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=4.907e^-2)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	2.8297	0.0925

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

894 significant hits at p-value < 0.001.

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	13184064	3R_13184064_SNP [dm3] 3R_17358342_SNP [dm6]	A	G	2.968e^-6	1	INTRON beat-IIa
2R	16836358	2R_16836358_SNP [dm3] 2R_20948853_SNP [dm6]	G	T	4.105e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	16836345	2R_16836345_SNP [dm3] 2R_20948840_SNP [dm6]	A	T	4.139e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	9835736	X_9835736_SNP [dm3] X_9941703_SNP [dm6]	T	A	6.435e^-6	1	INTERGENIC
2L	17941481	2L_17941481_SNP [dm3] 2L_17941481_SNP [dm6]	A	C	6.697e^-6	1	INTERGENIC
3L	8811352	3L_8811352_SNP [dm3] 3L_8818252_SNP [dm6]	C	T	7.217e^-6	1	INTERGENIC
3R	20232765	3R_20232765_SNP [dm3] 3R_24407043_SNP [dm6]	G	A	1.328e^-5	1	INTRON nAChRalpha1
X	2437875	X_2437875_SNP [dm3] X_2543842_SNP [dm6]	C	A	1.472e^-5	1	DOWNSTREAM mir-4955 INTRON trol
2L	4332941	2L_4332941_SNP [dm3] 2L_4332941_SNP [dm6]	T	A	1.715e^-5	1	UPSTREAM Atet INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens mE1_TFBS_Trl
X	17020608	X_17020608_SNP [dm3] X_17126575_SNP [dm6]	C	T	1.733e^-5	1	SYNONYMOUS_CODING CG5004	TF binding site mE1_TFBS_sens
X	16870005	X_16870005_SNP [dm3] X_16975972_SNP [dm6]	A	G	1.856e^-5	1	INTRON CG45002
3R	27155479	3R_27155479_SNP [dm3] 3R_31329757_SNP [dm6]	G	C	2.110e^-5	1	INTRON CG34347	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	19963493	2L_19963493_SNP [dm3] 2L_19963493_SNP [dm6]	C	T	2.364e^-5	1	NON_SYNONYMOUS_CODING CG16772 UPSTREAM CG10680 DOWNSTREAM CR45701
2L	2762285	2L_2762285_SNP [dm3] 2L_2762285_SNP [dm6]	T	G	2.409e^-5	1	SYNONYMOUS_CODING Trn-SR
2R	11742741	2R_11742741_SNP [dm3] 2R_15855236_SNP [dm6]	A	G	2.460e^-5	1	UTR_3_PRIME tun UPSTREAM CG12970 DOWNSTREAM tun
X	9835742	X_9835742_SNP [dm3] X_9941709_SNP [dm6]	T	C	2.518e^-5	1	INTERGENIC
X	9835728	X_9835728_SNP [dm3] X_9941695_SNP [dm6]	C	T	2.518e^-5	1	INTERGENIC
3R	24733735	3R_24733735_SNP [dm3] 3R_28908013_SNP [dm6]	C	A	2.575e^-5	1	SYNONYMOUS_CODING Doa INTRON Doa	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	16995715	X_16995715_SNP [dm3] X_17101682_SNP [dm6]	C	G	2.959e^-5	1	UPSTREAM CG4991 INTRON CG4991
3L	9176911	3L_9176911_SNP [dm3] 3L_9183811_SNP [dm6]	C	T	3.090e^-5	1	INTERGENIC
3L	2516376	3L_2516376_SNP [dm3] 3L_2516376_SNP [dm6]	G	A	3.359e^-5	1	UPSTREAM CR45170 INTRON Spn
2R	18146278	2R_18146278_SNP [dm3] 2R_22258773_SNP [dm6]	A	T	3.506e^-5	1	INTRON dve
X	16995751	X_16995751_DEL [dm3] X_17101718_DEL [dm6]	TGATTGTTCTGC...	T	3.566e^-5	1	UPSTREAM CG4991 INTRON CG4991
3R	17188241	3R_17188241_SNP [dm3] 3R_21362519_SNP [dm6]	G	A	3.607e^-5	1	UTR_3_PRIME mod_mdg4_ DOWNSTREAM mod_mdg4_ & 5 others INTRON mod_mdg4_
3L	3011919	3L_3011919_SNP [dm3] 3L_3011919_SNP [dm6]	C	T	3.730e^-5	1	DOWNSTREAM FMRFaR INTERGENIC
X	12400356	X_12400356_SNP [dm3] X_12506323_SNP [dm6]	G	C	3.788e^-5	1	INTRON CG2556
3R	22089690	3R_22089690_SNP [dm3] 3R_26263968_SNP [dm6]	G	T	3.892e^-5	1	INTRON CG6154
X	3994558	X_3994558_SNP [dm3] X_4100525_SNP [dm6]	C	T	3.922e^-5	1	SYNONYMOUS_CODING CG6379 UPSTREAM CG15375	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	3994561	X_3994561_SNP [dm3] X_4100528_SNP [dm6]	G	A	3.973e^-5	1	SYNONYMOUS_CODING CG6379 UPSTREAM CG15375	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	17941413	2L_17941413_INS [dm3] 2L_17941413_INS [dm6]	T	TGTAGA	4.106e^-5	1	INTERGENIC	transposable element FlyBase
2L	17941414	2L_17941414_DEL [dm3] 2L_17941414_DEL [dm6]	TGCC	T	4.106e^-5	1	INTERGENIC	transposable element FlyBase
2L	4890698	2L_4890698_SNP [dm3] 2L_4890698_SNP [dm6]	G	C	4.184e^-5	1	NON_SYNONYMOUS_CODING CG15625 DOWNSTREAM CR45716	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	5728446	X_5728446_SNP [dm3] X_5834413_SNP [dm6]	C	T	4.204e^-5	1	SYNONYMOUS_CODING CG15765
X	5728467	X_5728467_SNP [dm3] X_5834434_SNP [dm6]	T	C	4.204e^-5	1	SYNONYMOUS_CODING CG15765
2R	8631670	2R_8631670_DEL [dm3] 2R_12744165_DEL [dm6]	TCTGTTT	T	4.355e^-5	1	INTRON CG42663
3R	4224921	3R_4224921_SNP [dm3] 3R_8399199_SNP [dm6]	A	G	4.361e^-5	1	INTRON CG45263
2L	2538796	2L_2538796_SNP [dm3] 2L_2538796_SNP [dm6]	A	T	4.493e^-5	1	INTERGENIC
3L	15776793	3L_15776793_SNP [dm3] 3L_15783693_SNP [dm6]	C	G	4.511e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	1050333	X_1050333_SNP [dm3] X_1156300_SNP [dm6]	C	G	4.659e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	16387669	3R_16387669_SNP [dm3] 3R_20561947_SNP [dm6]	G	A	4.704e^-5	1	DOWNSTREAM CG10877 INTRON CG5191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10301073	3L_10301073_SNP [dm3] 3L_10307973_SNP [dm6]	G	A	4.775e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	7832474	3R_7832474_SNP [dm3] 3R_12006752_SNP [dm6]	C	T	4.854e^-5	1	DOWNSTREAM KLHL18 INTERGENIC
X	9835751	X_9835751_SNP [dm3] X_9941718_SNP [dm6]	A	G	4.859e^-5	1	INTERGENIC
X	9835756	X_9835756_SNP [dm3] X_9941723_SNP [dm6]	G	A	4.859e^-5	1	INTERGENIC
X	5728550	X_5728550_SNP [dm3] X_5834517_SNP [dm6]	C	T	5.097e^-5	1	INTRON CG15765
3R	16387165	3R_16387165_SNP [dm3] 3R_20561443_SNP [dm6]	C	T	5.210e^-5	1	INTRON CG5191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	16387177	3R_16387177_SNP [dm3] 3R_20561455_SNP [dm6]	A	G	5.215e^-5	1	INTRON CG5191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16995743	X_16995743_DEL [dm3] X_17101710_DEL [dm6]	GTTTT	G	5.319e^-5	1	UPSTREAM CG4991 INTRON CG4991
3L	1548584	3L_1548584_SNP [dm3] 3L_1548584_SNP [dm6]	G	A	5.424e^-5	1	INTRON Cct1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16870008	X_16870008_INS [dm3] X_16975975_INS [dm6]	T	TGATTCAACTAATTTTAGTT...	5.519e^-5	1	INTRON CG45002
3R	26180900	3R_26180900_SNP [dm3] 3R_30355178_SNP [dm6]	C	A	5.682e^-5	1	INTRON hdc
3L	10852327	3L_10852327_SNP [dm3] 3L_10859227_SNP [dm6]	T	C	5.750e^-5	1	INTRON tna	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_kn mE1_TFBS_sbb
3R	24626685	3R_24626685_SNP [dm3] 3R_28800963_SNP [dm6]	T	A	5.807e^-5	1	INTERGENIC
2R	8631576	2R_8631576_SNP [dm3] 2R_12744071_SNP [dm6]	G	C	5.811e^-5	1	INTRON CG42663	TF binding site mE1_TFBS_Trl
2R	8631598	2R_8631598_SNP [dm3] 2R_12744093_SNP [dm6]	G	T	5.811e^-5	1	INTRON CG42663	TF binding site mE1_TFBS_Trl
X	563639	X_563639_SNP [dm3] X_669606_SNP [dm6]	C	G	5.863e^-5	1	INTERGENIC
X	563659	X_563659_SNP [dm3] X_669626_SNP [dm6]	G	A	5.863e^-5	1	INTERGENIC
2R	13051943	2R_13051943_SNP [dm3] 2R_17164438_SNP [dm6]	G	T	5.885e^-5	1	DOWNSTREAM CG10953 INTERGENIC
3R	21179857	3R_21179857_SNP [dm3] 3R_25354135_SNP [dm6]	A	G	5.930e^-5	1	INTRON Fur1	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	6533305	2R_6533305_SNP [dm3] 2R_10645800_SNP [dm6]	A	T	6.300e^-5	1	UTR_5_PRIME Elp2 UPSTREAM Git	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Ubx
X	1050443	X_1050443_SNP [dm3] X_1156410_SNP [dm6]	G	C	6.366e^-5	1	INTERGENIC
2L	2761823	2L_2761823_SNP [dm3] 2L_2761823_SNP [dm6]	C	G	6.531e^-5	1	SYNONYMOUS_CODING Trn-SR
X	14015866	X_14015866_SNP [dm3] X_14121833_SNP [dm6]	C	T	6.629e^-5	1	INTERGENIC
3R	12921812	3R_12921812_SNP [dm3] 3R_17096090_SNP [dm6]	C	T	6.808e^-5	1	UPSTREAM cher INTRON cher
3R	25646305	3R_25646305_SNP [dm3] 3R_29820583_SNP [dm6]	T	A	6.879e^-5	1	INTRON neo
3R	17192411	3R_17192411_SNP [dm3] 3R_21366689_SNP [dm6]	C	T	6.962e^-5	1	STOP_GAINED pre-mod_mdg4_-X START_GAINED pre-mod_mdg4_-V & 4 others UTR_5_PRIME pre-mod_mdg4_-V & 4 others UTR_3_PRIME pre-mod_mdg4_-Y INTRON mod_mdg4_	TF binding site mE1_TFBS_sens
X	1050698	X_1050698_SNP [dm3] X_1156665_SNP [dm6]	C	A	7.005e^-5	1	INTERGENIC
3L	6106839	3L_6106839_DEL [dm3] 3L_6113739_DEL [dm6]	AA	A	7.149e^-5	1	INTRON Ets65A
2L	20120641	2L_20120641_DEL [dm3] 2L_20120641_DEL [dm6]	GT	G	7.239e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3R	9935496	3R_9935496_SNP [dm3] 3R_14109774_SNP [dm6]	C	T	7.305e^-5	1	SYNONYMOUS_CODING Or88a INTRON CR44237
3L	16059482	3L_16059482_SNP [dm3] 3L_16066382_SNP [dm6]	T	C	7.605e^-5	1	INTRON Mbs
3L	6114346	3L_6114346_SNP [dm3] 3L_6121246_SNP [dm6]	T	G	7.623e^-5	1	INTRON Ets65A	TF binding site mE1_TFBS_HSA
3L	6114362	3L_6114362_SNP [dm3] 3L_6121262_SNP [dm6]	C	A	7.678e^-5	1	INTRON Ets65A	TF binding site mE1_TFBS_HSA
3L	1059887	3L_1059887_SNP [dm3] 3L_1059887_SNP [dm6]	C	A	7.849e^-5	1	INTRON bab1
2R	8631649	2R_8631649_SNP [dm3] 2R_12744144_SNP [dm6]	A	T	8.077e^-5	1	INTRON CG42663
3L	4647279	3L_4647279_SNP [dm3] 3L_4647279_SNP [dm6]	G	T	8.381e^-5	1	UPSTREAM CG32238 INTRON axo
3R	4224940	3R_4224940_SNP [dm3] 3R_8399218_SNP [dm6]	A	G	8.539e^-5	1	INTRON CG45263
2R	9846894	2R_9846894_SNP [dm3] 2R_13959389_SNP [dm6]	C	T	9.023e^-5	1	SYNONYMOUS_CODING Rpn13	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2515931	3L_2515931_SNP [dm3] 3L_2515931_SNP [dm6]	C	T	9.098e^-5	1	INTRON Spn
3R	16440982	3R_16440982_SNP [dm3] 3R_20615260_SNP [dm6]	G	T	9.406e^-5	1	NON_SYNONYMOUS_CODING CG15923	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10878723	3R_10878723_SNP [dm3] 3R_15053001_SNP [dm6]	T	A	9.408e^-5	1	INTERGENIC
2R	9403406	2R_9403406_SNP [dm3] 2R_13515901_SNP [dm6]	T	A	9.627e^-5	1	SYNONYMOUS_CODING CG13330 UTR_3_PRIME Vmat	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4302348	3L_4302348_SNP [dm3] 3L_4302348_SNP [dm6]	C	G	9.830e^-5	1	INTRON dyl
3L	2354929	3L_2354929_INS [dm3] 3L_2354929_INS [dm6]	G	GG	9.890e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
3L	4573797	3L_4573797_SNP [dm3] 3L_4573797_SNP [dm6]	T	G	9.891e^-5	1	INTRON CG42540
3L	15491432	3L_15491432_SNP [dm3] 3L_15498332_SNP [dm6]	A	T	9.990e^-5	1	SYNONYMOUS_CODING CG7276 UPSTREAM CG7275 DOWNSTREAM CG13455	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2R	19368631	2R_19368631_SNP [dm3] 2R_23481108_SNP [dm6]	T	A	1.000e^-4	1	INTRON CG43795
3R	20232899	3R_20232899_INS [dm3] 3R_24407177_INS [dm6]	C	CCAA	1.010e^-4	1	INTRON nAChRalpha1
X	440331	X_440331_DEL [dm3] X_546298_DEL [dm6]	GCG	G	1.055e^-4	1	INTRON Appl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	18388064	2L_18388064_SNP [dm3] 2L_18388064_SNP [dm6]	T	A	1.065e^-4	1	DOWNSTREAM Fas3 INTRON Fas3
3L	9578360	3L_9578360_SNP [dm3] 3L_9585260_SNP [dm6]	T	G	1.093e^-4	1	INTRON CG42673
2R	15391461	2R_15391461_SNP [dm3] 2R_19503956_SNP [dm6]	A	G	1.108e^-4	1	NON_SYNONYMOUS_CODING CG11007 UPSTREAM CR44472
2R	19368445	2R_19368445_SNP [dm3] 2R_23480922_SNP [dm6]	A	G	1.145e^-4	1	INTRON CG43795
X	19367096	X_19367096_SNP [dm3] X_19473063_SNP [dm6]	T	G	1.158e^-4	1	INTERGENIC
2L	19922892	2L_19922892_SNP [dm3] 2L_19922892_SNP [dm6]	C	G	1.160e^-4	1	UPSTREAM CR43827 DOWNSTREAM CR43828 INTRON sick
X	14015881	X_14015881_SNP [dm3] X_14121848_SNP [dm6]	C	G	1.171e^-4	1	INTERGENIC
X	3445359	X_3445359_SNP [dm3] X_3551326_SNP [dm6]	T	G	1.174e^-4	1	INTRON CG32791
3L	8806878	3L_8806878_SNP [dm3] 3L_8813778_SNP [dm6]	C	T	1.197e^-4	1	INTERGENIC
3R	17148742	3R_17148742_SNP [dm3] 3R_21323020_SNP [dm6]	G	A	1.206e^-4	1	INTRON CG16791
X	586769	X_586769_SNP [dm3] X_692736_SNP [dm6]	G	A	1.212e^-4	1	INTRON sdk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi

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Phenotype distribution and association to known covariates

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GWAS results