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=4.128e^-9)
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

Covariate	χ²	p-value	Significance
wolba	5.7478	0.0165
In_2L_t	6.8071	0.0333

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

6835 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	10640543	2L_10640543_SNP [dm3] 2L_10640543_SNP [dm6]	G	A	2.141e^-9	0.002	NON_SYNONYMOUS_CODING CG31872 DOWNSTREAM CR45351
2R	18294499	2R_18294499_SNP [dm3] 2R_22406994_SNP [dm6]	C	T	2.435e^-9	0.002	INTRON CG6044	TF binding site BDTNP1_TFBS_twi
3L	1078558	3L_1078558_SNP [dm3] 3L_1078558_SNP [dm6]	A	G	2.417e^-8	0.012	INTRON bab1	TF binding site mE1_TFBS_HSA
3L	1078768	3L_1078768_SNP [dm3] 3L_1078768_SNP [dm6]	G	A	2.680e^-8	0.012	INTRON bab1	TF binding site mE1_TFBS_HSA
2L	10640411	2L_10640411_SNP [dm3] 2L_10640411_SNP [dm6]	G	A	4.837e^-8	0.012	NON_SYNONYMOUS_CODING CG31872 DOWNSTREAM CR45351
2R	12050760	2R_12050760_SNP [dm3] 2R_16163255_SNP [dm6]	C	T	5.142e^-8	0.012	INTRON lbk
3L	18839432	3L_18839432_SNP [dm3] 3L_18846332_SNP [dm6]	T	G	5.669e^-8	0.012	UPSTREAM Indy INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	2729066	X_2729066_SNP [dm3] X_2835033_SNP [dm6]	C	T	5.669e^-8	0.012	INTRON kirre
X	8947767	X_8947767_DEL [dm3] X_9053734_DEL [dm6]	GAA	T	5.669e^-8	0.012	UTR_3_PRIME CG42388 DOWNSTREAM CG42388 & 1 other
3L	1752641	3L_1752641_SNP [dm3] 3L_1752641_SNP [dm6]	C	T	9.108e^-8	0.017	NON_SYNONYMOUS_CODING Cht2 DOWNSTREAM CG13921	TF binding site mE1_TFBS_cad
3L	1078912	3L_1078912_SNP [dm3] 3L_1078912_SNP [dm6]	A	C	1.027e^-7	0.017	INTRON bab1	TF binding site mE1_TFBS_HSA
2L	6026813	2L_6026813_SNP [dm3] 2L_6026813_SNP [dm6]	A	T	1.791e^-7	0.022	INTRON CG9109
3L	12240608	3L_12240608_SNP [dm3] 3L_12247508_SNP [dm6]	C	T	1.860e^-7	0.022	INTRON app
3L	12240611	3L_12240611_SNP [dm3] 3L_12247511_SNP [dm6]	A	T	1.860e^-7	0.022	INTRON app
3L	12240612	3L_12240612_SNP [dm3] 3L_12247512_SNP [dm6]	C	T	1.860e^-7	0.022	INTRON app
3R	20521920	3R_20521920_DEL [dm3] 3R_24696198_DEL [dm6]	AACCAAAA	A	2.232e^-7	0.022	INTRON slo
2R	18643889	2R_18643889_SNP [dm3] 2R_22756384_SNP [dm6]	T	G	2.279e^-7	0.022	DOWNSTREAM CG13526 INTRON CG42260 EXON CR30267
3L	7066385	3L_7066385_SNP [dm3] 3L_7073285_SNP [dm6]	C	G	2.329e^-7	0.022	DOWNSTREAM CG34030 INTRON CG8641
X	3662251	X_3662251_SNP [dm3] X_3768218_SNP [dm6]	T	G	2.471e^-7	0.022	INTRON tlk
3L	12662721	3L_12662721_SNP [dm3] 3L_12669621_SNP [dm6]	T	C	2.551e^-7	0.022	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	10857656	2R_10857656_SNP [dm3] 2R_14970151_SNP [dm6]	A	G	3.079e^-7	0.022	INTRON ckn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	16095572	2R_16095572_DEL [dm3] 2R_20208067_DEL [dm6]	GGCTGT	G	3.079e^-7	0.022	INTERGENIC
2R	2971126	2R_2971126_SNP [dm3] 2R_7083621_SNP [dm6]	G	T	3.079e^-7	0.022	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7066059	3L_7066059_SNP [dm3] 3L_7072959_SNP [dm6]	G	A	3.079e^-7	0.022	DOWNSTREAM CG34030 INTRON CG8641	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	7066061	3L_7066061_SNP [dm3] 3L_7072961_SNP [dm6]	A	G	3.079e^-7	0.022	DOWNSTREAM CG34030 INTRON CG8641	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	7897771	3L_7897771_SNP [dm3] 3L_7904671_SNP [dm6]	A	G	3.079e^-7	0.022	INTRON pbl
2R	17930476	2R_17930476_DEL [dm3] 2R_22042971_DEL [dm6]	GT	G	3.418e^-7	0.022	UPSTREAM PpD5 INTERGENIC
2R	2995490	2R_2995490_SNP [dm3] 2R_7107985_SNP [dm6]	A	T	4.181e^-7	0.022	INTRON esn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	2999266	2R_2999266_SNP [dm3] 2R_7111761_SNP [dm6]	C	T	4.181e^-7	0.022	INTRON esn	TF binding site mE1_TFBS_inv
2R	3006289	2R_3006289_SNP [dm3] 2R_7118784_SNP [dm6]	C	T	4.181e^-7	0.022	SYNONYMOUS_CODING esn	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
X	15466647	X_15466647_SNP [dm3] X_15572614_SNP [dm6]	C	T	4.430e^-7	0.022	NON_SYNONYMOUS_CODING CG9213 UPSTREAM CG15643	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	2858906	2R_2858906_SNP [dm3] 2R_6971401_SNP [dm6]	G	A	4.628e^-7	0.022	UTR_5_PRIME mim & 1 other DOWNSTREAM Cyp6u1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	17930579	2R_17930579_SNP [dm3] 2R_22043074_SNP [dm6]	A	G	4.695e^-7	0.022	UPSTREAM PpD5 INTERGENIC
2R	17930585	2R_17930585_SNP [dm3] 2R_22043080_SNP [dm6]	G	T	4.695e^-7	0.022	UPSTREAM PpD5 INTERGENIC
2R	17930594	2R_17930594_SNP [dm3] 2R_22043089_SNP [dm6]	C	T	4.695e^-7	0.022	UPSTREAM PpD5 INTERGENIC
2L	18152890	2L_18152890_SNP [dm3] 2L_18152890_SNP [dm6]	T	C	4.851e^-7	0.022	UPSTREAM CG17681 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn
2L	13536113	2L_13536113_SNP [dm3] 2L_13536113_SNP [dm6]	T	G	4.944e^-7	0.022	UPSTREAM CG15638 INTRON B4
3L	1077822	3L_1077822_SNP [dm3] 3L_1077822_SNP [dm6]	C	T	5.249e^-7	0.022	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1077938	3L_1077938_SNP [dm3] 3L_1077938_SNP [dm6]	G	T	5.249e^-7	0.022	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1078420	3L_1078420_SNP [dm3] 3L_1078420_SNP [dm6]	C	T	5.249e^-7	0.022	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1078448	3L_1078448_INS [dm3] 3L_1078448_INS [dm6]	C	CTACC	5.249e^-7	0.022	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1078458	3L_1078458_INS [dm3] 3L_1078458_INS [dm6]	G	GC	5.249e^-7	0.022	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1078491	3L_1078491_SNP [dm3] 3L_1078491_SNP [dm6]	A	G	5.249e^-7	0.022	INTRON bab1	TF binding site mE1_TFBS_HSA
3L	17634480	3L_17634480_SNP [dm3] 3L_17641380_SNP [dm6]	A	C	5.372e^-7	0.022	INTRON Pep
3L	17644925	3L_17644925_DEL [dm3] 3L_17651825_DEL [dm6]	TGGC	T	5.372e^-7	0.022	INTRON Ndfip & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	10497272	2R_10497272_SNP [dm3] 2R_14609767_SNP [dm6]	C	G	5.467e^-7	0.022	SYNONYMOUS_CODING Su_var_2-HP2	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	9527549	2L_9527549_SNP [dm3] 2L_9527549_SNP [dm6]	G	C	5.835e^-7	0.022	UPSTREAM CG31883 INTRON Oatp30B
2R	3656950	2R_3656950_SNP [dm3] 2R_7769445_SNP [dm6]	C	T	5.835e^-7	0.022	INTRON CG30497 & 1 other
2R	17930908	2R_17930908_DEL [dm3] 2R_22043403_DEL [dm6]	GG	G	6.221e^-7	0.023	UPSTREAM PpD5 INTERGENIC
3L	18934617	3L_18934617_SNP [dm3] 3L_18941517_SNP [dm6]	C	T	6.597e^-7	0.024	INTRON CG32204
2R	13472399	2R_13472399_SNP [dm3] 2R_17584894_SNP [dm6]	A	G	6.768e^-7	0.024	UPSTREAM CG6484 & 1 other DOWNSTREAM CG14483 & 1 other INTERGENIC
2R	13472443	2R_13472443_DEL [dm3] 2R_17584938_DEL [dm6]	AG	A	6.768e^-7	0.024	UPSTREAM CG6484 & 1 other DOWNSTREAM CG14483 & 1 other INTERGENIC
3L	17643363	3L_17643363_SNP [dm3] 3L_17650263_SNP [dm6]	G	A	6.768e^-7	0.024	SYNONYMOUS_CODING Krn INTRON Ndfip	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 mE1_TFBS_sens
3L	13250181	3L_13250181_SNP [dm3] 3L_13257081_SNP [dm6]	C	T	7.087e^-7	0.024	INTRON caps
3L	13250184	3L_13250184_SNP [dm3] 3L_13257084_SNP [dm6]	G	A	7.087e^-7	0.024	INTRON caps
3L	1078426	3L_1078426_SNP [dm3] 3L_1078426_SNP [dm6]	C	A	8.050e^-7	0.024	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1078479	3L_1078479_SNP [dm3] 3L_1078479_SNP [dm6]	A	C	8.050e^-7	0.024	INTRON bab1	TF binding site mE1_TFBS_HSA
3L	1078482	3L_1078482_SNP [dm3] 3L_1078482_SNP [dm6]	T	A	8.050e^-7	0.024	INTRON bab1	TF binding site mE1_TFBS_HSA
3L	1080084	3L_1080084_SNP [dm3] 3L_1080084_SNP [dm6]	A	G	8.050e^-7	0.024	INTRON bab1	TF binding site mE1_TFBS_chinmo
3L	1080496	3L_1080496_SNP [dm3] 3L_1080496_SNP [dm6]	A	C	8.050e^-7	0.024	INTRON bab1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1080508	3L_1080508_SNP [dm3] 3L_1080508_SNP [dm6]	C	T	8.050e^-7	0.024	INTRON bab1	TF binding site mE1_TFBS_chinmo
X	2977476	X_2977476_SNP [dm3] X_3083443_SNP [dm6]	A	T	8.273e^-7	0.024	INTRON kirre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17628711	3L_17628711_SNP [dm3] 3L_17635611_SNP [dm6]	C	T	8.303e^-7	0.024	INTRON CG7497
2L	16800227	2L_16800227_SNP [dm3] 2L_16800227_SNP [dm6]	G	A	8.577e^-7	0.025	SYNONYMOUS_CODING Ugt36Bc
2L	17540736	2L_17540736_SNP [dm3] 2L_17540736_SNP [dm6]	T	G	8.785e^-7	0.025	INTERGENIC
3L	1078686	3L_1078686_SNP [dm3] 3L_1078686_SNP [dm6]	A	C	8.876e^-7	0.025	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13539214	2L_13539214_SNP [dm3] 2L_13539214_SNP [dm6]	A	G	9.629e^-7	0.026	INTRON B4
X	19137557	X_19137557_SNP [dm3] X_19243524_SNP [dm6]	T	G	9.634e^-7	0.026	UPSTREAM CG7889 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cad
2R	18198511	2R_18198511_SNP [dm3] 2R_22311006_SNP [dm6]	C	T	9.677e^-7	0.026	INTRON wdp
2L	8043171	2L_8043171_INS [dm3] 2L_8043171_INS [dm6]	C	TGAAACAATAA...	9.936e^-7	0.026	UPSTREAM snoRNA:Psi28S-2648 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
3L	4012147	3L_4012147_SNP [dm3] 3L_4012147_SNP [dm6]	C	G	1.003e^-6	0.026	INTERGENIC
X	1889917	X_1889917_INS [dm3] X_1995884_INS [dm6]	G	GCGTGTGTG	1.069e^-6	0.027	INTRON Hr4	TF binding site BDTNP1_TFBS_dl
3L	7909074	3L_7909074_SNP [dm3] 3L_7915974_SNP [dm6]	C	A	1.112e^-6	0.028	UPSTREAM CG8111 DOWNSTREAM syd & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	7909123	3L_7909123_SNP [dm3] 3L_7916023_SNP [dm6]	G	C	1.112e^-6	0.028	UPSTREAM CG8111 DOWNSTREAM syd & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	17704712	3L_17704712_SNP [dm3] 3L_17711612_SNP [dm6]	G	A	1.204e^-6	0.029	INTRON Ccn	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17704740	3L_17704740_SNP [dm3] 3L_17711640_SNP [dm6]	T	C	1.204e^-6	0.029	INTRON Ccn	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17760751	3L_17760751_SNP [dm3] 3L_17767651_SNP [dm6]	G	T	1.204e^-6	0.029	INTERGENIC
3L	1078427	3L_1078427_SNP [dm3] 3L_1078427_SNP [dm6]	C	T	1.228e^-6	0.029	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1080588	3L_1080588_SNP [dm3] 3L_1080588_SNP [dm6]	A	G	1.228e^-6	0.029	INTRON bab1	TF binding site mE1_TFBS_chinmo
2L	22491522	2L_22491522_SNP [dm3] 2L_22598790_SNP [dm6]	A	G	1.408e^-6	0.031	INTERGENIC
3L	10015208	3L_10015208_SNP [dm3] 3L_10022108_SNP [dm6]	G	T	1.449e^-6	0.031	INTRON dpr6
3L	17763209	3L_17763209_SNP [dm3] 3L_17770109_SNP [dm6]	G	T	1.449e^-6	0.031	INTERGENIC
3L	7352038	3L_7352038_SNP [dm3] 3L_7358938_SNP [dm6]	G	A	1.449e^-6	0.031	SYNONYMOUS_CODING pst	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8043231	2L_8043231_SNP [dm3] 2L_8043231_SNP [dm6]	T	G	1.481e^-6	0.031	UPSTREAM snoRNA:Psi28S-2648 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
2L	9048888	2L_9048888_SNP [dm3] 2L_9048888_SNP [dm6]	C	G	1.586e^-6	0.031	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	12876728	2R_12876728_SNP [dm3] 2R_16989223_SNP [dm6]	A	C	1.616e^-6	0.031	INTRON Cbp53E	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	1080989	3L_1080989_SNP [dm3] 3L_1080989_SNP [dm6]	C	T	1.631e^-6	0.031	INTRON bab1
2L	6531570	2L_6531570_SNP [dm3] 2L_6531570_SNP [dm6]	G	A	1.705e^-6	0.031	INTRON eya	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2L	20080899	2L_20080899_DEL [dm3] 2L_20080899_DEL [dm6]	TGTAT	T	1.709e^-6	0.031	UPSTREAM fok DOWNSTREAM fok INTRON neb & 1 other	TF binding site mE1_TFBS_inv
3L	1078685	3L_1078685_SNP [dm3] 3L_1078685_SNP [dm6]	A	C	1.718e^-6	0.031	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	6519878	X_6519878_SNP [dm3] X_6625845_SNP [dm6]	T	C	1.728e^-6	0.031	INTRON pigs
3L	7389139	3L_7389139_INS [dm3] 3L_7396039_INS [dm6]	T	TT	1.733e^-6	0.031	UPSTREAM CG32379 DOWNSTREAM CG8563 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	17646185	3L_17646185_SNP [dm3] 3L_17653085_SNP [dm6]	G	A	1.798e^-6	0.031	INTRON Ndfip & 1 other	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_HSA mE1_TFBS_Trl
3L	17704723	3L_17704723_SNP [dm3] 3L_17711623_SNP [dm6]	T	G	1.808e^-6	0.031	INTRON Ccn	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	5308583	2R_5308583_SNP [dm3] 2R_9421078_SNP [dm6]	C	T	1.821e^-6	0.031	DOWNSTREAM CG13955 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
4	981576	4_981576_DEL [dm3] 4_960950_DEL [dm6]	TT	T	1.825e^-6	0.031	INTRON CR44030	transposable element FlyBase
3L	1078645	3L_1078645_SNP [dm3] 3L_1078645_SNP [dm6]	G	T	1.825e^-6	0.031	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	4688747	3R_4688747_INS [dm3] 3R_8863025_INS [dm6]	T	TCTTTTTTTATTTTTT...	2.012e^-6	0.031	DOWNSTREAM tRNA:R:85Cb INTRON pyd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	13154578	2L_13154578_INS [dm3] 2L_13154578_INS [dm6]	G	GG	2.074e^-6	0.031	INTERGENIC
2R	5283802	2R_5283802_SNP [dm3] 2R_9396297_SNP [dm6]	A	C	2.074e^-6	0.031	UTR_3_PRIME CG8801 UPSTREAM CG8800 DOWNSTREAM CG8801	TF binding site mE1_TFBS_cad

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By genomic position
Variant impact
Gene name

pc_MB_Beta_Missing phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results