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=3.284e^-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	0.0179651

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1548 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	2.625e^-7	0.488	UPSTREAM CR45341 INTRON CG17292
3R	11181742	3R_11181742_SNP [dm3] 3R_15356020_SNP [dm6]	C	T	1.099e^-6	0.792	SYNONYMOUS_CODING Atg4b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	25264539	3R_25264539_SNP [dm3] 3R_29438817_SNP [dm6]	T	A	1.278e^-6	0.792	INTRON Ptp99A
3L	18820962	3L_18820962_SNP [dm3] 3L_18827862_SNP [dm6]	C	T	3.610e^-6	1	SYNONYMOUS_CODING Cat DOWNSTREAM Indy	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	25264633	3R_25264633_SNP [dm3] 3R_29438911_SNP [dm6]	T	C	4.206e^-6	1	INTRON Ptp99A
3R	25264625	3R_25264625_SNP [dm3] 3R_29438903_SNP [dm6]	A	C	5.768e^-6	1	INTRON Ptp99A
2L	11192334	2L_11192334_SNP [dm3] 2L_11192334_SNP [dm6]	T	A	8.315e^-6	1	INTRON Ca-beta
2R	7442907	2R_7442907_SNP [dm3] 2R_11555402_SNP [dm6]	T	C	1.013e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	2570058	2R_2570058_SNP [dm3] 2R_6682553_SNP [dm6]	C	T	1.018e^-5	1	UPSTREAM CG15909 DOWNSTREAM CR44164 INTRON CG9422 EXON CR44165
X	8471036	X_8471036_SNP [dm3] X_8577003_SNP [dm6]	G	T	1.045e^-5	1	INTRON CG12065
2L	8371537	2L_8371537_SNP [dm3] 2L_8371537_SNP [dm6]	T	A	1.156e^-5	1	UPSTREAM CR45341 & 1 other INTRON CG17292
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	1.192e^-5	1	INTERGENIC
2L	5381800	2L_5381800_SNP [dm3] 2L_5381800_SNP [dm6]	G	A	1.308e^-5	1	UPSTREAM CR42850 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	1.367e^-5	1	INTERGENIC
3L	12173728	3L_12173728_SNP [dm3] 3L_12180628_SNP [dm6]	T	C	1.416e^-5	1	INTRON CAH2
2L	21882791	2L_21882791_SNP [dm3] 2L_21882791_SNP [dm6]	G	C	1.465e^-5	1	INTERGENIC
3L	14420567	3L_14420567_SNP [dm3] 3L_14427467_SNP [dm6]	C	T	1.489e^-5	1	UPSTREAM bbg INTRON bbg	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	11303552	3L_11303552_SNP [dm3] 3L_11310452_SNP [dm6]	T	C	1.518e^-5	1	INTERGENIC
2L	11192164	2L_11192164_SNP [dm3] 2L_11192164_SNP [dm6]	A	G	1.881e^-5	1	INTRON Ca-beta
2L	3850703	2L_3850703_SNP [dm3] 2L_3850703_SNP [dm6]	A	T	2.009e^-5	1	INTERGENIC
2L	8370140	2L_8370140_SNP [dm3] 2L_8370140_SNP [dm6]	C	T	2.101e^-5	1	UPSTREAM CG17292 DOWNSTREAM CR45341 & 1 other INTERGENIC
2L	15759696	2L_15759696_SNP [dm3] 2L_15759696_SNP [dm6]	G	A	2.127e^-5	1	SYNONYMOUS_CODING Gli	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9646792	3L_9646792_SNP [dm3] 3L_9653692_SNP [dm6]	T	C	2.251e^-5	1	INTRON fry & 1 other
2L	20124924	2L_20124924_SNP [dm3] 2L_20124924_SNP [dm6]	A	G	2.253e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	5417071	3L_5417071_SNP [dm3] 3L_5423971_SNP [dm6]	A	G	2.311e^-5	1	UPSTREAM CG34391 INTERGENIC
3R	13569252	3R_13569252_SNP [dm3] 3R_17743530_SNP [dm6]	G	A	2.328e^-5	1	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	6555381	2R_6555381_SNP [dm3] 2R_10667876_SNP [dm6]	C	T	2.355e^-5	1	INTERGENIC
2R	16764707	2R_16764707_SNP [dm3] 2R_20877202_SNP [dm6]	A	T	2.631e^-5	1	INTRON Ipk1
3L	12194708	3L_12194708_SNP [dm3] 3L_12201608_SNP [dm6]	T	C	2.894e^-5	1	INTRON Adk1
2R	6726485	2R_6726485_SNP [dm3] 2R_10838980_SNP [dm6]	A	C	2.949e^-5	1	UPSTREAM CG7686 DOWNSTREAM CG30015 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8471345	X_8471345_SNP [dm3] X_8577312_SNP [dm6]	C	T	2.979e^-5	1	INTRON CG12065
X	8471356	X_8471356_SNP [dm3] X_8577323_SNP [dm6]	A	T	2.979e^-5	1	INTRON CG12065
2L	8372336	2L_8372336_SNP [dm3] 2L_8372336_SNP [dm6]	C	A	3.090e^-5	1	UPSTREAM CG17292 INTRON CG17292
2L	8398451	2L_8398451_DEL [dm3] 2L_8398451_DEL [dm6]	CAATAC	C	3.162e^-5	1	UPSTREAM CG13386 DOWNSTREAM CG13385 INTERGENIC
2R	13568808	2R_13568808_SNP [dm3] 2R_17681303_SNP [dm6]	T	C	3.174e^-5	1	INTRON Sema-1b	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2L	10030079	2L_10030079_SNP [dm3] 2L_10030079_SNP [dm6]	T	C	3.278e^-5	1	DOWNSTREAM CG13127 INTERGENIC
X	13768849	X_13768849_SNP [dm3] X_13874816_SNP [dm6]	T	A	3.284e^-5	1	INTRON mamo
X	15563687	X_15563687_SNP [dm3] X_15669654_SNP [dm6]	C	T	3.291e^-5	1	UTR_5_PRIME CG15646 INTRON CG15646	TF binding site BDTNP1_TFBS_dl
2L	5381702	2L_5381702_INS [dm3] 2L_5381702_INS [dm6]	A	AGCCA	3.424e^-5	1	UPSTREAM CR42850 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	3.452e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	9973092	3R_9973092_SNP [dm3] 3R_14147370_SNP [dm6]	A	T	3.658e^-5	1	INTERGENIC
2L	8367595	2L_8367595_SNP [dm3] 2L_8367595_SNP [dm6]	G	A	3.671e^-5	1	SYNONYMOUS_CODING Pp2A-29B	TF binding site mE1_TFBS_cad
2L	8370098	2L_8370098_SNP [dm3] 2L_8370098_SNP [dm6]	A	T	3.712e^-5	1	UPSTREAM CG17292 DOWNSTREAM CR45341 & 1 other INTERGENIC
2R	13385678	2R_13385678_SNP [dm3] 2R_17498173_SNP [dm6]	G	A	3.767e^-5	1	INTERGENIC
2R	10796875	2R_10796875_SNP [dm3] 2R_14909370_SNP [dm6]	C	A	3.851e^-5	1	INTRON CG10249
3L	14420578	3L_14420578_SNP [dm3] 3L_14427478_SNP [dm6]	G	A	3.990e^-5	1	UPSTREAM bbg INTRON bbg	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	10287406	3L_10287406_SNP [dm3] 3L_10294306_SNP [dm6]	C	G	4.006e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10030169	2L_10030169_SNP [dm3] 2L_10030169_SNP [dm6]	C	T	4.068e^-5	1	DOWNSTREAM CG13127 INTERGENIC
2L	8370131	2L_8370131_SNP [dm3] 2L_8370131_SNP [dm6]	T	A	4.112e^-5	1	UPSTREAM CG17292 DOWNSTREAM CR45341 & 1 other INTERGENIC
2L	8370138	2L_8370138_SNP [dm3] 2L_8370138_SNP [dm6]	C	G	4.112e^-5	1	UPSTREAM CG17292 DOWNSTREAM CR45341 & 1 other INTERGENIC
X	3875217	X_3875217_SNP [dm3] X_3981184_SNP [dm6]	G	C	4.332e^-5	1	INTERGENIC
2L	5261010	2L_5261010_SNP [dm3] 2L_5261010_SNP [dm6]	G	A	4.347e^-5	1	INTRON tkv
2L	3238057	2L_3238057_SNP [dm3] 2L_3238057_SNP [dm6]	C	T	4.512e^-5	1	INTERGENIC
2L	6488827	2L_6488827_SNP [dm3] 2L_6488827_SNP [dm6]	A	C	4.877e^-5	1	UPSTREAM epsilonCOP & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	15709360	3R_15709360_SNP [dm3] 3R_19883638_SNP [dm6]	C	T	5.004e^-5	1	SYNONYMOUS_CODING Pk92B	TF binding site mE1_TFBS_cad
3R	25451580	3R_25451580_SNP [dm3] 3R_29625858_SNP [dm6]	C	A	5.030e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25451581	3R_25451581_SNP [dm3] 3R_29625859_SNP [dm6]	C	A	5.030e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	16872533	3L_16872533_SNP [dm3] 3L_16879433_SNP [dm6]	C	T	5.102e^-5	1	DOWNSTREAM CG32170 INTRON Lmpt
2L	17797068	2L_17797068_SNP [dm3] 2L_17797068_SNP [dm6]	T	A	5.140e^-5	1	INTRON CadN2
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	5.237e^-5	1	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13380619	2R_13380619_SNP [dm3] 2R_17493114_SNP [dm6]	C	T	5.401e^-5	1	UTR_3_PRIME NT5E-2 UPSTREAM CG30103	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA
2R	14617661	2R_14617661_SNP [dm3] 2R_18730156_SNP [dm6]	A	G	5.447e^-5	1	SYNONYMOUS_CODING List INTRON Hs3st-A
3L	5229784	3L_5229784_SNP [dm3] 3L_5236684_SNP [dm6]	A	T	5.821e^-5	1	DOWNSTREAM CG4669 INTRON shep
3R	12896174	3R_12896174_SNP [dm3] 3R_17070452_SNP [dm6]	A	G	6.032e^-5	1	DOWNSTREAM Ns1 & 1 other INTERGENIC
3L	7497052	3L_7497052_SNP [dm3] 3L_7503952_SNP [dm6]	A	T	6.116e^-5	1	INTERGENIC
3L	16673300	3L_16673300_SNP [dm3] 3L_16680200_SNP [dm6]	G	A	6.157e^-5	1	INTRON Lasp & 1 other	TF binding site BDTNP1_TFBS_dl
3R	14239542	3R_14239542_INS [dm3] 3R_18413820_INS [dm6]	C	CCATCAGAAAAGTAAACTAG...	6.202e^-5	1	UPSTREAM CG31122 DOWNSTREAM fru INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	9868203	3R_9868203_SNP [dm3] 3R_14042481_SNP [dm6]	G	C	6.301e^-5	1	INTERGENIC
3R	18686709	3R_18686709_SNP [dm3] 3R_22860987_SNP [dm6]	G	A	6.335e^-5	1	INTERGENIC
2L	17797674	2L_17797674_SNP [dm3] 2L_17797674_SNP [dm6]	T	G	6.380e^-5	1	SYNONYMOUS_CODING CadN2
2L	3605590	2L_3605590_SNP [dm3] 2L_3605590_SNP [dm6]	G	A	6.425e^-5	1	SYNONYMOUS_CODING odd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	8471071	X_8471071_SNP [dm3] X_8577038_SNP [dm6]	C	A	6.458e^-5	1	INTRON CG12065
2R	19106397	2R_19106397_SNP [dm3] 2R_23218874_SNP [dm6]	T	C	6.476e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	18510730	2L_18510730_SNP [dm3] 2L_18510730_SNP [dm6]	G	T	6.542e^-5	1	INTRON CG10178
2R	5075321	2R_5075321_SNP [dm3] 2R_9187816_SNP [dm6]	A	T	7.032e^-5	1	UTR_3_PRIME CG8026 & 1 other INTRON CG8026 & 1 other
2L	17797240	2L_17797240_SNP [dm3] 2L_17797240_SNP [dm6]	C	A	7.047e^-5	1	INTRON CadN2
2R	2882279	2R_2882279_SNP [dm3] 2R_6994774_SNP [dm6]	T	C	7.086e^-5	1	DOWNSTREAM CG30159 INTRON Tsp42Ea	TF binding site mE1_TFBS_Trl
3R	14043969	3R_14043969_SNP [dm3] 3R_18218247_SNP [dm6]	C	A	7.088e^-5	1	UTR_3_PRIME CG7183 DOWNSTREAM CG14314
X	5582697	X_5582697_SNP [dm3] X_5688664_SNP [dm6]	C	G	7.231e^-5	1	SYNONYMOUS_CODING CG3160	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	25264775	3R_25264775_SNP [dm3] 3R_29439053_SNP [dm6]	A	G	7.253e^-5	1	INTRON Ptp99A
X	3136845	X_3136845_SNP [dm3] X_3242812_SNP [dm6]	A	G	7.261e^-5	1	UTR_3_PRIME ng1 UPSTREAM ng3 INTRON dnc
X	18358953	X_18358953_SNP [dm3] X_18464920_SNP [dm6]	C	G	7.283e^-5	1	INTRON CG32547	TF binding site mE1_TFBS_chinmo
3R	17689923	3R_17689923_SNP [dm3] 3R_21864201_SNP [dm6]	G	A	7.322e^-5	1	UPSTREAM lsn INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11308479	2L_11308479_INS [dm3] 2L_11308479_INS [dm6]	G	GG	7.332e^-5	1	DOWNSTREAM CR43721 INTERGENIC
2L	17936426	2L_17936426_SNP [dm3] 2L_17936426_SNP [dm6]	T	C	7.580e^-5	1	INTERGENIC
3L	7732289	3L_7732289_SNP [dm3] 3L_7739189_SNP [dm6]	C	T	7.677e^-5	1	INTRON CG32373 & 1 other
2L	1510210	2L_1510210_SNP [dm3] 2L_1510210_SNP [dm6]	T	C	7.690e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	18823274	3L_18823274_SNP [dm3] 3L_18830174_SNP [dm6]	G	A	7.906e^-5	1	INTRON Indy	TF binding site mE1_TFBS_inv
2L	4187058	2L_4187058_SNP [dm3] 2L_4187058_SNP [dm6]	C	T	8.093e^-5	1	SYNONYMOUS_CODING CG31961 DOWNSTREAM CR44057	TF binding site mE1_TFBS_sens
3R	26199432	3R_26199432_SNP [dm3] 3R_30373710_SNP [dm6]	G	A	8.187e^-5	1	INTERGENIC
2R	17866839	2R_17866839_SNP [dm3] 2R_21979334_SNP [dm6]	T	C	8.187e^-5	1	SYNONYMOUS_CODING Gr58b UPSTREAM Gr58a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	12904883	3R_12904883_SNP [dm3] 3R_17079161_SNP [dm6]	A	G	8.268e^-5	1	INTRON Keap1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_Trl mE1_TFBS_zfh1
3L	7403072	3L_7403072_SNP [dm3] 3L_7409972_SNP [dm6]	G	T	8.409e^-5	1	UPSTREAM CR44525 INTERGENIC
2L	4807215	2L_4807215_SNP [dm3] 2L_4807215_SNP [dm6]	G	A	8.437e^-5	1	INTERGENIC
3L	8895277	3L_8895277_SNP [dm3] 3L_8902177_SNP [dm6]	G	A	8.506e^-5	1	UPSTREAM TrpA1 INTRON TrpA1
2R	5801867	2R_5801867_SNP [dm3] 2R_9914362_SNP [dm6]	G	A	8.560e^-5	1	UTR_3_PRIME Mef2 DOWNSTREAM Etf-QO
X	8471487	X_8471487_SNP [dm3] X_8577454_SNP [dm6]	G	T	8.801e^-5	1	INTRON CG12065
3L	18824273	3L_18824273_SNP [dm3] 3L_18831173_SNP [dm6]	G	A	8.804e^-5	1	SYNONYMOUS_CODING Indy	TF binding site mE1_TFBS_cad
X	13696983	X_13696983_SNP [dm3] X_13802950_SNP [dm6]	C	T	8.812e^-5	1	SYNONYMOUS_CODING inaE
3L	2559730	3L_2559730_SNP [dm3] 3L_2559730_SNP [dm6]	C	T	8.824e^-5	1	INTRON msn

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By genomic position
Variant impact
Gene name

pc_Comamonadaceae phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results