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=1.469e^-5)
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_2L_t	0.01394

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.5064	0.0142

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3003 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	9114956	2L_9114956_SNP [dm3] 2L_9114956_SNP [dm6]	A	T	6.421e^-9	0.006	INTERGENIC
2L	9114957	2L_9114957_SNP [dm3] 2L_9114957_SNP [dm6]	C	A	6.421e^-9	0.006	INTERGENIC
2L	13731198	2L_13731198_SNP [dm3] 2L_13731198_SNP [dm6]	A	C	2.509e^-7	0.153	INTERGENIC
2L	11584570	2L_11584570_SNP [dm3] 2L_11584570_SNP [dm6]	G	A	5.313e^-7	0.182	DOWNSTREAM Mst33A INTRON kek2
2R	18978521	2R_18978521_SNP [dm3] 2R_23090998_SNP [dm6]	G	T	5.313e^-7	0.182	SYNONYMOUS_CODING CG9876	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	19561390	2L_19561390_SNP [dm3] 2L_19561390_SNP [dm6]	A	G	5.976e^-7	0.182	SYNONYMOUS_CODING Tep5
2R	11246343	2R_11246343_SNP [dm3] 2R_15358838_SNP [dm6]	T	A	7.043e^-7	0.184	INTRON unc-5	TF binding site mE1_TFBS_chinmo
3L	7748277	3L_7748277_SNP [dm3] 3L_7755177_SNP [dm6]	C	T	1.368e^-6	0.282	DOWNSTREAM CG7409 INTRON CG32373
2L	6694167	2L_6694167_SNP [dm3] 2L_6694167_SNP [dm6]	G	A	1.511e^-6	0.282	INTRON Tsp
3R	16634541	3R_16634541_SNP [dm3] 3R_20808819_SNP [dm6]	G	T	1.637e^-6	0.282	UTR_3_PRIME Syp
2L	16447653	2L_16447653_SNP [dm3] 2L_16447653_SNP [dm6]	A	G	2.219e^-6	0.282	DOWNSTREAM Idgf1 INTRON CG5888 & 1 other
3R	18595583	3R_18595583_SNP [dm3] 3R_22769861_SNP [dm6]	T	A	2.442e^-6	0.282	UTR_3_PRIME CG43093 UPSTREAM CG43092 DOWNSTREAM CG43094 INTRON Usp12-46 & 1 other
3R	18595619	3R_18595619_SNP [dm3] 3R_22769897_SNP [dm6]	G	A	2.442e^-6	0.282	SYNONYMOUS_CODING CG43093 UPSTREAM CG43092 DOWNSTREAM CG43094 INTRON Usp12-46 & 1 other
2L	13376616	2L_13376616_SNP [dm3] 2L_13376616_SNP [dm6]	T	A	3.499e^-6	0.282	UTR_3_PRIME CG9302 DOWNSTREAM CG6565
2R	3766379	2R_3766379_SNP [dm3] 2R_7878874_SNP [dm6]	A	T	3.510e^-6	0.282	INTRON Dgk
3R	18595575	3R_18595575_SNP [dm3] 3R_22769853_SNP [dm6]	A	C	3.601e^-6	0.282	UTR_3_PRIME CG43093 UPSTREAM CG43092 DOWNSTREAM CG43094 INTRON Usp12-46 & 1 other
3R	18595578	3R_18595578_SNP [dm3] 3R_22769856_SNP [dm6]	G	A	3.601e^-6	0.282	UTR_3_PRIME CG43093 UPSTREAM CG43092 DOWNSTREAM CG43094 INTRON Usp12-46 & 1 other
3R	26018212	3R_26018212_DEL [dm3] 3R_30192490_DEL [dm6]	AA	A	3.752e^-6	0.282	INTERGENIC
2L	14070523	2L_14070523_INS [dm3] 2L_14070523_INS [dm6]	A	ATA	3.808e^-6	0.282	INTRON nAChRalpha5
2L	8842551	2L_8842551_SNP [dm3] 2L_8842551_SNP [dm6]	A	T	6.506e^-6	0.282	INTERGENIC	silencer mE1_HDAC_PRE 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_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E
3L	7748502	3L_7748502_SNP [dm3] 3L_7755402_SNP [dm6]	T	C	6.506e^-6	0.282	DOWNSTREAM CG7409 INTRON CG32373
2L	12370692	2L_12370692_SNP [dm3] 2L_12370692_SNP [dm6]	A	G	6.860e^-6	0.282	INTRON bru-2
3L	3261062	3L_3261062_SNP [dm3] 3L_3261062_SNP [dm6]	G	A	7.194e^-6	0.282	INTRON ckd
4	1238504	4_1238504_SNP [dm3] 4_1234778_SNP [dm6]	A	G	8.027e^-6	0.282	SYNONYMOUS_CODING Caps	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	16388616	2L_16388616_SNP [dm3] 2L_16388616_SNP [dm6]	G	C	8.033e^-6	0.282	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	9291552	X_9291552_SNP [dm3] X_9397519_SNP [dm6]	T	C	8.630e^-6	0.282	INTRON mgl
2L	16258113	2L_16258113_SNP [dm3] 2L_16258113_SNP [dm6]	A	C	8.668e^-6	0.282	UTR_5_PRIME EndoGI UPSTREAM PRL-1	TF binding site BDTNP1_TFBS_dl
3R	10261693	3R_10261693_SNP [dm3] 3R_14435971_SNP [dm6]	T	C	1.005e^-5	0.282	INTRON cv-c
2L	13103749	2L_13103749_SNP [dm3] 2L_13103749_SNP [dm6]	C	A	1.046e^-5	0.282	UPSTREAM CR45461 INTERGENIC
2L	12539112	2L_12539112_SNP [dm3] 2L_12539112_SNP [dm6]	A	G	1.179e^-5	0.282	SYNONYMOUS_CODING bun	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2R	12179615	2R_12179615_SNP [dm3] 2R_16292110_SNP [dm6]	A	G	1.220e^-5	0.282	NON_SYNONYMOUS_CODING CG30100 UTR_3_PRIME CG42372 UPSTREAM CR43730 DOWNSTREAM CG7747 & 1 other	TF binding site mE1_TFBS_HSA
3L	21460495	3L_21460495_SNP [dm3] 3L_21467395_SNP [dm6]	A	C	1.376e^-5	0.282	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	9392532	2R_9392532_SNP [dm3] 2R_13505027_SNP [dm6]	C	A	1.386e^-5	0.282	SYNONYMOUS_CODING mars	TF binding site mE1_TFBS_chinmo
X	12451748	X_12451748_INS [dm3] X_12557715_INS [dm6]	A	AAA	1.476e^-5	0.282	INTRON CG43921
2L	1048553	2L_1048553_SNP [dm3] 2L_1048553_SNP [dm6]	G	A	1.598e^-5	0.282	UPSTREAM IA-2 INTERGENIC
2L	1048559	2L_1048559_SNP [dm3] 2L_1048559_SNP [dm6]	G	A	1.598e^-5	0.282	UPSTREAM IA-2 INTERGENIC
2L	1048568	2L_1048568_SNP [dm3] 2L_1048568_SNP [dm6]	C	A	1.598e^-5	0.282	UPSTREAM IA-2 INTERGENIC
2L	1048578	2L_1048578_SNP [dm3] 2L_1048578_SNP [dm6]	T	A	1.598e^-5	0.282	UPSTREAM IA-2 INTERGENIC
2L	1048583	2L_1048583_SNP [dm3] 2L_1048583_SNP [dm6]	A	G	1.598e^-5	0.282	UPSTREAM IA-2 INTERGENIC
3L	7818184	3L_7818184_INS [dm3] 3L_7825084_INS [dm6]	A	ATTCC	1.598e^-5	0.282	INTRON Pdp1
3L	7818186	3L_7818186_SNP [dm3] 3L_7825086_SNP [dm6]	G	C	1.598e^-5	0.282	INTRON Pdp1
3L	7818188	3L_7818188_INS [dm3] 3L_7825088_INS [dm6]	G	GTTGC	1.598e^-5	0.282	INTRON Pdp1
3L	7818191	3L_7818191_SNP [dm3] 3L_7825091_SNP [dm6]	A	G	1.598e^-5	0.282	INTRON Pdp1
3L	7818195	3L_7818195_DEL [dm3] 3L_7825095_DEL [dm6]	ATG	A	1.598e^-5	0.282	INTRON Pdp1
3L	8554439	3L_8554439_SNP [dm3] 3L_8561339_SNP [dm6]	C	G	1.598e^-5	0.282	INTRON rhea
3L	8554474	3L_8554474_SNP [dm3] 3L_8561374_SNP [dm6]	T	C	1.598e^-5	0.282	UTR_5_PRIME rhea
2L	9188842	2L_9188842_SNP [dm3] 2L_9188842_SNP [dm6]	C	T	1.615e^-5	0.282	INTRON tai
X	2170730	X_2170730_SNP [dm3] X_2276697_SNP [dm6]	A	C	1.632e^-5	0.282	NON_SYNONYMOUS_CODING Vml	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	10706313	3L_10706313_SNP [dm3] 3L_10713213_SNP [dm6]	T	C	1.778e^-5	0.282	INTERGENIC
2L	14549334	2L_14549334_SNP [dm3] 2L_14549334_SNP [dm6]	G	A	1.870e^-5	0.282	UPSTREAM CG4218 INTERGENIC	TF binding site mE1_TFBS_cad
4	1070161	4_1070161_SNP [dm3] 4_1049535_SNP [dm6]	A	C	1.870e^-5	0.282	INTRON CaMKII
3L	7818203	3L_7818203_SNP [dm3] 3L_7825103_SNP [dm6]	G	T	2.008e^-5	0.282	INTRON Pdp1
2R	14408171	2R_14408171_SNP [dm3] 2R_18520666_SNP [dm6]	T	C	2.011e^-5	0.282	SPLICE_SITE_REGION CG43066 INTRON CG43066	TF binding site mE1_TFBS_chinmo
3L	21453439	3L_21453439_SNP [dm3] 3L_21460339_SNP [dm6]	G	A	2.046e^-5	0.282	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	11360755	3L_11360755_SNP [dm3] 3L_11367655_SNP [dm6]	T	C	2.189e^-5	0.282	INTERGENIC	TF binding site mE1_TFBS_inv
2L	12254750	2L_12254750_SNP [dm3] 2L_12254750_SNP [dm6]	C	T	2.252e^-5	0.282	INTRON aret
2R	18070289	2R_18070289_INS [dm3] 2R_22182784_INS [dm6]	A	ACACCTGCGTCGGCG...	2.279e^-5	0.282	UTR_5_PRIME CG11170 UPSTREAM MED16 DOWNSTREAM CG11275 INTRON CG11170	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9865085	3R_9865085_SNP [dm3] 3R_14039363_SNP [dm6]	T	C	2.335e^-5	0.282	INTERGENIC
3L	18759018	3L_18759018_SNP [dm3] 3L_18765918_SNP [dm6]	C	T	2.340e^-5	0.282	UPSTREAM ftz-f1 INTRON ftz-f1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	9122103	2L_9122103_SNP [dm3] 2L_9122103_SNP [dm6]	G	A	2.373e^-5	0.282	UPSTREAM CR44616 INTERGENIC	TF binding site BDTNP1_TFBS_hb
4	1066900	4_1066900_SNP [dm3] 4_1046274_SNP [dm6]	A	G	2.373e^-5	0.282	INTRON CaMKII	transposable element FlyBase
4	908535	4_908535_SNP [dm3] 4_887909_SNP [dm6]	A	G	2.373e^-5	0.282	NON_SYNONYMOUS_CODING unc-13 INTRON unc-13	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	13103729	2L_13103729_SNP [dm3] 2L_13103729_SNP [dm6]	C	A	2.531e^-5	0.282	UPSTREAM CR45461 INTERGENIC
2L	6694003	2L_6694003_SNP [dm3] 2L_6694003_SNP [dm6]	T	A	2.630e^-5	0.282	INTRON Tsp
2R	10822536	2R_10822536_INS [dm3] 2R_14935031_INS [dm6]	A	AAA	2.699e^-5	0.282	UPSTREAM Lap1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_bab1
2L	18506752	2L_18506752_SNP [dm3] 2L_18506752_SNP [dm6]	G	T	2.753e^-5	0.282	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	14070421	2L_14070421_SNP [dm3] 2L_14070421_SNP [dm6]	C	G	2.819e^-5	0.282	INTRON nAChRalpha5
2L	13358705	2L_13358705_SNP [dm3] 2L_13358705_SNP [dm6]	A	G	2.929e^-5	0.282	INTERGENIC
X	14046009	X_14046009_SNP [dm3] X_14151976_SNP [dm6]	T	G	2.943e^-5	0.282	UTR_5_PRIME CG12479
X	14046001	X_14046001_SNP [dm3] X_14151968_SNP [dm6]	C	G	3.191e^-5	0.282	UTR_5_PRIME CG12479
3L	12056550	3L_12056550_DEL [dm3] 3L_12063450_DEL [dm6]	AAAAGCGG	A	3.380e^-5	0.282	INTRON rols	TF binding site mE1_TFBS_HSA
3L	12856850	3L_12856850_SNP [dm3] 3L_12863750_SNP [dm6]	T	C	3.380e^-5	0.282	UPSTREAM CG10943 INTERGENIC
3R	13857285	3R_13857285_SNP [dm3] 3R_18031563_SNP [dm6]	G	T	3.380e^-5	0.282	INTERGENIC
X	10296227	X_10296227_SNP [dm3] X_10402194_SNP [dm6]	T	C	3.380e^-5	0.282	INTRON flw
2R	19493775	2R_19493775_SNP [dm3] 2R_23606252_SNP [dm6]	T	C	3.397e^-5	0.282	NON_SYNONYMOUS_CODING CG17662 INTRON CG17664	TF binding site mE1_TFBS_chinmo
2L	13358799	2L_13358799_SNP [dm3] 2L_13358799_SNP [dm6]	T	C	3.415e^-5	0.282	INTERGENIC
3L	3028127	3L_3028127_SNP [dm3] 3L_3028127_SNP [dm6]	T	C	3.464e^-5	0.282	INTERGENIC
2L	20165775	2L_20165775_SNP [dm3] 2L_20165775_SNP [dm6]	G	A	3.467e^-5	0.282	INTERGENIC	transposable element FlyBase
2R	9775801	2R_9775801_SNP [dm3] 2R_13888296_SNP [dm6]	G	T	3.566e^-5	0.282	NON_SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad
2R	9775828	2R_9775828_SNP [dm3] 2R_13888323_SNP [dm6]	G	T	3.566e^-5	0.282	NON_SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad
2L	14164783	2L_14164783_SNP [dm3] 2L_14164783_SNP [dm6]	C	T	3.761e^-5	0.282	SYNONYMOUS_CODING CG43333
2L	14165005	2L_14165005_SNP [dm3] 2L_14165005_SNP [dm6]	C	T	3.761e^-5	0.282	SYNONYMOUS_CODING CG43333	TF binding site mE1_TFBS_cad
2L	14165202	2L_14165202_SNP [dm3] 2L_14165202_SNP [dm6]	T	C	3.761e^-5	0.282	NON_SYNONYMOUS_CODING CG43333	TF binding site mE1_TFBS_cad
2L	4657135	2L_4657135_SNP [dm3] 2L_4657135_SNP [dm6]	T	C	3.761e^-5	0.282	INTERGENIC
2L	9846569	2L_9846569_SNP [dm3] 2L_9846569_SNP [dm6]	A	G	3.761e^-5	0.282	INTRON nAChRalpha6
2L	9940433	2L_9940433_SNP [dm3] 2L_9940433_SNP [dm6]	A	C	3.761e^-5	0.282	SYNONYMOUS_CODING CG4619 DOWNSTREAM CG5853
2L	9995743	2L_9995743_DEL [dm3] 2L_9995743_DEL [dm6]	CAAGGCCTTTTTTATG...	C	3.761e^-5	0.282	UTR_3_PRIME CG31875 DOWNSTREAM bib & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	11484632	2R_11484632_SNP [dm3] 2R_15597127_SNP [dm6]	G	A	3.761e^-5	0.282	INTERGENIC
2R	11972364	2R_11972364_SNP [dm3] 2R_16084859_SNP [dm6]	T	C	3.761e^-5	0.282	SYNONYMOUS_CODING Dg	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	6111986	2R_6111986_SNP [dm3] 2R_10224481_SNP [dm6]	G	A	3.761e^-5	0.282	INTRON Hr46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	6111996	2R_6111996_INS [dm3] 2R_10224491_INS [dm6]	T	TGA	3.761e^-5	0.282	INTRON Hr46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	6112003	2R_6112003_SNP [dm3] 2R_10224498_SNP [dm6]	G	A	3.761e^-5	0.282	INTRON Hr46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	6112004	2R_6112004_SNP [dm3] 2R_10224499_SNP [dm6]	T	C	3.761e^-5	0.282	INTRON Hr46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	11060730	3L_11060730_SNP [dm3] 3L_11067630_SNP [dm6]	T	C	3.761e^-5	0.282	SYNONYMOUS_CODING SuUR UTR_3_PRIME CG45101	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1144160	3L_1144160_SNP [dm3] 3L_1144160_SNP [dm6]	G	T	3.761e^-5	0.282	INTRON bab2
3L	15707684	3L_15707684_SNP [dm3] 3L_15714584_SNP [dm6]	T	A	3.761e^-5	0.282	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	16477873	3L_16477873_SNP [dm3] 3L_16484773_SNP [dm6]	A	G	3.761e^-5	0.282	INTRON CG33158	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	16477887	3L_16477887_SNP [dm3] 3L_16484787_SNP [dm6]	T	C	3.761e^-5	0.282	INTRON CG33158	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	16477910	3L_16477910_SNP [dm3] 3L_16484810_SNP [dm6]	G	T	3.761e^-5	0.282	INTRON CG33158	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	16477914	3L_16477914_SNP [dm3] 3L_16484814_SNP [dm6]	A	G	3.761e^-5	0.282	INTRON CG33158	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl

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Phenotype distribution and association to known covariates

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GWAS results