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=2.002e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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
In_2L_t	4.7782	0.0917

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1061 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
X	11111178	X_11111178_SNP [dm3] X_11217145_SNP [dm6]	T	C	2.957e^-6	0.917	INTERGENIC
2R	8911925	2R_8911925_SNP [dm3] 2R_13024420_SNP [dm6]	A	G	4.192e^-6	0.917	INTERGENIC
3L	18492202	3L_18492202_SNP [dm3] 3L_18499102_SNP [dm6]	G	A	4.192e^-6	0.917	INTRON AstC-R2
2R	5427749	2R_5427749_SNP [dm3] 2R_9540244_SNP [dm6]	G	A	5.124e^-6	0.917	UTR_3_PRIME brp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14527380	3L_14527380_SNP [dm3] 3L_14534280_SNP [dm6]	G	C	6.915e^-6	0.917	INTRON bbg	TF binding site mE1_TFBS_Trl
2R	17436228	2R_17436228_SNP [dm3] 2R_21548723_SNP [dm6]	C	A	1.092e^-5	0.917	INTRON Egfr	TF binding site BDTNP1_TFBS_dl
2R	11844909	2R_11844909_SNP [dm3] 2R_15957404_SNP [dm6]	A	G	1.237e^-5	0.917	UPSTREAM Strn-Mlck DOWNSTREAM CG8366 INTRON Strn-Mlck	TF binding site mE1_TFBS_cad
2R	11844926	2R_11844926_SNP [dm3] 2R_15957421_SNP [dm6]	T	C	1.237e^-5	0.917	UPSTREAM Strn-Mlck DOWNSTREAM CG8366 INTRON Strn-Mlck	TF binding site mE1_TFBS_cad
2R	5444062	2R_5444062_SNP [dm3] 2R_9556557_SNP [dm6]	T	G	1.237e^-5	0.917	INTERGENIC
X	11111129	X_11111129_SNP [dm3] X_11217096_SNP [dm6]	T	C	1.343e^-5	0.917	INTERGENIC
2L	4794246	2L_4794246_SNP [dm3] 2L_4794246_SNP [dm6]	A	C	1.360e^-5	0.917	UPSTREAM CG3294 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	9620785	3L_9620785_SNP [dm3] 3L_9627685_SNP [dm6]	A	G	1.538e^-5	0.917	SPLICE_SITE_REGION Or67b UPSTREAM CG8336 DOWNSTREAM CG3335 INTRON Or67b
2L	21916487	2L_21916487_SNP [dm3] 2L_21916487_SNP [dm6]	T	A	1.624e^-5	0.917	NON_SYNONYMOUS_CODING CG11634
3L	4978489	3L_4978489_SNP [dm3] 3L_4978489_SNP [dm6]	A	G	1.716e^-5	0.917	INTRON Con
2R	11415155	2R_11415155_SNP [dm3] 2R_15527650_SNP [dm6]	C	T	1.945e^-5	0.917	SYNONYMOUS_CODING Khc-73	TF binding site BDTNP1_TFBS_dl
2R	11416422	2R_11416422_SNP [dm3] 2R_15528917_SNP [dm6]	T	C	1.945e^-5	0.917	INTRON Khc-73	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8911929	2R_8911929_SNP [dm3] 2R_13024424_SNP [dm6]	C	A	2.228e^-5	0.917	INTERGENIC
3R	15327713	3R_15327713_SNP [dm3] 3R_19501991_SNP [dm6]	G	T	2.228e^-5	0.917	INTRON Dys
3R	18328932	3R_18328932_SNP [dm3] 3R_22503210_SNP [dm6]	T	A	2.228e^-5	0.917	INTRON Octbeta1R
3R	25265193	3R_25265193_SNP [dm3] 3R_29439471_SNP [dm6]	A	T	2.228e^-5	0.917	INTRON Ptp99A
2L	7189211	2L_7189211_SNP [dm3] 2L_7189211_SNP [dm6]	G	C	2.324e^-5	0.917	INTRON CG4496	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	14268854	2R_14268854_SNP [dm3] 2R_18381349_SNP [dm6]	T	C	2.343e^-5	0.917	DOWNSTREAM CG43202 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	9444999	2R_9444999_SNP [dm3] 2R_13557494_SNP [dm6]	T	C	2.404e^-5	0.917	DOWNSTREAM snoRNA:Psi28S-1153 & 3 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	19973851	2R_19973851_SNP [dm3] 2R_24086328_SNP [dm6]	G	C	2.736e^-5	0.917	UPSTREAM snama DOWNSTREAM CG16786 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx
2R	5427731	2R_5427731_SNP [dm3] 2R_9540226_SNP [dm6]	G	T	3.030e^-5	0.917	UTR_3_PRIME brp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7956155	3L_7956155_SNP [dm3] 3L_7963055_SNP [dm6]	C	A	3.226e^-5	0.917	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	8913789	3L_8913789_SNP [dm3] 3L_8920689_SNP [dm6]	A	T	3.243e^-5	0.917	INTRON Tsp66E
3R	18704146	3R_18704146_SNP [dm3] 3R_22878424_SNP [dm6]	T	G	3.301e^-5	0.917	INTERGENIC	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	4978443	3L_4978443_SNP [dm3] 3L_4978443_SNP [dm6]	T	G	3.341e^-5	0.917	INTRON Con
2L	6566375	2L_6566375_SNP [dm3] 2L_6566375_SNP [dm6]	G	C	3.513e^-5	0.917	UPSTREAM CG13766 INTERGENIC
2L	6140895	2L_6140895_SNP [dm3] 2L_6140895_SNP [dm6]	C	T	3.568e^-5	0.917	SYNONYMOUS_CODING CG13991	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	6140901	2L_6140901_SNP [dm3] 2L_6140901_SNP [dm6]	G	T	3.568e^-5	0.917	SYNONYMOUS_CODING CG13991	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	20823341	3R_20823341_SNP [dm3] 3R_24997619_SNP [dm6]	G	A	3.730e^-5	0.917	INTRON tnc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	20391131	X_20391131_SNP [dm3] X_20520104_SNP [dm6]	T	G	3.730e^-5	0.917	INTRON Tak1
3L	3297604	3L_3297604_SNP [dm3] 3L_3297604_SNP [dm6]	C	T	3.912e^-5	0.917	SYNONYMOUS_CODING CG12009
2R	17599721	2R_17599721_SNP [dm3] 2R_21712216_SNP [dm6]	T	G	4.062e^-5	0.917	UPSTREAM CG30403 INTRON HmgD	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	3783026	3L_3783026_SNP [dm3] 3L_3783026_SNP [dm6]	C	A	4.242e^-5	0.917	INTRON CG32264	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	22848917	3R_22848917_SNP [dm3] 3R_27023195_SNP [dm6]	C	T	4.317e^-5	0.917	UTR_5_PRIME CG6277 INTRON RYa-R
3R	22848918	3R_22848918_SNP [dm3] 3R_27023196_SNP [dm6]	G	A	4.317e^-5	0.917	START_GAINED CG6277 UTR_5_PRIME CG6277 INTRON RYa-R
2R	11653566	2R_11653566_SNP [dm3] 2R_15766061_SNP [dm6]	T	G	4.449e^-5	0.917	SYNONYMOUS_CODING Zasp52 INTRON Zasp52	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	9832299	X_9832299_SNP [dm3] X_9938266_SNP [dm6]	G	T	4.540e^-5	0.917	INTERGENIC
X	9832310	X_9832310_SNP [dm3] X_9938277_SNP [dm6]	G	C	4.540e^-5	0.917	INTERGENIC
X	9832314	X_9832314_SNP [dm3] X_9938281_SNP [dm6]	G	T	4.540e^-5	0.917	INTERGENIC
2R	11423956	2R_11423956_SNP [dm3] 2R_15536451_SNP [dm6]	C	A	4.895e^-5	0.917	INTRON CG30471
X	14829020	X_14829020_SNP [dm3] X_14934987_SNP [dm6]	G	C	5.003e^-5	0.917	SYNONYMOUS_CODING pdgy	TF binding site mE1_TFBS_sens
2L	6567218	2L_6567218_SNP [dm3] 2L_6567218_SNP [dm6]	T	C	5.006e^-5	0.917	INTERGENIC
3R	22890521	3R_22890521_DEL [dm3] 3R_27064799_DEL [dm6]	AA	C	5.215e^-5	0.917	UPSTREAM Nep5 & 1 other DOWNSTREAM spz INTERGENIC
3R	9839233	3R_9839233_SNP [dm3] 3R_14013511_SNP [dm6]	A	C	5.334e^-5	0.917	INTRON rdx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	4135877	2R_4135877_SNP [dm3] 2R_8248372_SNP [dm6]	A	C	5.395e^-5	0.917	DOWNSTREAM CG44439 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni 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_D mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
X	20340275	X_20340275_SNP [dm3] X_20469248_SNP [dm6]	C	T	5.465e^-5	0.917	NON_SYNONYMOUS_CODING GstT3 DOWNSTREAM RhoGAP19D	TF binding site mE1_TFBS_HSA
2R	11418437	2R_11418437_SNP [dm3] 2R_15530932_SNP [dm6]	C	G	5.928e^-5	0.917	INTRON Khc-73	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	770261	2L_770261_SNP [dm3] 2L_770261_SNP [dm6]	C	T	5.993e^-5	0.917	INTERGENIC
3L	5820932	3L_5820932_SNP [dm3] 3L_5827832_SNP [dm6]	A	T	6.004e^-5	0.917	INTRON vn
2R	7403149	2R_7403149_SNP [dm3] 2R_11515644_SNP [dm6]	C	T	6.233e^-5	0.917	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	13941266	3L_13941266_SNP [dm3] 3L_13948166_SNP [dm6]	G	T	6.233e^-5	0.917	INTRON CG32137
3L	8124936	3L_8124936_SNP [dm3] 3L_8131836_SNP [dm6]	T	C	6.233e^-5	0.917	SYNONYMOUS_CODING CG7504 DOWNSTREAM CdsA
3L	8124987	3L_8124987_SNP [dm3] 3L_8131887_SNP [dm6]	T	A	6.233e^-5	0.917	NON_SYNONYMOUS_CODING CG7504 DOWNSTREAM CdsA
3R	26538524	3R_26538524_SNP [dm3] 3R_30712802_SNP [dm6]	C	T	6.425e^-5	0.917	INTERGENIC
3L	2431992	3L_2431992_SNP [dm3] 3L_2431992_SNP [dm6]	G	A	6.458e^-5	0.917	INTRON CG45186
3L	2619676	3L_2619676_SNP [dm3] 3L_2619676_SNP [dm6]	C	T	6.458e^-5	0.917	INTRON Pxn
3L	3453265	3L_3453265_SNP [dm3] 3L_3453265_SNP [dm6]	G	T	6.458e^-5	0.917	INTRON eIF5B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	17812630	3R_17812630_SNP [dm3] 3R_21986908_SNP [dm6]	T	C	6.633e^-5	0.917	INTRON Eip93F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	4292804	2L_4292804_INS [dm3] 2L_4292804_INS [dm6]	A	AA	6.753e^-5	0.917	INTRON tutl
2R	6228370	2R_6228370_SNP [dm3] 2R_10340865_SNP [dm6]	C	T	6.769e^-5	0.917	INTRON CG42732
2L	6558215	2L_6558215_SNP [dm3] 2L_6558215_SNP [dm6]	A	G	6.936e^-5	0.917	UPSTREAM Osm6 INTRON CoVb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	22894759	3R_22894759_SNP [dm3] 3R_27069037_SNP [dm6]	T	C	7.086e^-5	0.917	INTRON spz
3L	16257560	3L_16257560_SNP [dm3] 3L_16264460_SNP [dm6]	G	T	7.169e^-5	0.917	UPSTREAM CG13069 DOWNSTREAM CG13051 & 1 other INTERGENIC	TF binding site mE1_TFBS_inv
2R	17025724	2R_17025724_SNP [dm3] 2R_21138219_SNP [dm6]	G	C	7.171e^-5	0.917	SPLICE_SITE_REGION Magi INTRON Magi	TF binding site mE1_TFBS_chinmo
3L	3080579	3L_3080579_DEL [dm3] 3L_3080579_DEL [dm6]	ACGCGT	A	7.172e^-5	0.917	UPSTREAM CG11486 INTRON CG11486	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	3080587	3L_3080587_SNP [dm3] 3L_3080587_SNP [dm6]	G	T	7.172e^-5	0.917	UPSTREAM CG11486 INTRON CG11486	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	4978723	3L_4978723_SNP [dm3] 3L_4978723_SNP [dm6]	A	C	7.172e^-5	0.917	INTRON Con
3R	22727094	3R_22727094_SNP [dm3] 3R_26901372_SNP [dm6]	G	C	7.288e^-5	0.917	INTRON T48	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
3R	25321020	3R_25321020_SNP [dm3] 3R_29495298_SNP [dm6]	G	T	7.518e^-5	0.917	INTRON CG2010	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2L	18234409	2L_18234409_SNP [dm3] 2L_18234409_SNP [dm6]	C	A	7.743e^-5	0.917	INTRON CG42750
2L	7071872	2L_7071872_INS [dm3] 2L_7071872_INS [dm6]	G	GG	7.882e^-5	0.917	INTRON Pvf2
2R	10795398	2R_10795398_SNP [dm3] 2R_14907893_SNP [dm6]	A	G	8.207e^-5	0.917	UTR_5_PRIME CG10249 INTRON CG10249	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	5954596	2L_5954596_SNP [dm3] 2L_5954596_SNP [dm6]	G	T	8.348e^-5	0.917	NON_SYNONYMOUS_CODING CG9044 DOWNSTREAM CG13999	TF binding site mE1_TFBS_inv
2R	5648610	2R_5648610_SNP [dm3] 2R_9761105_SNP [dm6]	T	A	8.628e^-5	0.917	INTRON trpl
2R	5648613	2R_5648613_SNP [dm3] 2R_9761108_SNP [dm6]	A	T	8.628e^-5	0.917	INTRON trpl
2L	8496071	2L_8496071_SNP [dm3] 2L_8496071_SNP [dm6]	A	G	8.764e^-5	0.917	SYNONYMOUS_CODING Bace INTRON Dh31	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	8497308	2L_8497308_SNP [dm3] 2L_8497308_SNP [dm6]	C	T	8.764e^-5	0.917	INTRON Dh31
2L	8497327	2L_8497327_DEL [dm3] 2L_8497327_DEL [dm6]	AA	A	8.764e^-5	0.917	INTRON Dh31
2L	3750983	2L_3750983_SNP [dm3] 2L_3750983_SNP [dm6]	C	G	9.494e^-5	0.917	INTRON CG10019
2L	19936799	2L_19936799_SNP [dm3] 2L_19936799_SNP [dm6]	C	G	9.645e^-5	0.917	INTRON sick	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	11419011	2R_11419011_SNP [dm3] 2R_15531506_SNP [dm6]	A	G	9.718e^-5	0.917	INTRON Khc-73	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	9832281	X_9832281_SNP [dm3] X_9938248_SNP [dm6]	G	A	9.795e^-5	0.917	INTERGENIC
2R	14939481	2R_14939481_SNP [dm3] 2R_19051976_SNP [dm6]	C	T	9.865e^-5	0.917	INTERGENIC
X	6388208	X_6388208_SNP [dm3] X_6494175_SNP [dm6]	G	A	9.865e^-5	0.917	INTRON CG42340
2R	5427803	2R_5427803_DEL [dm3] 2R_9540298_DEL [dm6]	TTATG	T	1.005e^-4	0.917	UTR_3_PRIME brp	TF binding site BDTNP1_TFBS_dl
3L	10520198	3L_10520198_SNP [dm3] 3L_10527098_SNP [dm6]	G	A	1.007e^-4	0.917	INTRON A2bp1
2L	18234340	2L_18234340_SNP [dm3] 2L_18234340_SNP [dm6]	T	C	1.009e^-4	0.917	INTRON CG42750
2L	6559264	2L_6559264_INS [dm3] 2L_6559264_INS [dm6]	A	AT	1.024e^-4	0.917	UTR_3_PRIME CoVb UPSTREAM CG11043 DOWNSTREAM CG9596 & 1 other
2L	770067	2L_770067_INS [dm3] 2L_770067_INS [dm6]	T	TTACTAT	1.024e^-4	0.917	INTERGENIC
2L	770213	2L_770213_SNP [dm3] 2L_770213_SNP [dm6]	A	G	1.024e^-4	0.917	INTERGENIC
2L	770255	2L_770255_SNP [dm3] 2L_770255_SNP [dm6]	T	C	1.024e^-4	0.917	INTERGENIC
2L	770287	2L_770287_SNP [dm3] 2L_770287_SNP [dm6]	G	A	1.024e^-4	0.917	INTERGENIC
2R	18813149	2R_18813149_SNP [dm3] 2R_22925626_SNP [dm6]	G	A	1.026e^-4	0.917	UPSTREAM Nup214 & 1 other INTRON CG42678	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	18813162	2R_18813162_SNP [dm3] 2R_22925639_SNP [dm6]	G	A	1.026e^-4	0.917	UPSTREAM Nup214 & 1 other INTRON CG42678	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	18813170	2R_18813170_SNP [dm3] 2R_22925647_SNP [dm6]	C	A	1.026e^-4	0.917	UPSTREAM Nup214 & 1 other INTRON CG42678	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	14993536	3L_14993536_INS [dm3] 3L_15000436_INS [dm6]	A	AAAA	1.026e^-4	0.917	UPSTREAM mRpL39 DOWNSTREAM Reck INTRON Prosbeta2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA

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By genomic position
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MedianLS phenotype

Phenotype distribution and association to known covariates

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GWAS results