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=2.430e^-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

2410 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	6245013	2L_6245013_SNP [dm3] 2L_6245013_SNP [dm6]	C	A	4.491e^-7	0.312	INTERGENIC
3R	23937052	3R_23937052_SNP [dm3] 3R_28111330_SNP [dm6]	C	G	7.719e^-7	0.312	INTERGENIC
3R	23937038	3R_23937038_SNP [dm3] 3R_28111316_SNP [dm6]	T	G	7.758e^-7	0.312	INTERGENIC
3L	2835271	3L_2835271_SNP [dm3] 3L_2835271_SNP [dm6]	T	A	1.001e^-6	0.312	INTRON CG43444
3L	2424179	3L_2424179_DEL [dm3] 3L_2424179_DEL [dm6]	TT	T	1.070e^-6	0.312	INTRON CG45186
3R	4677071	3R_4677071_SNP [dm3] 3R_8851349_SNP [dm6]	G	A	1.075e^-6	0.312	INTRON pyd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	3615107	X_3615107_SNP [dm3] X_3721074_SNP [dm6]	G	A	1.736e^-6	0.312	INTRON tlk	TF binding site BDTNP1_TFBS_dl
2L	15734504	2L_15734504_SNP [dm3] 2L_15734504_SNP [dm6]	C	T	1.891e^-6	0.312	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Kr
X	3615088	X_3615088_SNP [dm3] X_3721055_SNP [dm6]	G	T	1.906e^-6	0.312	INTRON tlk	TF binding site BDTNP1_TFBS_dl
X	3617257	X_3617257_SNP [dm3] X_3723224_SNP [dm6]	C	A	1.929e^-6	0.312	INTRON tlk	TF binding site BDTNP1_TFBS_dl
X	3615106	X_3615106_SNP [dm3] X_3721073_SNP [dm6]	A	G	2.191e^-6	0.312	INTRON tlk	TF binding site BDTNP1_TFBS_dl
2L	7440910	2L_7440910_SNP [dm3] 2L_7440910_SNP [dm6]	G	T	2.490e^-6	0.312	UTR_5_PRIME CG5973 INTRON CG5973
3R	14678071	3R_14678071_SNP [dm3] 3R_18852349_SNP [dm6]	G	T	2.604e^-6	0.312	UPSTREAM CG31226 INTERGENIC
3L	3576742	3L_3576742_SNP [dm3] 3L_3576742_SNP [dm6]	C	T	2.644e^-6	0.312	INTRON Eip63E
3R	14678909	3R_14678909_DEL [dm3] 3R_18853187_DEL [dm6]	CC	C	2.699e^-6	0.312	INTERGENIC
2L	17048510	2L_17048510_SNP [dm3] 2L_17048510_SNP [dm6]	T	G	2.751e^-6	0.312	UPSTREAM CG15136 INTERGENIC
3R	24130310	3R_24130310_SNP [dm3] 3R_28304588_SNP [dm6]	T	C	2.829e^-6	0.312	START_GAINED CG12516 UTR_5_PRIME CG12516
3R	12903335	3R_12903335_SNP [dm3] 3R_17077613_SNP [dm6]	A	G	3.786e^-6	0.395	INTRON Keap1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
X	3617480	X_3617480_SNP [dm3] X_3723447_SNP [dm6]	T	C	4.305e^-6	0.425	INTRON tlk	TF binding site BDTNP1_TFBS_dl
2L	3267116	2L_3267116_SNP [dm3] 2L_3267116_SNP [dm6]	A	T	4.754e^-6	0.446	INTERGENIC
3R	14543660	3R_14543660_SNP [dm3] 3R_18717938_SNP [dm6]	A	G	5.289e^-6	0.472	UTR_3_PRIME VAChT INTRON Cha
3L	9808756	3L_9808756_SNP [dm3] 3L_9815656_SNP [dm6]	A	T	6.721e^-6	0.573	UPSTREAM CG43897 INTRON CG43897
3L	10760378	3L_10760378_SNP [dm3] 3L_10767278_SNP [dm6]	A	T	7.138e^-6	0.582	INTERGENIC
3L	9344968	3L_9344968_SNP [dm3] 3L_9351868_SNP [dm6]	G	C	7.503e^-6	0.586	DOWNSTREAM PGRP-LF INTRON UGP
X	5855639	X_5855639_SNP [dm3] X_5961606_SNP [dm6]	T	A	8.419e^-6	0.632	SYNONYMOUS_CODING fs_1_M3
X	3617340	X_3617340_SNP [dm3] X_3723307_SNP [dm6]	T	C	9.357e^-6	0.647	INTRON tlk	TF binding site BDTNP1_TFBS_dl
3L	9344969	3L_9344969_SNP [dm3] 3L_9351869_SNP [dm6]	A	G	1.113e^-5	0.647	DOWNSTREAM PGRP-LF INTRON UGP
3R	19565253	3R_19565253_SNP [dm3] 3R_23739531_SNP [dm6]	C	T	1.136e^-5	0.647	INTRON Hmgcr
2L	5878808	2L_5878808_SNP [dm3] 2L_5878808_SNP [dm6]	G	A	1.165e^-5	0.647	INTRON rau	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	9416993	2L_9416993_SNP [dm3] 2L_9416993_SNP [dm6]	T	A	1.178e^-5	0.647	INTRON Mco1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	9344973	3L_9344973_SNP [dm3] 3L_9351873_SNP [dm6]	G	T	1.263e^-5	0.647	DOWNSTREAM PGRP-LF INTRON UGP
3L	9344978	3L_9344978_SNP [dm3] 3L_9351878_SNP [dm6]	T	A	1.265e^-5	0.647	DOWNSTREAM PGRP-LF INTRON UGP
3L	15825028	3L_15825028_SNP [dm3] 3L_15831928_SNP [dm6]	A	T	1.277e^-5	0.647	UTR_3_PRIME dbo UPSTREAM CG12713 DOWNSTREAM dbo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
2L	5403099	2L_5403099_SNP [dm3] 2L_5403099_SNP [dm6]	A	T	1.300e^-5	0.647	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2L	5403108	2L_5403108_SNP [dm3] 2L_5403108_SNP [dm6]	C	A	1.300e^-5	0.647	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2R	9916555	2R_9916555_SNP [dm3] 2R_14029050_SNP [dm6]	C	T	1.317e^-5	0.647	NON_SYNONYMOUS_CODING CG18371 INTRON mam
2L	4336150	2L_4336150_SNP [dm3] 2L_4336150_SNP [dm6]	T	G	1.371e^-5	0.647	INTRON Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9344980	3L_9344980_SNP [dm3] 3L_9351880_SNP [dm6]	G	A	1.432e^-5	0.647	DOWNSTREAM PGRP-LF INTRON UGP
3R	5806070	3R_5806070_SNP [dm3] 3R_9980348_SNP [dm6]	T	A	1.437e^-5	0.647	INTRON Glut4EF
3R	10590302	3R_10590302_SNP [dm3] 3R_14764580_SNP [dm6]	G	T	1.450e^-5	0.647	INTRON jvl
3R	1927929	3R_1927929_SNP [dm3] 3R_6102207_SNP [dm6]	A	G	1.453e^-5	0.647	EXON CR44929
2L	11982032	2L_11982032_SNP [dm3] 2L_11982032_SNP [dm6]	A	T	1.580e^-5	0.647	SYNONYMOUS_CODING CG16965
2L	14236437	2L_14236437_INS [dm3] 2L_14236437_INS [dm6]	G	AAAGCACATTTTACACTGTC...	1.643e^-5	0.647	DOWNSTREAM CR44728 INTERGENIC
X	10185840	X_10185840_SNP [dm3] X_10291807_SNP [dm6]	G	T	1.657e^-5	0.647	INTRON alpha-Man-I
2L	2880132	2L_2880132_SNP [dm3] 2L_2880132_SNP [dm6]	G	A	1.658e^-5	0.647	SYNONYMOUS_CODING betaggt-II DOWNSTREAM NTPase	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo
2L	3267295	2L_3267295_SNP [dm3] 2L_3267295_SNP [dm6]	A	T	1.661e^-5	0.647	UPSTREAM CR44484 INTERGENIC
3R	14676984	3R_14676984_SNP [dm3] 3R_18851262_SNP [dm6]	C	T	1.756e^-5	0.647	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
3L	9344982	3L_9344982_SNP [dm3] 3L_9351882_SNP [dm6]	G	A	1.819e^-5	0.647	DOWNSTREAM PGRP-LF INTRON UGP
3L	14145464	3L_14145464_SNP [dm3] 3L_14152364_SNP [dm6]	A	C	1.823e^-5	0.647	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	5512470	3L_5512470_SNP [dm3] 3L_5519370_SNP [dm6]	C	T	1.870e^-5	0.647	INTRON Lkr
2R	17204093	2R_17204093_SNP [dm3] 2R_21316588_SNP [dm6]	A	C	1.870e^-5	0.647	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	15818261	3L_15818261_SNP [dm3] 3L_15825161_SNP [dm6]	G	A	1.944e^-5	0.647	UPSTREAM Dcp2 INTRON Dcp2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	7496901	3L_7496901_SNP [dm3] 3L_7503801_SNP [dm6]	T	A	2.006e^-5	0.647	INTERGENIC
X	10185982	X_10185982_SNP [dm3] X_10291949_SNP [dm6]	T	C	2.146e^-5	0.647	INTRON alpha-Man-I
3R	24138819	3R_24138819_SNP [dm3] 3R_28313097_SNP [dm6]	G	C	2.190e^-5	0.647	INTERGENIC	TF binding site mE1_TFBS_cad
2L	4011813	2L_4011813_SNP [dm3] 2L_4011813_SNP [dm6]	G	A	2.208e^-5	0.647	INTERGENIC
3L	2835279	3L_2835279_SNP [dm3] 3L_2835279_SNP [dm6]	A	T	2.209e^-5	0.647	INTRON CG43444
3R	5944856	3R_5944856_SNP [dm3] 3R_10119134_SNP [dm6]	A	G	2.234e^-5	0.647	NON_SYNONYMOUS_CODING CG3940
3L	2192677	3L_2192677_INS [dm3] 3L_2192677_INS [dm6]	C	CT	2.241e^-5	0.647	UPSTREAM CG5707 INTERGENIC
3L	7579199	3L_7579199_SNP [dm3] 3L_7586099_SNP [dm6]	C	G	2.279e^-5	0.647	SPLICE_SITE_REGION CG14838 SYNONYMOUS_CODING CG14838
2L	4514683	2L_4514683_SNP [dm3] 2L_4514683_SNP [dm6]	G	T	2.302e^-5	0.647	INTRON dp
X	3615145	X_3615145_SNP [dm3] X_3721112_SNP [dm6]	T	C	2.405e^-5	0.647	INTRON tlk	TF binding site BDTNP1_TFBS_dl
3L	2192681	3L_2192681_SNP [dm3] 3L_2192681_SNP [dm6]	T	A	2.418e^-5	0.647	UPSTREAM CG5707 INTERGENIC
2L	1714758	2L_1714758_SNP [dm3] 2L_1714758_SNP [dm6]	C	G	2.419e^-5	0.647	INTRON frtz	TF binding site mE1_TFBS_chinmo
3L	1320779	3L_1320779_SNP [dm3] 3L_1320779_SNP [dm6]	T	A	2.421e^-5	0.647	UPSTREAM Myo61F INTRON Myo61F
3L	2192611	3L_2192611_SNP [dm3] 3L_2192611_SNP [dm6]	C	A	2.451e^-5	0.647	UPSTREAM CG5707 INTERGENIC
2L	5592368	2L_5592368_SNP [dm3] 2L_5592368_SNP [dm6]	A	G	2.466e^-5	0.647	INTERGENIC
2R	20374772	2R_20374772_SNP [dm3] 2R_24487249_SNP [dm6]	T	C	2.492e^-5	0.647	INTRON CG13579	TF binding site mE1_TFBS_cad
3R	4676506	3R_4676506_SNP [dm3] 3R_8850784_SNP [dm6]	T	A	2.495e^-5	0.647	INTRON pyd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4906869	2L_4906869_DEL [dm3] 2L_4906869_DEL [dm6]	TACTACTACTTACT...	T	2.538e^-5	0.647	UPSTREAM CG2837 INTERGENIC
3L	9567598	3L_9567598_SNP [dm3] 3L_9574498_SNP [dm6]	C	T	2.607e^-5	0.647	INTRON CG42673
3L	5876508	3L_5876508_SNP [dm3] 3L_5883408_SNP [dm6]	C	T	2.660e^-5	0.647	SYNONYMOUS_CODING CG13287	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	7257030	2R_7257030_SNP [dm3] 2R_11369525_SNP [dm6]	G	A	2.664e^-5	0.647	SYNONYMOUS_CODING CG13204 DOWNSTREAM Tapdelta	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
2L	9515186	2L_9515186_SNP [dm3] 2L_9515186_SNP [dm6]	G	A	2.664e^-5	0.647	INTRON CG33298
3L	2424172	3L_2424172_SNP [dm3] 3L_2424172_SNP [dm6]	C	T	2.723e^-5	0.647	INTRON CG45186
2L	4011868	2L_4011868_SNP [dm3] 2L_4011868_SNP [dm6]	C	T	2.725e^-5	0.647	INTERGENIC
X	4685359	X_4685359_SNP [dm3] X_4791326_SNP [dm6]	C	G	2.779e^-5	0.647	INTERGENIC
2L	3930095	2L_3930095_SNP [dm3] 2L_3930095_SNP [dm6]	G	C	2.787e^-5	0.647	INTRON fred
3R	24705381	3R_24705381_SNP [dm3] 3R_28879659_SNP [dm6]	T	C	2.788e^-5	0.647	SYNONYMOUS_CODING CG14523 INTRON CG33203	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15195786	3R_15195786_SNP [dm3] 3R_19370064_SNP [dm6]	A	C	2.793e^-5	0.647	INTRON Ino80
3R	14676991	3R_14676991_DEL [dm3] 3R_18851269_DEL [dm6]	CG	T	2.815e^-5	0.647	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
2L	5403133	2L_5403133_SNP [dm3] 2L_5403133_SNP [dm6]	A	G	2.904e^-5	0.647	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
3R	14543634	3R_14543634_SNP [dm3] 3R_18717912_SNP [dm6]	G	A	2.930e^-5	0.647	UTR_3_PRIME VAChT INTRON Cha
3R	24138878	3R_24138878_SNP [dm3] 3R_28313156_SNP [dm6]	G	T	2.957e^-5	0.647	INTERGENIC	TF binding site mE1_TFBS_cad
3L	2186226	3L_2186226_SNP [dm3] 3L_2186226_SNP [dm6]	G	T	2.976e^-5	0.647	SYNONYMOUS_CODING CG13810	TF binding site BDTNP1_TFBS_twi
3L	12306535	3L_12306535_SNP [dm3] 3L_12313435_SNP [dm6]	G	A	2.984e^-5	0.647	INTERGENIC
X	10186020	X_10186020_SNP [dm3] X_10291987_SNP [dm6]	A	T	3.015e^-5	0.647	INTRON alpha-Man-I
3L	6524221	3L_6524221_SNP [dm3] 3L_6531121_SNP [dm6]	G	A	3.047e^-5	0.647	SYNONYMOUS_CODING CG32396 INTRON sfl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	15758061	3L_15758061_INS [dm3] 3L_15764961_INS [dm6]	A	ACGA	3.074e^-5	0.647	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7496902	3L_7496902_SNP [dm3] 3L_7503802_SNP [dm6]	A	C	3.103e^-5	0.647	INTERGENIC
3L	2439565	3L_2439565_SNP [dm3] 3L_2439565_SNP [dm6]	G	C	3.248e^-5	0.662	SYNONYMOUS_CODING CG45186 UTR_5_PRIME CG45186	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	15819384	3L_15819384_SNP [dm3] 3L_15826284_SNP [dm6]	A	G	3.307e^-5	0.662	SPLICE_SITE_DONOR Dcp2 UTR_5_PRIME Dcp2 UPSTREAM dbo INTRON Dcp2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
2L	4546212	2L_4546212_SNP [dm3] 2L_4546212_SNP [dm6]	G	C	3.384e^-5	0.662	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	9281728	2L_9281728_SNP [dm3] 2L_9281728_SNP [dm6]	T	C	3.432e^-5	0.662	INTRON Ggamma30A
X	10401495	X_10401495_SNP [dm3] X_10507462_SNP [dm6]	C	A	3.443e^-5	0.662	INTRON spri
2R	8345647	2R_8345647_SNP [dm3] 2R_12458142_SNP [dm6]	G	T	3.445e^-5	0.662	INTRON Lac	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	24835273	3R_24835273_SNP [dm3] 3R_29009551_SNP [dm6]	C	A	3.469e^-5	0.662	UPSTREAM mir-4947 INTRON wat
2L	4501756	2L_4501756_SNP [dm3] 2L_4501756_SNP [dm6]	T	A	3.510e^-5	0.662	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	10945098	2L_10945098_SNP [dm3] 2L_10945098_SNP [dm6]	A	G	3.514e^-5	0.662	INTRON dpr2
2L	5591753	2L_5591753_SNP [dm3] 2L_5591753_SNP [dm6]	A	G	3.556e^-5	0.662	INTERGENIC

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Phenotype distribution and association to known covariates

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GWAS results