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=4.213e^-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_3R_K	0.0219249
In_3R_Mo	0.0698955

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	5.1207	0.0773

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1789 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	8371319	2L_8371319_INS [dm3] 2L_8371319_INS [dm6]	A	ATCTA	1.727e^-6	0.945	UPSTREAM CR45341 INTRON CG17292
2R	2882279	2R_2882279_SNP [dm3] 2R_6994774_SNP [dm6]	T	C	3.516e^-6	0.945	DOWNSTREAM CG30159 INTRON Tsp42Ea	TF binding site mE1_TFBS_Trl
3R	9973092	3R_9973092_SNP [dm3] 3R_14147370_SNP [dm6]	A	T	4.954e^-6	0.945	INTERGENIC
X	16226823	X_16226823_SNP [dm3] X_16332790_SNP [dm6]	A	C	7.942e^-6	0.945	UPSTREAM CG9921 & 1 other INTRON CG9921	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_zfh1
2R	2570058	2R_2570058_SNP [dm3] 2R_6682553_SNP [dm6]	C	T	8.245e^-6	0.945	UPSTREAM CG15909 DOWNSTREAM CR44164 INTRON CG9422 EXON CR44165
3L	4357029	3L_4357029_SNP [dm3] 3L_4357029_SNP [dm6]	C	G	8.838e^-6	0.945	INTRON Cip4
2L	8398451	2L_8398451_DEL [dm3] 2L_8398451_DEL [dm6]	CAATAC	C	1.027e^-5	0.945	UPSTREAM CG13386 DOWNSTREAM CG13385 INTERGENIC
3R	9855212	3R_9855212_SNP [dm3] 3R_14029490_SNP [dm6]	T	A	1.079e^-5	0.945	SYNONYMOUS_CODING Cyp6d5 INTRON rdx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
3L	4722156	3L_4722156_SNP [dm3] 3L_4722156_SNP [dm6]	T	A	1.125e^-5	0.945	INTRON RhoGEF64C
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	1.182e^-5	0.945	INTERGENIC
3L	5350075	3L_5350075_SNP [dm3] 3L_5356975_SNP [dm6]	A	G	1.228e^-5	0.945	UTR_3_PRIME Klp64D UPSTREAM tRNA:CR32421 DOWNSTREAM tRNA:CR32420
X	3875217	X_3875217_SNP [dm3] X_3981184_SNP [dm6]	G	C	1.303e^-5	0.945	INTERGENIC
2L	21882791	2L_21882791_SNP [dm3] 2L_21882791_SNP [dm6]	G	C	1.509e^-5	0.945	INTERGENIC
2L	15759696	2L_15759696_SNP [dm3] 2L_15759696_SNP [dm6]	G	A	1.635e^-5	0.945	SYNONYMOUS_CODING Gli	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	3136845	X_3136845_SNP [dm3] X_3242812_SNP [dm6]	A	G	1.785e^-5	0.945	UTR_3_PRIME ng1 UPSTREAM ng3 INTRON dnc
3L	12173728	3L_12173728_SNP [dm3] 3L_12180628_SNP [dm6]	T	C	1.804e^-5	0.945	INTRON CAH2
2R	6555381	2R_6555381_SNP [dm3] 2R_10667876_SNP [dm6]	C	T	1.825e^-5	0.945	INTERGENIC
X	8471036	X_8471036_SNP [dm3] X_8577003_SNP [dm6]	G	T	1.893e^-5	0.945	INTRON CG12065
2R	6726485	2R_6726485_SNP [dm3] 2R_10838980_SNP [dm6]	A	C	1.966e^-5	0.945	UPSTREAM CG7686 DOWNSTREAM CG30015 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16872533	3L_16872533_SNP [dm3] 3L_16879433_SNP [dm6]	C	T	1.973e^-5	0.945	DOWNSTREAM CG32170 INTRON Lmpt
3R	11181742	3R_11181742_SNP [dm3] 3R_15356020_SNP [dm6]	C	T	2.034e^-5	0.945	SYNONYMOUS_CODING Atg4b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	11295413	2L_11295413_SNP [dm3] 2L_11295413_SNP [dm6]	C	A	2.442e^-5	0.945	INTERGENIC
X	15486296	X_15486296_INS [dm3] X_15592263_INS [dm6]	G	GAGG	2.448e^-5	0.945	INTRON CG9220	TF binding site BDTNP1_TFBS_dl
3L	12175390	3L_12175390_SNP [dm3] 3L_12182290_SNP [dm6]	T	C	2.475e^-5	0.945	SYNONYMOUS_CODING CAH2
2R	5801867	2R_5801867_SNP [dm3] 2R_9914362_SNP [dm6]	G	A	2.527e^-5	0.945	UTR_3_PRIME Mef2 DOWNSTREAM Etf-QO
3R	16005337	3R_16005337_INS [dm3] 3R_20179615_INS [dm6]	A	ATGTA	2.570e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_sbb
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	2.611e^-5	0.945	INTERGENIC
3R	15992223	3R_15992223_SNP [dm3] 3R_20166501_SNP [dm6]	A	G	2.617e^-5	0.945	INTERGENIC
3L	18820962	3L_18820962_SNP [dm3] 3L_18827862_SNP [dm6]	C	T	2.629e^-5	0.945	SYNONYMOUS_CODING Cat DOWNSTREAM Indy	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	17346119	X_17346119_SNP [dm3] X_17452086_SNP [dm6]	A	G	2.701e^-5	0.945	SYNONYMOUS_CODING CG8568
3L	10241531	3L_10241531_INS [dm3] 3L_10248431_INS [dm6]	C	CTTTTTTTGTT...	2.702e^-5	0.945	DOWNSTREAM CR44539 EXON CR44540
3R	9868203	3R_9868203_SNP [dm3] 3R_14042481_SNP [dm6]	G	C	2.757e^-5	0.945	INTERGENIC
3R	14856001	3R_14856001_SNP [dm3] 3R_19030279_SNP [dm6]	T	C	2.768e^-5	0.945	SYNONYMOUS_CODING Prp18 DOWNSTREAM P5cr	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	2.914e^-5	0.945	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	14239542	3R_14239542_INS [dm3] 3R_18413820_INS [dm6]	C	CCATCAGAAAAGTAAACTAG...	2.918e^-5	0.945	UPSTREAM CG31122 DOWNSTREAM fru INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	10712198	3L_10712198_SNP [dm3] 3L_10719098_SNP [dm6]	G	A	2.943e^-5	0.945	INTERGENIC
2L	8098939	2L_8098939_SNP [dm3] 2L_8098939_SNP [dm6]	T	C	3.039e^-5	0.945	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	16673300	3L_16673300_SNP [dm3] 3L_16680200_SNP [dm6]	G	A	3.062e^-5	0.945	INTRON Lasp & 1 other	TF binding site BDTNP1_TFBS_dl
3R	16005541	3R_16005541_SNP [dm3] 3R_20179819_SNP [dm6]	G	T	3.094e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	3.191e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	8115095	3L_8115095_SNP [dm3] 3L_8121995_SNP [dm6]	T	A	3.230e^-5	0.945	NON_SYNONYMOUS_CODING ldbr DOWNSTREAM msk	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
X	3136851	X_3136851_SNP [dm3] X_3242818_SNP [dm6]	G	C	3.249e^-5	0.945	UTR_3_PRIME ng1 UPSTREAM ng3 INTRON dnc
2L	11292363	2L_11292363_SNP [dm3] 2L_11292363_SNP [dm6]	G	A	3.367e^-5	0.945	INTERGENIC
3L	10287406	3L_10287406_SNP [dm3] 3L_10294306_SNP [dm6]	C	G	3.390e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17772302	2R_17772302_INS [dm3] 2R_21884797_INS [dm6]	A	AA	3.419e^-5	0.945	INTRON Fili	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20336420	2L_20336420_SNP [dm3] 2L_20336420_SNP [dm6]	G	A	3.521e^-5	0.945	INTRON spir
2L	4073253	2L_4073253_SNP [dm3] 2L_4073253_SNP [dm6]	C	G	3.674e^-5	0.945	INTRON ed
3R	12922495	3R_12922495_SNP [dm3] 3R_17096773_SNP [dm6]	A	G	3.774e^-5	0.945	INTRON cher
3L	16673400	3L_16673400_SNP [dm3] 3L_16680300_SNP [dm6]	G	A	3.879e^-5	0.945	INTRON Lasp & 1 other
3L	8895277	3L_8895277_SNP [dm3] 3L_8902177_SNP [dm6]	G	A	3.909e^-5	0.945	UPSTREAM TrpA1 INTRON TrpA1
2L	20331677	2L_20331677_SNP [dm3] 2L_20331677_SNP [dm6]	A	G	4.277e^-5	0.945	INTRON spir
2L	8113189	2L_8113189_SNP [dm3] 2L_8113189_SNP [dm6]	C	A	4.313e^-5	0.945	UTR_3_PRIME Bsg
3R	5307674	3R_5307674_SNP [dm3] 3R_9481952_SNP [dm6]	C	G	4.619e^-5	0.945	INTRON CG16779
3L	12478358	3L_12478358_SNP [dm3] 3L_12485258_SNP [dm6]	C	T	4.697e^-5	0.945	UPSTREAM CG33725 & 1 other INTRON CG33725	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5582697	X_5582697_SNP [dm3] X_5688664_SNP [dm6]	C	G	4.704e^-5	0.945	SYNONYMOUS_CODING CG3160	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	18531658	3R_18531658_SNP [dm3] 3R_22705936_SNP [dm6]	G	A	4.709e^-5	0.945	SYNONYMOUS_CODING CG13842
3L	3823377	3L_3823377_SNP [dm3] 3L_3823377_SNP [dm6]	T	C	4.755e^-5	0.945	INTRON enc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	11342771	3R_11342771_DEL [dm3] 3R_15517049_DEL [dm6]	TCTCCACAGACT...	T	4.803e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	26620810	3R_26620810_SNP [dm3] 3R_30795088_SNP [dm6]	C	T	4.970e^-5	0.945	INTRON wts	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	20587062	3L_20587062_SNP [dm3] 3L_20593962_SNP [dm6]	T	C	4.982e^-5	0.945	INTERGENIC
X	9507713	X_9507713_SNP [dm3] X_9613680_SNP [dm6]	C	G	5.065e^-5	0.945	INTRON CG42797
X	9507717	X_9507717_SNP [dm3] X_9613684_SNP [dm6]	T	G	5.065e^-5	0.945	INTRON CG42797
2L	8371537	2L_8371537_SNP [dm3] 2L_8371537_SNP [dm6]	T	A	5.109e^-5	0.945	UPSTREAM CR45341 & 1 other INTRON CG17292
2L	3238057	2L_3238057_SNP [dm3] 2L_3238057_SNP [dm6]	C	T	5.149e^-5	0.945	INTERGENIC
3R	13418787	3R_13418787_SNP [dm3] 3R_17593065_SNP [dm6]	A	T	5.154e^-5	0.945	INTERGENIC
2L	11296751	2L_11296751_SNP [dm3] 2L_11296751_SNP [dm6]	T	A	5.276e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3L	11804001	3L_11804001_SNP [dm3] 3L_11810901_SNP [dm6]	A	T	5.407e^-5	0.945	SYNONYMOUS_CODING CG42255
3R	25069064	3R_25069064_SNP [dm3] 3R_29243342_SNP [dm6]	A	G	5.411e^-5	0.945	INTRON CG31445
3R	25264539	3R_25264539_SNP [dm3] 3R_29438817_SNP [dm6]	T	A	5.413e^-5	0.945	INTRON Ptp99A
3R	25451580	3R_25451580_SNP [dm3] 3R_29625858_SNP [dm6]	C	A	5.433e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25451581	3R_25451581_SNP [dm3] 3R_29625859_SNP [dm6]	C	A	5.433e^-5	0.945	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	16794067	2L_16794067_SNP [dm3] 2L_16794067_SNP [dm6]	G	A	5.457e^-5	0.945	UPSTREAM Ugt36Ba DOWNSTREAM CG17928 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	16042681	2R_16042681_SNP [dm3] 2R_20155176_SNP [dm6]	C	A	5.472e^-5	0.945	INTERGENIC
2L	6488827	2L_6488827_SNP [dm3] 2L_6488827_SNP [dm6]	A	C	5.792e^-5	0.945	UPSTREAM epsilonCOP & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
X	6728895	X_6728895_SNP [dm3] X_6834862_SNP [dm6]	T	C	5.892e^-5	0.945	SYNONYMOUS_CODING nonC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	11472329	2R_11472329_SNP [dm3] 2R_15584824_SNP [dm6]	T	A	6.119e^-5	0.945	INTERGENIC
3R	11108010	3R_11108010_SNP [dm3] 3R_15282288_SNP [dm6]	A	G	6.154e^-5	0.945	INTRON Tm1	TF binding site mE1_TFBS_Trl
X	16160435	X_16160435_SNP [dm3] X_16266402_SNP [dm6]	A	G	6.213e^-5	0.945	SYNONYMOUS_CODING CG12507 DOWNSTREAM kat80
3L	9647191	3L_9647191_SNP [dm3] 3L_9654091_SNP [dm6]	G	C	6.215e^-5	0.945	INTRON fry & 1 other
2L	8353554	2L_8353554_SNP [dm3] 2L_8353554_SNP [dm6]	C	T	6.216e^-5	0.945	INTRON Mur29B	TF binding site mE1_TFBS_sens
X	18358953	X_18358953_SNP [dm3] X_18464920_SNP [dm6]	C	G	6.227e^-5	0.945	INTRON CG32547	TF binding site mE1_TFBS_chinmo
3R	25981552	3R_25981552_SNP [dm3] 3R_30155830_SNP [dm6]	G	T	6.409e^-5	0.945	SPLICE_SITE_REGION CG11498 INTRON CG11498	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8372336	2L_8372336_SNP [dm3] 2L_8372336_SNP [dm6]	C	A	6.429e^-5	0.945	UPSTREAM CG17292 INTRON CG17292
3L	14420567	3L_14420567_SNP [dm3] 3L_14427467_SNP [dm6]	C	T	6.455e^-5	0.945	UPSTREAM bbg INTRON bbg	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	8471071	X_8471071_SNP [dm3] X_8577038_SNP [dm6]	C	A	6.485e^-5	0.945	INTRON CG12065
3L	7395804	3L_7395804_SNP [dm3] 3L_7402704_SNP [dm6]	C	A	6.573e^-5	0.945	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	10047101	3R_10047101_SNP [dm3] 3R_14221379_SNP [dm6]	C	T	6.587e^-5	0.945	SYNONYMOUS_CODING CG33109 DOWNSTREAM Sp212
2L	11192334	2L_11192334_SNP [dm3] 2L_11192334_SNP [dm6]	T	A	6.617e^-5	0.945	INTRON Ca-beta
2R	5801871	2R_5801871_SNP [dm3] 2R_9914366_SNP [dm6]	T	C	6.649e^-5	0.945	UTR_3_PRIME Mef2 DOWNSTREAM Etf-QO
3R	26634046	3R_26634046_SNP [dm3] 3R_30808324_SNP [dm6]	G	T	6.678e^-5	0.945	UPSTREAM cindr DOWNSTREAM dj-1beta INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad
3R	12386148	3R_12386148_SNP [dm3] 3R_16560426_SNP [dm6]	C	G	6.691e^-5	0.945	INTRON CG42342	TF binding site BDTNP1_TFBS_twi
3L	7921417	3L_7921417_SNP [dm3] 3L_7928317_SNP [dm6]	G	T	6.797e^-5	0.945	SYNONYMOUS_CODING syd	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	20847874	X_20847874_SNP [dm3] X_20976847_SNP [dm6]	T	C	6.822e^-5	0.945	INTERGENIC
2L	13433604	2L_13433604_SNP [dm3] 2L_13433604_SNP [dm6]	G	C	7.004e^-5	0.945	INTRON CG42784
2L	1509860	2L_1509860_DEL [dm3] 2L_1509860_DEL [dm6]	TT	T	7.007e^-5	0.945	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_inv
2L	11292759	2L_11292759_SNP [dm3] 2L_11292759_SNP [dm6]	C	T	7.185e^-5	0.945	INTERGENIC
2R	5979670	2R_5979670_SNP [dm3] 2R_10092165_SNP [dm6]	C	T	7.208e^-5	0.945	INTRON CG2269
3L	12478303	3L_12478303_SNP [dm3] 3L_12485203_SNP [dm6]	G	T	7.232e^-5	0.945	UPSTREAM CG33725 & 1 other INTRON CG33725	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18889465	2R_18889465_SNP [dm3] 2R_23001942_SNP [dm6]	A	T	7.267e^-5	0.945	INTRON twi	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3R	25460307	3R_25460307_SNP [dm3] 3R_29634585_SNP [dm6]	T	C	7.338e^-5	0.945	INTRON Dop1R2

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By genomic position
Variant impact
Gene name

pc_Xanthomonadaceae phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results