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=6.541e^-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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1963 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
3R	15012988	3R_15012988_INS [dm3] 3R_19187266_INS [dm6]	C	GCTCT	1.879e^-6	0.943	INTRON CG31475	TF binding site mE1_TFBS_inv
3R	15012994	3R_15012994_SNP [dm3] 3R_19187272_SNP [dm6]	T	G	2.930e^-6	0.943	INTRON CG31475	TF binding site mE1_TFBS_inv
3R	15852506	3R_15852506_SNP [dm3] 3R_20026784_SNP [dm6]	C	T	3.957e^-6	0.943	DOWNSTREAM psidin INTRON CG4424
2L	19856691	2L_19856691_SNP [dm3] 2L_19856691_SNP [dm6]	G	A	4.531e^-6	0.943	INTRON sick
2R	13771330	2R_13771330_SNP [dm3] 2R_17883825_SNP [dm6]	G	A	6.942e^-6	0.943	INTRON Elk
3L	9946310	3L_9946310_SNP [dm3] 3L_9953210_SNP [dm6]	C	T	6.983e^-6	0.943	INTRON CG34356
2R	10171811	2R_10171811_SNP [dm3] 2R_14284306_SNP [dm6]	T	A	7.047e^-6	0.943	INTRON Ih	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	19923189	2L_19923189_SNP [dm3] 2L_19923189_SNP [dm6]	T	C	7.072e^-6	0.943	INTRON sick & 1 other EXON CR43827
2L	20335041	2L_20335041_SNP [dm3] 2L_20335041_SNP [dm6]	A	C	7.225e^-6	0.943	INTRON spir
2L	20862470	2L_20862470_SNP [dm3] 2L_20862470_SNP [dm6]	G	A	7.734e^-6	0.943	DOWNSTREAM CR9337 INTERGENIC
3R	9585911	3R_9585911_SNP [dm3] 3R_13760189_SNP [dm6]	C	T	9.158e^-6	0.943	INTRON CG34383
2R	13628030	2R_13628030_SNP [dm3] 2R_17740525_SNP [dm6]	G	A	1.199e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	13628009	2R_13628009_SNP [dm3] 2R_17740504_SNP [dm6]	G	A	1.216e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	13628012	2R_13628012_SNP [dm3] 2R_17740507_SNP [dm6]	C	G	1.218e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	7701220	2L_7701220_SNP [dm3] 2L_7701220_SNP [dm6]	T	A	1.236e^-5	0.943	INTRON Tep2	TF binding site mE1_TFBS_Trl
3L	17919798	3L_17919798_SNP [dm3] 3L_17926698_SNP [dm6]	G	A	1.252e^-5	0.943	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	3516415	X_3516415_DEL [dm3] X_3622382_DEL [dm6]	TT	T	1.354e^-5	0.943	INTRON AstA-R1
3L	10775124	3L_10775124_SNP [dm3] 3L_10782024_SNP [dm6]	A	T	1.445e^-5	0.943	INTERGENIC
2L	6107755	2L_6107755_SNP [dm3] 2L_6107755_SNP [dm6]	A	T	1.628e^-5	0.943	INTRON stai
2R	6464832	2R_6464832_SNP [dm3] 2R_10577327_SNP [dm6]	A	G	1.702e^-5	0.943	INTRON psq
2R	8672361	2R_8672361_SNP [dm3] 2R_12784856_SNP [dm6]	A	T	1.709e^-5	0.943	INTRON sca & 1 other	regulatory region REDfly_CRMs
3R	25208577	3R_25208577_INS [dm3] 3R_29382855_INS [dm6]	A	ATACA	1.716e^-5	0.943	INTRON Ptp99A
2L	18882851	2L_18882851_SNP [dm3] 2L_18882851_SNP [dm6]	T	C	1.938e^-5	0.943	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	16479528	3R_16479528_SNP [dm3] 3R_20653806_SNP [dm6]	G	T	2.111e^-5	0.943	SYNONYMOUS_CODING Nep4	TF binding site mE1_TFBS_cad
3L	14731962	3L_14731962_SNP [dm3] 3L_14738862_SNP [dm6]	T	C	2.136e^-5	0.943	INTRON ome
X	11629664	X_11629664_SNP [dm3] X_11735631_SNP [dm6]	C	G	2.175e^-5	0.943	NON_SYNONYMOUS_CODING CG15221
2L	13274279	2L_13274279_SNP [dm3] 2L_13274279_SNP [dm6]	T	A	2.179e^-5	0.943	INTRON CG44085
3L	3412396	3L_3412396_SNP [dm3] 3L_3412396_SNP [dm6]	T	C	2.243e^-5	0.943	UPSTREAM mir-2282 INTRON sty
3R	16479675	3R_16479675_SNP [dm3] 3R_20653953_SNP [dm6]	A	G	2.278e^-5	0.943	SYNONYMOUS_CODING Nep4	TF binding site mE1_TFBS_cad
2L	5913141	2L_5913141_SNP [dm3] 2L_5913141_SNP [dm6]	C	T	2.341e^-5	0.943	SYNONYMOUS_CODING bchs
2R	13627997	2R_13627997_SNP [dm3] 2R_17740492_SNP [dm6]	T	C	2.372e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
3L	4325125	3L_4325125_SNP [dm3] 3L_4325125_SNP [dm6]	G	A	2.423e^-5	0.943	NON_SYNONYMOUS_CODING Cip4
2L	6834406	2L_6834406_SNP [dm3] 2L_6834406_SNP [dm6]	A	G	2.462e^-5	0.943	INTRON sens-2	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	25520225	3R_25520225_SNP [dm3] 3R_29694503_SNP [dm6]	A	T	2.487e^-5	0.943	INTRON dmrt99B
2R	7451746	2R_7451746_SNP [dm3] 2R_11564241_SNP [dm6]	G	T	2.510e^-5	0.943	INTERGENIC
2R	6965120	2R_6965120_SNP [dm3] 2R_11077615_SNP [dm6]	C	T	2.514e^-5	0.943	INTRON luna	TF binding site mE1_TFBS_HSA
3R	25515655	3R_25515655_SNP [dm3] 3R_29689933_SNP [dm6]	A	C	2.572e^-5	0.943	UPSTREAM Obp99c INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_Trl
X	14426280	X_14426280_SNP [dm3] X_14532247_SNP [dm6]	G	A	2.628e^-5	0.943	INTERGENIC
2R	4978866	2R_4978866_SNP [dm3] 2R_9091361_SNP [dm6]	G	A	2.696e^-5	0.943	INTRON CG8080
2R	4978872	2R_4978872_SNP [dm3] 2R_9091367_SNP [dm6]	C	A	2.696e^-5	0.943	INTRON CG8080
3L	3463947	3L_3463947_SNP [dm3] 3L_3463947_SNP [dm6]	G	A	2.730e^-5	0.943	SYNONYMOUS_CODING armi
2L	20327490	2L_20327490_SNP [dm3] 2L_20327490_SNP [dm6]	T	A	2.801e^-5	0.943	INTRON spir
3L	15402265	3L_15402265_SNP [dm3] 3L_15409165_SNP [dm6]	T	A	2.896e^-5	0.943	DOWNSTREAM CG33259 INTERGENIC
3R	6504570	3R_6504570_SNP [dm3] 3R_10678848_SNP [dm6]	G	T	2.972e^-5	0.943	NON_SYNONYMOUS_CODING CG14688	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2R	4978850	2R_4978850_SNP [dm3] 2R_9091345_SNP [dm6]	T	G	3.013e^-5	0.943	INTRON CG8080
3L	3463659	3L_3463659_SNP [dm3] 3L_3463659_SNP [dm6]	G	A	3.047e^-5	0.943	SYNONYMOUS_CODING armi
X	10026153	X_10026153_SNP [dm3] X_10132120_SNP [dm6]	T	C	3.068e^-5	0.943	INTRON CR44894 & 1 other
3L	11038442	3L_11038442_SNP [dm3] 3L_11045342_SNP [dm6]	A	G	3.071e^-5	0.943	INTRON CG43693	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
3R	19431381	3R_19431381_SNP [dm3] 3R_23605659_SNP [dm6]	A	G	3.109e^-5	0.943	UPSTREAM CG10184 DOWNSTREAM CG31145 INTERGENIC
2L	20388956	2L_20388956_SNP [dm3] 2L_20388956_SNP [dm6]	G	A	3.270e^-5	0.943	INTRON CG10947
3L	12335189	3L_12335189_SNP [dm3] 3L_12342089_SNP [dm6]	T	C	3.358e^-5	0.943	INTRON CrzR
3R	25316690	3R_25316690_SNP [dm3] 3R_29490968_SNP [dm6]	G	A	3.448e^-5	0.943	UTR_3_PRIME CG2006 DOWNSTREAM CG2310 & 1 other INTRON Spase12	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	20226742	2L_20226742_SNP [dm3] 2L_20226742_SNP [dm6]	C	A	3.686e^-5	0.943	INTERGENIC
2R	17583321	2R_17583321_SNP [dm3] 2R_21695816_SNP [dm6]	G	A	3.691e^-5	0.943	SYNONYMOUS_CODING CngB	TF binding site mE1_TFBS_cad
2R	13628162	2R_13628162_SNP [dm3] 2R_17740657_SNP [dm6]	G	A	3.759e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	13627976	2R_13627976_SNP [dm3] 2R_17740471_SNP [dm6]	G	A	3.760e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	3552794	2R_3552794_SNP [dm3] 2R_7665289_SNP [dm6]	T	A	3.805e^-5	0.943	UPSTREAM CG2064 DOWNSTREAM CG2065 INTERGENIC	TF binding site BDTNP1_TFBS_Med
3L	5914586	3L_5914586_DEL [dm3] 3L_5921486_DEL [dm6]	ACAACA	A	3.807e^-5	0.943	UPSTREAM CG32407 & 1 other INTERGENIC
2L	14051068	2L_14051068_SNP [dm3] 2L_14051068_SNP [dm6]	C	A	3.846e^-5	0.943	INTRON nAChRalpha5	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3R	19181525	3R_19181525_SNP [dm3] 3R_23355803_SNP [dm6]	T	A	3.901e^-5	0.943	UPSTREAM Sec13 DOWNSTREAM DNApol-epsilon INTRON ATPsyn-Cf6	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
2L	16374926	2L_16374926_SNP [dm3] 2L_16374926_SNP [dm6]	A	T	3.923e^-5	0.943	INTERGENIC
2R	8672444	2R_8672444_SNP [dm3] 2R_12784939_SNP [dm6]	C	G	3.964e^-5	0.943	INTRON sca EXON CR45137	regulatory region REDfly_CRMs
3L	3462787	3L_3462787_SNP [dm3] 3L_3462787_SNP [dm6]	A	T	4.007e^-5	0.943	SPLICE_SITE_REGION armi INTRON armi	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	5914965	3L_5914965_SNP [dm3] 3L_5921865_SNP [dm6]	A	T	4.065e^-5	0.943	UPSTREAM CG32407 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
3R	25723445	3R_25723445_DEL [dm3] 3R_29897723_DEL [dm6]	ATA	A	4.095e^-5	0.943	UTR_3_PRIME CG31038 INTRON CG31038	TF binding site mE1_TFBS_chinmo
2R	13628027	2R_13628027_SNP [dm3] 2R_17740522_SNP [dm6]	G	A	4.125e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	9983800	2L_9983800_SNP [dm3] 2L_9983800_SNP [dm6]	C	T	4.211e^-5	0.943	UPSTREAM bib EXON CR13130	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	11349631	3L_11349631_SNP [dm3] 3L_11356531_SNP [dm6]	C	A	4.488e^-5	0.943	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12946422	X_12946422_SNP [dm3] X_13052389_SNP [dm6]	G	A	4.778e^-5	0.943	DOWNSTREAM CG12715 INTRON rad
2L	6042641	2L_6042641_SNP [dm3] 2L_6042641_SNP [dm6]	C	G	4.912e^-5	0.943	NON_SYNONYMOUS_CODING ade2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	2754643	X_2754643_SNP [dm3] X_2860610_SNP [dm6]	A	T	4.993e^-5	0.943	INTRON kirre
3L	12017812	3L_12017812_SNP [dm3] 3L_12024712_SNP [dm6]	G	A	5.010e^-5	0.943	INTRON rols
2R	19668908	2R_19668908_SNP [dm3] 2R_23781385_SNP [dm6]	G	T	5.097e^-5	0.943	INTRON CG9850
3R	10962657	3R_10962657_SNP [dm3] 3R_15136935_SNP [dm6]	C	G	5.113e^-5	0.943	UTR_5_PRIME CG6912 UPSTREAM CG3984 DOWNSTREAM CR45600	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad
3R	26796056	3R_26796056_SNP [dm3] 3R_30970334_SNP [dm6]	T	A	5.157e^-5	0.943	SYNONYMOUS_CODING 5-HT7	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	9192101	2L_9192101_SNP [dm3] 2L_9192101_SNP [dm6]	C	T	5.220e^-5	0.943	INTRON tai
2R	13628078	2R_13628078_SNP [dm3] 2R_17740573_SNP [dm6]	G	A	5.240e^-5	0.943	SYNONYMOUS_CODING CG4996 UPSTREAM CG6401	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
X	13808652	X_13808652_SNP [dm3] X_13914619_SNP [dm6]	T	C	5.250e^-5	0.943	INTRON mamo
2R	14646899	2R_14646899_SNP [dm3] 2R_18759394_SNP [dm6]	A	C	5.258e^-5	0.943	SYNONYMOUS_CODING Jabba
3L	5373981	3L_5373981_SNP [dm3] 3L_5380881_SNP [dm6]	G	A	5.268e^-5	0.943	INTRON Ir64a
X	21138053	X_21138053_SNP [dm3] X_21267026_SNP [dm6]	T	C	5.362e^-5	0.943	INTRON CG32521
3L	10775115	3L_10775115_SNP [dm3] 3L_10782015_SNP [dm6]	G	A	5.417e^-5	0.943	INTERGENIC
3R	25316616	3R_25316616_SNP [dm3] 3R_29490894_SNP [dm6]	A	G	5.455e^-5	0.943	SYNONYMOUS_CODING Spase12 UTR_3_PRIME CG2006 DOWNSTREAM CG2310 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	14732064	3L_14732064_SNP [dm3] 3L_14738964_SNP [dm6]	C	T	5.478e^-5	0.943	INTRON ome	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	17993103	3R_17993103_SNP [dm3] 3R_22167381_SNP [dm6]	G	C	5.491e^-5	0.943	INTRON SKIP	TF binding site mE1_TFBS_Kr
2L	16195018	2L_16195018_SNP [dm3] 2L_16195018_SNP [dm6]	G	A	5.509e^-5	0.943	DOWNSTREAM CR44735 EXON CR44734
2R	19791700	2R_19791700_SNP [dm3] 2R_23904177_SNP [dm6]	T	C	5.532e^-5	0.943	SYNONYMOUS_CODING CG13562 DOWNSTREAM Lpt & 1 other
3R	15843652	3R_15843652_SNP [dm3] 3R_20017930_SNP [dm6]	A	T	5.540e^-5	0.943	SYNONYMOUS_CODING CG4836 UTR_3_PRIME CG4836 DOWNSTREAM CG4433	TF binding site mE1_TFBS_cad
X	21138054	X_21138054_SNP [dm3] X_21267027_SNP [dm6]	T	C	5.577e^-5	0.943	INTRON CG32521
3R	26459341	3R_26459341_SNP [dm3] 3R_30633619_SNP [dm6]	C	T	5.630e^-5	0.943	INTERGENIC
3R	16479672	3R_16479672_SNP [dm3] 3R_20653950_SNP [dm6]	C	T	5.639e^-5	0.943	SYNONYMOUS_CODING Nep4	TF binding site mE1_TFBS_cad
2R	7570166	2R_7570166_SNP [dm3] 2R_11682661_SNP [dm6]	T	C	5.659e^-5	0.943	INTRON Buffy
X	13808627	X_13808627_SNP [dm3] X_13914594_SNP [dm6]	A	G	5.791e^-5	0.943	INTRON mamo
3R	16479570	3R_16479570_SNP [dm3] 3R_20653848_SNP [dm6]	A	G	5.818e^-5	0.943	SYNONYMOUS_CODING Nep4	TF binding site mE1_TFBS_cad
3L	16981484	3L_16981484_SNP [dm3] 3L_16988384_SNP [dm6]	C	T	5.830e^-5	0.943	INTRON Exn
3L	3446253	3L_3446253_SNP [dm3] 3L_3446253_SNP [dm6]	G	C	5.854e^-5	0.943	INTRON eIF5B
2L	14000232	2L_14000232_SNP [dm3] 2L_14000232_SNP [dm6]	T	A	5.868e^-5	0.943	INTRON rk
X	18368681	X_18368681_INS [dm3] X_18474648_INS [dm6]	C	CTC	5.956e^-5	0.943	INTRON CG32547
3L	1521077	3L_1521077_SNP [dm3] 3L_1521077_SNP [dm6]	A	T	5.959e^-5	0.943	INTRON Psa	TF binding site mE1_TFBS_cad
X	12780558	X_12780558_SNP [dm3] X_12886525_SNP [dm6]	A	T	5.976e^-5	0.943	INTRON Pde9

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By genomic position
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Susceptibility_C_PQ phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results