21855509_SNP [dm6]	T	C	1.449e^-6	0.128	INTRON CR44917	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	22233658	3R_22233658_SNP [dm3] 3R_26407936_SNP [dm6]	C	T	1.503e^-6	0.128	INTERGENIC
2L	21746958	2L_21746958_SNP [dm3] 2L_21746958_SNP [dm6]	A	G	1.506e^-6	0.128	SYNONYMOUS_CODING step INTRON step	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	21747825	2L_21747825_SNP [dm3] 2L_21747825_SNP [dm6]	C	A	1.544e^-6	0.128	INTRON step	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	13653464	3R_13653464_DEL [dm3] 3R_17827742_DEL [dm6]	TT	T	1.584e^-6	0.128	INTRON tinc	TF binding site mE1_TFBS_cad
2L	21858780	2L_21858780_SNP [dm3] 2L_21858780_SNP [dm6]	C	T	1.785e^-6	0.128	INTRON CR44917	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3L	12638597	3L_12638597_SNP [dm3] 3L_12645497_SNP [dm6]	C	A	1.785e^-6	0.128	EXON CR32111
2R	18603310	2R_18603310_SNP [dm3] 2R_22715805_SNP [dm6]	T	C	1.829e^-6	0.128	SYNONYMOUS_CODING CG30268	TF binding site BDTNP1_TFBS_twi
3R	9226941	3R_9226941_SNP [dm3] 3R_13401219_SNP [dm6]	G	T	1.911e^-6	0.128	INTRON CG9796	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	14059489	2L_14059489_SNP [dm3] 2L_14059489_SNP [dm6]	C	A	1.947e^-6	0.128	INTRON nAChRalpha5
2L	21759091	2L_21759091_SNP [dm3] 2L_21759091_SNP [dm6]	C	A	1.978e^-6	0.128	INTRON CG1416
3L	10503033	3L_10503033_SNP [dm3] 3L_10509933_SNP [dm6]	G	A	2.039e^-6	0.128	INTRON A2bp1
3L	12638161	3L_12638161_SNP [dm3] 3L_12645061_SNP [dm6]	G	T	2.044e^-6	0.128	INTRON CR32111	regulatory region REDfly_CRMs
3L	12638598	3L_12638598_SNP [dm3] 3L_12645498_SNP [dm6]	T	G	2.333e^-6	0.137	EXON CR32111
2R	3141826	2R_3141826_DEL [dm3] 2R_7254321_DEL [dm6]	AA	A	2.438e^-6	0.137	UPSTREAM CR45280 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	18746859	2L_18746859_SNP [dm3] 2L_18746859_SNP [dm6]	G	T	2.486e^-6	0.137	INTERGENIC
2L	9047596	2L_9047596_SNP [dm3] 2L_9047596_SNP [dm6]	C	G	2.490e^-6	0.137	INTERGENIC
2R	4101991	2R_4101991_SNP [dm3] 2R_8214486_SNP [dm6]	C	A	2.625e^-6	0.141	SYNONYMOUS_CODING LRP1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	5505862	2R_5505862_SNP [dm3] 2R_9618357_SNP [dm6]	A	G	2.713e^-6	0.141	INTRON Mmp2
3R	18581582	3R_18581582_SNP [dm3] 3R_22755860_SNP [dm6]	C	T	3.019e^-6	0.148	INTRON Usp12-46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	11391599	2L_11391599_SNP [dm3] 2L_11391599_SNP [dm6]	C	T	3.023e^-6	0.148	INTRON CR43681	regulatory region REDfly_CRMs
3L	1300670	3L_1300670_DEL [dm3] 3L_1300670_DEL [dm6]	GTAAG	G	3.084e^-6	0.148	DOWNSTREAM Rac1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	13652649	3R_13652649_SNP [dm3] 3R_17826927_SNP [dm6]	G	C	3.165e^-6	0.148	INTRON tinc	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_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	5505869	2R_5505869_SNP [dm3] 2R_9618364_SNP [dm6]	C	T	3.255e^-6	0.148	INTRON Mmp2
3R	9226136	3R_9226136_DEL [dm3] 3R_13400414_DEL [dm6]	TTAGTTAT	T	3.325e^-6	0.148	INTRON CG9796
X	12184484	X_12184484_SNP [dm3] X_12290451_SNP [dm6]	C	T	3.401e^-6	0.148	INTRON Ten-a
3R	18581576	3R_18581576_SNP [dm3] 3R_22755854_SNP [dm6]	T	C	3.511e^-6	0.15	INTRON Usp12-46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	7457994	2R_7457994_SNP [dm3] 2R_11570489_SNP [dm6]	C	T	3.721e^-6	0.151	INTERGENIC
2L	3605858	2L_3605858_SNP [dm3] 2L_3605858_SNP [dm6]	T	C	3.754e^-6	0.151	SYNONYMOUS_CODING odd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12638615	3L_12638615_SNP [dm3] 3L_12645515_SNP [dm6]	T	G	3.784e^-6	0.151	EXON CR32111
2L	21793557	2L_21793557_SNP [dm3] 2L_21793557_SNP [dm6]	G	T	4.028e^-6	0.156	INTRON CG31612	TF binding site BDTNP1_TFBS_z
X	12111468	X_12111468_SNP [dm3] X_12217435_SNP [dm6]	C	G	4.284e^-6	0.156	INTRON Ten-a	TF binding site mE1_TFBS_cad
2L	21747861	2L_21747861_SNP [dm3] 2L_21747861_SNP [dm6]	C	T	4.355e^-6	0.156	INTRON step	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	9396708	2L_9396708_SNP [dm3] 2L_9396708_SNP [dm6]	C	T	4.378e^-6	0.156	DOWNSTREAM CG4438 INTRON Shawl
3L	17579947	3L_17579947_SNP [dm3] 3L_17586847_SNP [dm6]	T	G	4.572e^-6	0.156	INTRON Eip74EF
3L	12638570	3L_12638570_SNP [dm3] 3L_12645470_SNP [dm6]	G	A	4.689e^-6	0.156	EXON CR32111
3L	12638612	3L_12638612_SNP [dm3] 3L_12645512_SNP [dm6]	G	A	4.707e^-6	0.156	EXON CR32111
2R	16332555	2R_16332555_SNP [dm3] 2R_20445050_SNP [dm6]	G	A	4.771e^-6	0.156	INTRON CG12484
3L	12638608	3L_12638608_SNP [dm3] 3L_12645508_SNP [dm6]	A	T	4.875e^-6	0.156	EXON CR32111
2R	2877700	2R_2877700_SNP [dm3] 2R_6990195_SNP [dm6]	T	A	5.087e^-6	0.156	INTERGENIC	transposable element FlyBase
2L	20097173	2L_20097173_SNP [dm3] 2L_20097173_SNP [dm6]	T	A	5.128e^-6	0.156	UTR_5_PRIME mRpS18B UPSTREAM Kua DOWNSTREAM nesd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
X	16613414	X_16613414_SNP [dm3] X_16719381_SNP [dm6]	T	G	5.195e^-6	0.156	INTRON CG34325	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
3R	23563740	3R_23563740_SNP [dm3] 3R_27738018_SNP [dm6]	G	A	5.219e^-6	0.156	INTRON Ets98B	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	20233640	2L_20233640_SNP [dm3] 2L_20233640_SNP [dm6]	A	G	5.264e^-6	0.156	INTERGENIC
3L	12638607	3L_12638607_SNP [dm3] 3L_12645507_SNP [dm6]	G	T	5.290e^-6	0.156	EXON CR32111
3L	12638617	3L_12638617_SNP [dm3] 3L_12645517_SNP [dm6]	T	G	5.350e^-6	0.156	EXON CR32111
3L	2401408	3L_2401408_SNP [dm3] 3L_2401408_SNP [dm6]	C	G	5.451e^-6	0.156	INTRON CG45186
2L	20097653	2L_20097653_SNP [dm3] 2L_20097653_SNP [dm6]	C	T	5.501e^-6	0.156	START_GAINED Kua UTR_5_PRIME Kua UPSTREAM Kua & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_Ubx
3R	25404976	3R_25404976_SNP [dm3] 3R_29579254_SNP [dm6]	C	T	5.583e^-6	0.156	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	5505897	2R_5505897_SNP [dm3] 2R_9618392_SNP [dm6]	A	T	5.660e^-6	0.156	INTRON Mmp2
3L	12638611	3L_12638611_SNP [dm3] 3L_12645511_SNP [dm6]	C	G	5.708e^-6	0.156	EXON CR32111
2L	20086170	2L_20086170_SNP [dm3] 2L_20086170_SNP [dm6]	G	A	5.754e^-6	0.156	INTRON neb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_GATAe mE1_TFBS_HSA
3L	10503050	3L_10503050_SNP [dm3] 3L_10509950_SNP [dm6]	T	C	6.168e^-6	0.165	INTRON A2bp1
2L	15473588	2L_15473588_SNP [dm3] 2L_15473588_SNP [dm6]	T	A	6.245e^-6	0.165	INTERGENIC
X	11274048	X_11274048_SNP [dm3] X_11380015_SNP [dm6]	T	C	6.401e^-6	0.166	INTRON dlg1
2L	11624083	2L_11624083_SNP [dm3] 2L_11624083_SNP [dm6]	A	G	6.469e^-6	0.166	SYNONYMOUS_CODING kek2	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2R	15873349	2R_15873349_SNP [dm3] 2R_19985844_SNP [dm6]	T	G	6.550e^-6	0.166	DOWNSTREAM CG8654 INTERGENIC
2R	1305234	2R_1305234_SNP [dm3] 2R_5417729_SNP [dm6]	G	A	6.649e^-6	0.166	INTRON laccase2	TF binding site BDTNP1_TFBS_dl
3L	12638413	3L_12638413_SNP [dm3] 3L_12645313_SNP [dm6]	G	A	6.896e^-6	0.17	SPLICE_SITE_REGION CR32111 INTRON CR32111
2L	20086068	2L_20086068_SNP [dm3] 2L_20086068_SNP [dm6]	T	C	7.248e^-6	0.177	UPSTREAM fok INTRON neb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_GATAe mE1_TFBS_HSA
2L	4341047	2L_4341047_SNP [dm3] 2L_4341047_SNP [dm6]	G	A	8.142e^-6	0.19	INTRON Atet
2L	1669689	2L_1669689_SNP [dm3] 2L_1669689_SNP [dm6]	A	T	8.145e^-6	0.19	INTRON chinmo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2R	18267494	2R_18267494_SNP [dm3] 2R_22379989_SNP [dm6]	T	A	8.269e^-6	0.19	UPSTREAM CR45327 INTRON wrapper
2L	20095550	2L_20095550_SNP [dm3] 2L_20095550_SNP [dm6]	G	C	8.336e^-6	0.19	NON_SYNONYMOUS_CODING nesd DOWNSTREAM mRpS18B	TF binding site mE1_TFBS_sens
2L	9588278	2L_9588278_SNP [dm3] 2L_9588278_SNP [dm6]	C	A	8.383e^-6	0.19	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9838804	2L_9838804_SNP [dm3] 2L_9838804_SNP [dm6]	A	C	8.503e^-6	0.19	INTRON nAChRalpha6
2L	21840208	2L_21840208_SNP [dm3] 2L_21840208_SNP [dm6]	T	C	8.558e^-6	0.19	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	2936925	X_2936925_SNP [dm3] X_3042892_SNP [dm6]	T	G	8.829e^-6	0.19	INTRON kirre
2L	20097573	2L_20097573_SNP [dm3] 2L_20097573_SNP [dm6]	T	A	8.945e^-6	0.19	UPSTREAM Kua & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_Ubx
2R	19180344	2R_19180344_SNP [dm3] 2R_23292821_SNP [dm6]	C	T	9.048e^-6	0.19	INTERGENIC
2L	14336797	2L_14336797_SNP [dm3] 2L_14336797_SNP [dm6]	T	A	9.061e^-6	0.19	INTRON CG33090	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	5540895	2R_5540895_INS [dm3] 2R_9653390_INS [dm6]	T	TT	9.062e^-6	0.19	INTRON Mmp2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12637790	3L_12637790_SNP [dm3] 3L_12644690_SNP [dm6]	T	A	9.096e^-6	0.19	INTRON CR32111	regulatory region REDfly_CRMs
3L	17610836	3L_17610836_SNP [dm3] 3L_17617736_SNP [dm6]	A	T	9.511e^-6	0.192	INTRON Eip74EF
3R	18839102	3R_18839102_SNP [dm3] 3R_23013380_SNP [dm6]	A	T	9.529e^-6	0.192	INTRON CG6688	TF binding site mE1_TFBS_zfh1
2L	21941505	2L_21941505_SNP [dm3] 2L_21941505_SNP [dm6]	T	G	9.626e^-6	0.192	INTERGENIC
2R	13185394	2R_13185394_SNP [dm3] 2R_17297889_SNP [dm6]	A	T	9.740e^-6	0.192	INTRON mbl
3R	25614470	3R_25614470_SNP [dm3] 3R_29788748_SNP [dm6]	C	A	1.003e^-5	0.192	UPSTREAM kay INTRON kay
3L	11657996	3L_11657996_SNP [dm3] 3L_11664896_SNP [dm6]	C	T	1.008e^-5	0.192	INTRON CG32085
2R	12874793	2R_12874793_SNP [dm3] 2R_16987288_SNP [dm6]	G	A	1.021e^-5	0.192	INTRON Cbp53E
2L	21852049	2L_21852049_SNP [dm3] 2L_21852049_SNP [dm6]	A	G	1.047e^-5	0.192	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17580000	3L_17580000_SNP [dm3] 3L_17586900_SNP [dm6]	T	A	1.047e^-5	0.192	INTRON Eip74EF
3R	9629972	3R_9629972_SNP [dm3] 3R_13804250_SNP [dm6]	T	C	1.056e^-5	0.192	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
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TotalVariants_2R phenotype

Phenotype distribution and association to known covariates

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GWAS results