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=1.108e^-8)
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	0.04816

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	8.108	0.0174

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2154 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	10497741	2L_10497741_SNP [dm3] 2L_10497741_SNP [dm6]	T	A	2.989e^-7	0.384	INTRON Myo31DF
3R	17404507	3R_17404507_SNP [dm3] 3R_21578785_SNP [dm6]	C	G	4.094e^-7	0.384	INTRON InR	TF binding site mE1_TFBS_sens
2L	4207638	2L_4207638_SNP [dm3] 2L_4207638_SNP [dm6]	T	C	6.550e^-7	0.385	SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	17404450	3R_17404450_SNP [dm3] 3R_21578728_SNP [dm6]	T	C	8.215e^-7	0.385	SPLICE_SITE_REGION InR SYNONYMOUS_CODING InR	TF binding site mE1_TFBS_sens
3L	10159369	3L_10159369_SNP [dm3] 3L_10166269_SNP [dm6]	C	T	1.390e^-6	0.463	SYNONYMOUS_CODING CG6628 INTRON dpr10
2L	4998127	2L_4998127_SNP [dm3] 2L_4998127_SNP [dm6]	G	C	2.096e^-6	0.463	UPSTREAM Rtnl1 INTRON Rtnl1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
3R	13893798	3R_13893798_INS [dm3] 3R_18068076_INS [dm6]	A	AA	2.109e^-6	0.463	INTERGENIC
3L	10159375	3L_10159375_SNP [dm3] 3L_10166275_SNP [dm6]	G	A	2.299e^-6	0.463	SYNONYMOUS_CODING CG6628 INTRON dpr10
3L	16660767	3L_16660767_SNP [dm3] 3L_16667667_SNP [dm6]	T	C	2.485e^-6	0.463	UTR_5_PRIME Galphaf	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	7869451	2L_7869451_SNP [dm3] 2L_7869451_SNP [dm6]	C	T	2.888e^-6	0.463	INTRON Proc
3R	17406267	3R_17406267_INS [dm3] 3R_21580545_INS [dm6]	T	TTCT	3.420e^-6	0.463	UTR_5_PRIME InR	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens
3R	17404580	3R_17404580_SNP [dm3] 3R_21578858_SNP [dm6]	A	G	4.320e^-6	0.463	SYNONYMOUS_CODING InR	TF binding site mE1_TFBS_sens
3R	9497020	3R_9497020_SNP [dm3] 3R_13671298_SNP [dm6]	G	T	4.437e^-6	0.463	SPLICE_SITE_REGION Task6 INTRON Task6	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18799941	2R_18799941_SNP [dm3] 2R_22912418_SNP [dm6]	C	G	4.740e^-6	0.463	NON_SYNONYMOUS_CODING nahoda SPLICE_SITE_REGION nahoda	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2R	18787514	2R_18787514_SNP [dm3] 2R_22899991_SNP [dm6]	C	T	4.884e^-6	0.463	INTRON nahoda
2R	20166819	2R_20166819_SNP [dm3] 2R_24279296_SNP [dm6]	T	C	4.969e^-6	0.463	INTRON nvy	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
3R	17384407	3R_17384407_SNP [dm3] 3R_21558685_SNP [dm6]	C	A	5.625e^-6	0.463	INTERGENIC	regulatory region FlyBase TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
3R	6352463	3R_6352463_SNP [dm3] 3R_10526741_SNP [dm6]	T	A	5.646e^-6	0.463	INTRON hth
3L	21558474	3L_21558474_SNP [dm3] 3L_21565374_SNP [dm6]	A	G	5.721e^-6	0.463	UPSTREAM CG7634 INTERGENIC
2R	19150426	2R_19150426_SNP [dm3] 2R_23262903_SNP [dm6]	T	C	5.951e^-6	0.463	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	3561531	2L_3561531_SNP [dm3] 2L_3561531_SNP [dm6]	T	A	6.258e^-6	0.463	UPSTREAM CR44309 INTERGENIC	TF binding site mE1_TFBS_HSA
X	7489757	X_7489757_SNP [dm3] X_7595724_SNP [dm6]	C	T	6.429e^-6	0.463	INTERGENIC	regulatory region REDfly_CRMs
2R	14133827	2R_14133827_INS [dm3] 2R_18246322_INS [dm6]	A	AA	6.598e^-6	0.463	EXON CR44420	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
2R	18800503	2R_18800503_SNP [dm3] 2R_22912980_SNP [dm6]	A	G	6.636e^-6	0.463	INTRON nahoda	TF binding site mE1_TFBS_HSA
X	19250301	X_19250301_SNP [dm3] X_19356268_SNP [dm6]	C	A	6.683e^-6	0.463	INTRON kek5
3L	5860166	3L_5860166_SNP [dm3] 3L_5867066_SNP [dm6]	G	C	6.824e^-6	0.463	INTERGENIC
3R	17404429	3R_17404429_SNP [dm3] 3R_21578707_SNP [dm6]	A	G	6.956e^-6	0.463	SYNONYMOUS_CODING InR	TF binding site mE1_TFBS_sens
2R	6246394	2R_6246394_SNP [dm3] 2R_10358889_SNP [dm6]	G	C	7.720e^-6	0.463	INTRON CG42732
2L	4780253	2L_4780253_DEL [dm3] 2L_4780253_DEL [dm6]	TA	T	7.802e^-6	0.463	INTRON CG15630
2R	16868203	2R_16868203_SNP [dm3] 2R_20980698_SNP [dm6]	A	C	8.257e^-6	0.463	INTRON CG9313
2R	14133830	2R_14133830_SNP [dm3] 2R_18246325_SNP [dm6]	C	T	8.603e^-6	0.463	EXON CR44420	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
2R	8983447	2R_8983447_SNP [dm3] 2R_13095942_SNP [dm6]	C	T	8.801e^-6	0.463	INTERGENIC	TF binding site mE1_TFBS_inv
2L	7574530	2L_7574530_DEL [dm3] 2L_7574530_DEL [dm6]	TG	T	9.060e^-6	0.463	INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl
2R	18786360	2R_18786360_SNP [dm3] 2R_22898837_SNP [dm6]	G	A	9.203e^-6	0.463	INTRON nahoda
3R	17410863	3R_17410863_SNP [dm3] 3R_21585141_SNP [dm6]	T	C	9.258e^-6	0.463	INTRON InR
2L	4035769	2L_4035769_SNP [dm3] 2L_4035769_SNP [dm6]	C	T	9.295e^-6	0.463	INTRON ed	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi
3R	13893801	3R_13893801_SNP [dm3] 3R_18068079_SNP [dm6]	A	G	9.733e^-6	0.463	INTERGENIC
2R	18017568	2R_18017568_SNP [dm3] 2R_22130063_SNP [dm6]	A	G	9.841e^-6	0.463	NON_SYNONYMOUS_CODING NtR DOWNSTREAM CG34205	TF binding site BDTNP1_TFBS_twi
3L	9614760	3L_9614760_SNP [dm3] 3L_9621660_SNP [dm6]	C	T	9.955e^-6	0.463	SYNONYMOUS_CODING LanB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	9975423	3L_9975423_SNP [dm3] 3L_9982323_SNP [dm6]	A	T	1.007e^-5	0.463	INTRON dpr6
3R	4224974	3R_4224974_SNP [dm3] 3R_8399252_SNP [dm6]	G	T	1.026e^-5	0.463	INTRON CG45263
3L	20565475	3L_20565475_SNP [dm3] 3L_20572375_SNP [dm6]	A	T	1.069e^-5	0.463	INTERGENIC
3L	1440946	3L_1440946_SNP [dm3] 3L_1440946_SNP [dm6]	C	A	1.086e^-5	0.463	INTRON Ptp61F	TF binding site mE1_TFBS_chinmo
3R	22328693	3R_22328693_SNP [dm3] 3R_26502971_SNP [dm6]	A	G	1.087e^-5	0.463	INTRON plum	TF binding site BDTNP1_TFBS_dl
3L	9975407	3L_9975407_SNP [dm3] 3L_9982307_SNP [dm6]	A	T	1.134e^-5	0.472	INTRON dpr6
2L	16412293	2L_16412293_SNP [dm3] 2L_16412293_SNP [dm6]	T	C	1.159e^-5	0.472	INTRON CG5888	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	9975413	3L_9975413_SNP [dm3] 3L_9982313_SNP [dm6]	C	T	1.210e^-5	0.483	INTRON dpr6
2L	16412374	2L_16412374_SNP [dm3] 2L_16412374_SNP [dm6]	T	A	1.244e^-5	0.486	INTRON CG5888	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
X	9412556	X_9412556_SNP [dm3] X_9518523_SNP [dm6]	A	T	1.280e^-5	0.49	INTRON CG32700	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	20565303	3L_20565303_SNP [dm3] 3L_20572203_SNP [dm6]	A	G	1.370e^-5	0.5	INTERGENIC
X	7489758	X_7489758_SNP [dm3] X_7595725_SNP [dm6]	A	G	1.388e^-5	0.5	INTERGENIC	regulatory region REDfly_CRMs
3R	17406239	3R_17406239_SNP [dm3] 3R_21580517_SNP [dm6]	C	T	1.411e^-5	0.5	UTR_5_PRIME InR	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens
2R	19150480	2R_19150480_INS [dm3] 2R_23262957_INS [dm6]	T	TGTATGATATGACTTGATAT...	1.423e^-5	0.5	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	9615168	3L_9615168_SNP [dm3] 3L_9622068_SNP [dm6]	G	C	1.439e^-5	0.5	SYNONYMOUS_CODING LanB2	TF binding site mE1_TFBS_cad
3L	20565474	3L_20565474_SNP [dm3] 3L_20572374_SNP [dm6]	A	T	1.492e^-5	0.501	INTERGENIC
3L	12162331	3L_12162331_SNP [dm3] 3L_12169231_SNP [dm6]	G	A	1.495e^-5	0.501	INTRON Rh7
2R	18787138	2R_18787138_SNP [dm3] 2R_22899615_SNP [dm6]	C	A	1.546e^-5	0.508	INTRON nahoda
3R	15246849	3R_15246849_SNP [dm3] 3R_19421127_SNP [dm6]	T	G	1.570e^-5	0.508	INTRON CG31221
2R	14514286	2R_14514286_SNP [dm3] 2R_18626781_SNP [dm6]	G	C	1.597e^-5	0.508	SYNONYMOUS_CODING Sec6	TF binding site mE1_TFBS_sens
2L	12247709	2L_12247709_SNP [dm3] 2L_12247709_SNP [dm6]	G	A	1.660e^-5	0.519	INTRON aret
3L	14589912	3L_14589912_SNP [dm3] 3L_14596812_SNP [dm6]	A	C	1.760e^-5	0.541	INTRON HGTX
2R	17642560	2R_17642560_SNP [dm3] 2R_21755055_SNP [dm6]	A	G	1.847e^-5	0.559	INTERGENIC
X	9882411	X_9882411_SNP [dm3] X_9988378_SNP [dm6]	G	A	1.918e^-5	0.571	INTERGENIC
3L	9735159	3L_9735159_SNP [dm3] 3L_9742059_SNP [dm6]	T	A	1.948e^-5	0.571	INTRON CG42268 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	4780274	2L_4780274_SNP [dm3] 2L_4780274_SNP [dm6]	A	T	2.009e^-5	0.58	INTRON CG15630
2L	1652315	2L_1652315_SNP [dm3] 2L_1652315_SNP [dm6]	A	C	2.061e^-5	0.586	INTRON chinmo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	2249279	X_2249279_SNP [dm3] X_2355246_SNP [dm6]	G	T	2.175e^-5	0.609	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl
2L	14094913	2L_14094913_SNP [dm3] 2L_14094913_SNP [dm6]	A	T	2.211e^-5	0.61	DOWNSTREAM nAChRalpha5 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	16442765	3R_16442765_SNP [dm3] 3R_20617043_SNP [dm6]	G	A	2.308e^-5	0.625	UPSTREAM CG5466 & 1 other INTERGENIC
X	7490704	X_7490704_SNP [dm3] X_7596671_SNP [dm6]	T	A	2.333e^-5	0.625	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2L	16412297	2L_16412297_INS [dm3] 2L_16412297_INS [dm6]	C	CC	2.464e^-5	0.627	INTRON CG5888	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	3237774	2L_3237774_SNP [dm3] 2L_3237774_SNP [dm6]	A	G	2.467e^-5	0.627	INTERGENIC
X	11237885	X_11237885_SNP [dm3] X_11343852_SNP [dm6]	G	A	2.473e^-5	0.627	SYNONYMOUS_CODING CG34348 DOWNSTREAM CG1597	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	9960959	3L_9960959_SNP [dm3] 3L_9967859_SNP [dm6]	T	C	2.475e^-5	0.627	NON_SYNONYMOUS_CODING CG6685 UPSTREAM Nc DOWNSTREAM CG34356	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk mE1_TFBS_Ubx
X	7489608	X_7489608_DEL [dm3] X_7595575_DEL [dm6]	CTCGGCTACCTTTTCAC...	C	2.563e^-5	0.637	INTERGENIC	regulatory region REDfly_CRMs
X	7745874	X_7745874_SNP [dm3] X_7851841_SNP [dm6]	G	A	2.596e^-5	0.637	DOWNSTREAM CG10920 INTERGENIC
X	17834681	X_17834681_INS [dm3] X_17940648_INS [dm6]	T	TTGT	2.645e^-5	0.637	INTRON Sh	TF binding site BDTNP1_TFBS_dl
X	20891019	X_20891019_SNP [dm3] X_21019992_SNP [dm6]	C	T	2.648e^-5	0.637	INTERGENIC
X	9829149	X_9829149_SNP [dm3] X_9935116_SNP [dm6]	G	A	2.685e^-5	0.638	INTERGENIC
2L	5715442	2L_5715442_SNP [dm3] 2L_5715442_SNP [dm6]	G	T	2.833e^-5	0.66	UTR_3_PRIME CG14007 UPSTREAM CR44818
2L	9995390	2L_9995390_SNP [dm3] 2L_9995390_SNP [dm6]	A	C	2.851e^-5	0.66	UTR_3_PRIME bib DOWNSTREAM CG31875	TF binding site BDTNP1_TFBS_dl
2R	20217082	2R_20217082_SNP [dm3] 2R_24329559_SNP [dm6]	T	A	2.915e^-5	0.665	UPSTREAM CR44810 INTRON CR44810 EXON CR44810	TF binding site mE1_TFBS_Trl
X	2585010	X_2585010_SNP [dm3] X_2690977_SNP [dm6]	C	A	3.003e^-5	0.665	SYNONYMOUS_CODING per	TF binding site mE1_TFBS_chinmo
3R	22791079	3R_22791079_SNP [dm3] 3R_26965357_SNP [dm6]	T	C	3.021e^-5	0.665	SYNONYMOUS_CODING Gr97a UPSTREAM Tsp97E	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	9829148	X_9829148_SNP [dm3] X_9935115_SNP [dm6]	G	A	3.024e^-5	0.665	INTERGENIC
3R	10604825	3R_10604825_SNP [dm3] 3R_14779103_SNP [dm6]	T	A	3.094e^-5	0.665	INTRON jvl
X	9829172	X_9829172_DEL [dm3] X_9935139_DEL [dm6]	AA	A	3.126e^-5	0.665	INTERGENIC
X	7489241	X_7489241_SNP [dm3] X_7595208_SNP [dm6]	G	T	3.127e^-5	0.665	INTERGENIC	regulatory region REDfly_CRMs
3R	17410898	3R_17410898_SNP [dm3] 3R_21585176_SNP [dm6]	A	G	3.278e^-5	0.665	INTRON InR
3R	17409538	3R_17409538_SNP [dm3] 3R_21583816_SNP [dm6]	C	T	3.328e^-5	0.665	INTRON InR	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	15969017	3R_15969017_SNP [dm3] 3R_20143295_SNP [dm6]	T	G	3.334e^-5	0.665	INTERGENIC
2R	20336548	2R_20336548_SNP [dm3] 2R_24449025_SNP [dm6]	A	C	3.368e^-5	0.665	INTERGENIC
2L	13034019	2L_13034019_SNP [dm3] 2L_13034019_SNP [dm6]	T	A	3.456e^-5	0.665	INTRON CG9932
3L	16665669	3L_16665669_SNP [dm3] 3L_16672569_SNP [dm6]	T	A	3.486e^-5	0.665	INTRON zetaCOP
X	9829126	X_9829126_SNP [dm3] X_9935093_SNP [dm6]	T	C	3.539e^-5	0.665	INTERGENIC
3L	10045669	3L_10045669_SNP [dm3] 3L_10052569_SNP [dm6]	G	A	3.550e^-5	0.665	INTRON dpr6
3R	17408208	3R_17408208_SNP [dm3] 3R_21582486_SNP [dm6]	C	A	3.564e^-5	0.665	INTRON InR	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	18786124	2R_18786124_SNP [dm3] 2R_22898601_SNP [dm6]	C	T	3.591e^-5	0.665	INTRON nahoda
2R	20161452	2R_20161452_SNP [dm3] 2R_24273929_SNP [dm6]	C	T	3.622e^-5	0.665	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_chinmo
2R	16732163	2R_16732163_SNP [dm3] 2R_20844658_SNP [dm6]	G	A	3.639e^-5	0.665	INTERGENIC

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By genomic position
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SE phenotype

Phenotype distribution and association to known covariates

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GWAS results