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=9.495e^-18)
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_3R_P	4.7989	0.0908

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4486 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
3L	6293706	3L_6293706_INS [dm3] 3L_6300606_INS [dm6]	T	TAG	5.859e^-9	0.011	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	27235324	3R_27235324_DEL [dm3] 3R_31409602_DEL [dm6]	TAAACGTATTT...	T	1.968e^-8	0.018	INTRON Gprk2
X	11479413	X_11479413_SNP [dm3] X_11585380_SNP [dm6]	C	G	3.490e^-8	0.02	NON_SYNONYMOUS_CODING nod UPSTREAM CR43217	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	6678460	3R_6678460_DEL [dm3] 3R_10852738_DEL [dm6]	AA	G	4.267e^-8	0.02	UTR_5_PRIME CG4565 DOWNSTREAM CG42394 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
X	19496052	X_19496052_INS [dm3] X_19602019_INS [dm6]	T	TTT	8.456e^-8	0.032	UPSTREAM CG14220 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	1216328	2R_1216328_INS [dm3] 2R_5328823_INS [dm6]	G	GTTGTGCAGTAGG...	1.054e^-7	0.033	INTRON sxc
3R	15892162	3R_15892162_SNP [dm3] 3R_20066440_SNP [dm6]	A	G	1.846e^-7	0.039	INTERGENIC
X	7599741	X_7599741_DEL [dm3] X_7705708_DEL [dm6]	AAA	A	2.113e^-7	0.039	UPSTREAM CHES-1-like INTRON CHES-1-like	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	17481255	X_17481255_DEL [dm3] X_17587222_DEL [dm6]	TACAT	T	2.174e^-7	0.039	INTRON CG12991
3L	473509	3L_473509_INS [dm3] 3L_473509_INS [dm6]	C	CTTTTC	2.288e^-7	0.039	INTRON klar
3L	6293700	3L_6293700_SNP [dm3] 3L_6300600_SNP [dm6]	T	A	2.298e^-7	0.039	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	18213458	3L_18213458_SNP [dm3] 3L_18220358_SNP [dm6]	G	T	2.478e^-7	0.039	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3R	15892036	3R_15892036_SNP [dm3] 3R_20066314_SNP [dm6]	A	G	2.844e^-7	0.041	INTERGENIC
X	17635879	X_17635879_DEL [dm3] X_17741846_DEL [dm6]	CC	C	4.091e^-7	0.047	INTRON CG42684	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	18213468	3L_18213468_SNP [dm3] 3L_18220368_SNP [dm6]	A	G	4.254e^-7	0.047	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	18213472	3L_18213472_SNP [dm3] 3L_18220372_SNP [dm6]	T	A	4.254e^-7	0.047	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	18213459	3L_18213459_DEL [dm3] 3L_18220359_DEL [dm6]	GAACCA	G	4.321e^-7	0.047	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3L	18329829	3L_18329829_INS [dm3] 3L_18336729_INS [dm6]	T	TT	4.722e^-7	0.047	INTERGENIC
X	11479401	X_11479401_SNP [dm3] X_11585368_SNP [dm6]	G	A	5.273e^-7	0.047	NON_SYNONYMOUS_CODING nod UPSTREAM CR43217	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15882905	3R_15882905_SNP [dm3] 3R_20057183_SNP [dm6]	G	T	5.275e^-7	0.047	SYNONYMOUS_CODING CG4390 UPSTREAM mdlc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	7600034	X_7600034_DEL [dm3] X_7706001_DEL [dm6]	TT	T	5.276e^-7	0.047	INTRON CHES-1-like	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	6293702	3L_6293702_SNP [dm3] 3L_6300602_SNP [dm6]	T	G	5.648e^-7	0.047	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	18730258	3L_18730258_SNP [dm3] 3L_18737158_SNP [dm6]	G	A	6.055e^-7	0.047	INTERGENIC
X	21364686	X_21364686_INS [dm3] X_21493659_INS [dm6]	A	ACATA	6.094e^-7	0.047	INTERGENIC
3L	12056313	3L_12056313_DEL [dm3] 3L_12063213_DEL [dm6]	CC	C	6.214e^-7	0.047	INTRON rols	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	3268579	2R_3268579_DEL [dm3] 2R_7381074_DEL [dm6]	CC	C	7.528e^-7	0.052	INTRON Dscam1	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	12367468	2R_12367468_INS [dm3] 2R_16479963_INS [dm6]	C	CA	7.793e^-7	0.052	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	21946825	X_21946825_INS [dm3] X_22544989_INS [dm6]	G	GG	8.043e^-7	0.052	UPSTREAM CG17599 INTERGENIC
2R	1141073	2R_1141073_INS [dm3] 2R_5253568_INS [dm6]	G	GG	8.116e^-7	0.052	UPSTREAM CR41443 INTERGENIC
2L	21070330	2L_21070330_SNP [dm3] 2L_21070330_SNP [dm6]	A	G	8.904e^-7	0.053	UPSTREAM CG9265 INTRON CG9265
2L	10072028	2L_10072028_SNP [dm3] 2L_10072028_SNP [dm6]	G	C	9.030e^-7	0.053	INTRON CG44153
X	12939490	X_12939490_DEL [dm3] X_13045457_DEL [dm6]	TG	T	9.286e^-7	0.053	INTRON rad
X	7682833	X_7682833_SNP [dm3] X_7788800_SNP [dm6]	A	T	9.338e^-7	0.053	INTERGENIC
X	16519235	X_16519235_DEL [dm3] X_16625202_DEL [dm6]	AA	A	1.012e^-6	0.054	UTR_3_PRIME Rok INTRON Rok
X	7682834	X_7682834_SNP [dm3] X_7788801_SNP [dm6]	T	G	1.029e^-6	0.054	INTERGENIC
3R	15882866	3R_15882866_SNP [dm3] 3R_20057144_SNP [dm6]	G	A	1.037e^-6	0.054	SYNONYMOUS_CODING CG4390 UPSTREAM mdlc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	15892179	3R_15892179_SNP [dm3] 3R_20066457_SNP [dm6]	A	T	1.112e^-6	0.055	INTERGENIC
3R	10628531	3R_10628531_SNP [dm3] 3R_14802809_SNP [dm6]	C	A	1.117e^-6	0.055	SYNONYMOUS_CODING CG14857
2R	19616121	2R_19616121_DEL [dm3] 2R_23728598_DEL [dm6]	GG	A	1.167e^-6	0.055	INTRON Sesn
3R	15892155	3R_15892155_SNP [dm3] 3R_20066433_SNP [dm6]	G	A	1.211e^-6	0.055	INTERGENIC
3R	15877380	3R_15877380_SNP [dm3] 3R_20051658_SNP [dm6]	T	A	1.243e^-6	0.055	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	25605188	3R_25605188_SNP [dm3] 3R_29779466_SNP [dm6]	C	T	1.259e^-6	0.055	SYNONYMOUS_CODING fig INTRON kay	TF binding site BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15892115	3R_15892115_SNP [dm3] 3R_20066393_SNP [dm6]	T	A	1.314e^-6	0.055	INTERGENIC
3R	15892266	3R_15892266_SNP [dm3] 3R_20066544_SNP [dm6]	G	A	1.318e^-6	0.055	INTERGENIC
3L	18213474	3L_18213474_SNP [dm3] 3L_18220374_SNP [dm6]	C	G	1.341e^-6	0.055	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
2L	14078423	2L_14078423_SNP [dm3] 2L_14078423_SNP [dm6]	C	A	1.358e^-6	0.055	INTRON nAChRalpha5
2R	18524741	2R_18524741_INS [dm3] 2R_22637236_INS [dm6]	T	TAT	1.390e^-6	0.055	UPSTREAM bonsai INTRON Cdk9	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	8397999	X_8397999_DEL [dm3] X_8503966_DEL [dm6]	TT	T	1.406e^-6	0.055	INTRON CG33181
3R	15892071	3R_15892071_INS [dm3] 3R_20066349_INS [dm6]	A	AA	1.483e^-6	0.056	INTERGENIC
3R	26174550	3R_26174550_SNP [dm3] 3R_30348828_SNP [dm6]	A	T	1.484e^-6	0.056	INTRON hdc
3L	18213445	3L_18213445_MNP [dm3] 3L_18220345_MNP [dm6]	CAT	TGG	1.592e^-6	0.058	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
3R	10140762	3R_10140762_SNP [dm3] 3R_14315040_SNP [dm6]	T	C	1.606e^-6	0.058	SYNONYMOUS_CODING Crz UPSTREAM pr-set7 DOWNSTREAM CG31321	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15892122	3R_15892122_SNP [dm3] 3R_20066400_SNP [dm6]	T	A	1.680e^-6	0.059	INTERGENIC
3L	6293695	3L_6293695_INS [dm3] 3L_6300595_INS [dm6]	A	AAAAAAAAC	1.752e^-6	0.06	INTERGENIC	TF binding site mE1_TFBS_HSA
X	13365303	X_13365303_INS [dm3] X_13471270_INS [dm6]	T	TATGGTGTT	1.756e^-6	0.06	INTRON Neto
3R	15892176	3R_15892176_SNP [dm3] 3R_20066454_SNP [dm6]	T	C	1.785e^-6	0.06	INTERGENIC
3R	15892161	3R_15892161_SNP [dm3] 3R_20066439_SNP [dm6]	A	G	1.849e^-6	0.061	INTERGENIC
X	11368748	X_11368748_SNP [dm3] X_11474715_SNP [dm6]	T	A	2.011e^-6	0.062	INTRON CG43155
2L	9320520	2L_9320520_INS [dm3] 2L_9320520_INS [dm6]	C	CTTGAA	2.012e^-6	0.062	INTERGENIC
2R	15912687	2R_15912687_SNP [dm3] 2R_20025182_SNP [dm6]	G	A	2.026e^-6	0.062	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	20966354	X_20966354_DEL [dm3] X_21095327_DEL [dm6]	ACA	A	2.082e^-6	0.062	DOWNSTREAM CG15446 INTRON stg1 & 1 other
X	19600727	X_19600727_INS [dm3] X_19706694_INS [dm6]	T	TGT	2.084e^-6	0.062	UTR_3_PRIME meso18E DOWNSTREAM CG14230	TF binding site mE1_TFBS_HSA
3L	21136719	3L_21136719_SNP [dm3] 3L_21143619_SNP [dm6]	T	C	2.163e^-6	0.062	INTRON Ac78C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	4336566	2L_4336566_DEL [dm3] 2L_4336566_DEL [dm6]	AAA	A	2.188e^-6	0.062	UTR_5_PRIME Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	12107229	3L_12107229_SNP [dm3] 3L_12114129_SNP [dm6]	A	T	2.204e^-6	0.062	INTERGENIC
3R	15891906	3R_15891906_SNP [dm3] 3R_20066184_SNP [dm6]	G	T	2.207e^-6	0.062	INTERGENIC
3R	15891978	3R_15891978_SNP [dm3] 3R_20066256_SNP [dm6]	A	T	2.227e^-6	0.062	INTERGENIC
X	4488608	X_4488608_DEL [dm3] X_4594575_DEL [dm6]	GCTTGGCATCG...	G	2.284e^-6	0.063	INTRON CR32773	TF binding site BDTNP1_TFBS_dl
3R	15891270	3R_15891270_SNP [dm3] 3R_20065548_SNP [dm6]	C	T	2.428e^-6	0.065	INTERGENIC
2R	18133151	2R_18133151_SNP [dm3] 2R_22245646_SNP [dm6]	G	C	2.431e^-6	0.065	INTRON dve
3R	15891982	3R_15891982_SNP [dm3] 3R_20066260_SNP [dm6]	G	C	2.630e^-6	0.069	INTERGENIC
2L	12301408	2L_12301408_SNP [dm3] 2L_12301408_SNP [dm6]	G	A	2.936e^-6	0.076	INTRON aret
3R	12185008	3R_12185008_DEL [dm3] 3R_16359286_DEL [dm6]	TT	T	2.975e^-6	0.076	UTR_5_PRIME CG17931 INTRON CG42446	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	14974159	3R_14974159_SNP [dm3] 3R_19148437_SNP [dm6]	G	A	3.018e^-6	0.076	UPSTREAM Ppcs & 1 other DOWNSTREAM CG5835 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Ubx
3R	22520225	3R_22520225_INS [dm3] 3R_26694503_INS [dm6]	G	GTTGG	3.127e^-6	0.078	UPSTREAM TwdlQ INTERGENIC
3L	6317088	3L_6317088_SNP [dm3] 3L_6323988_SNP [dm6]	T	C	3.209e^-6	0.079	INTERGENIC
3R	15892601	3R_15892601_SNP [dm3] 3R_20066879_SNP [dm6]	G	A	3.435e^-6	0.084	INTERGENIC
3R	848071	3R_848071_INS [dm3] 3R_5022349_INS [dm6]	T	TTT	3.764e^-6	0.09	DOWNSTREAM CR45585 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15891876	3R_15891876_SNP [dm3] 3R_20066154_SNP [dm6]	T	A	3.822e^-6	0.09	INTERGENIC
3R	15892378	3R_15892378_SNP [dm3] 3R_20066656_SNP [dm6]	T	A	3.962e^-6	0.09	INTERGENIC
3L	18840695	3L_18840695_INS [dm3] 3L_18847595_INS [dm6]	T	TCTTA	3.973e^-6	0.09	INTERGENIC
3R	15892009	3R_15892009_SNP [dm3] 3R_20066287_SNP [dm6]	C	T	4.030e^-6	0.09	INTERGENIC
3L	18730262	3L_18730262_SNP [dm3] 3L_18737162_SNP [dm6]	C	T	4.040e^-6	0.09	INTERGENIC
3L	18730260	3L_18730260_SNP [dm3] 3L_18737160_SNP [dm6]	G	A	4.071e^-6	0.09	INTERGENIC
2R	18133354	2R_18133354_SNP [dm3] 2R_22245849_SNP [dm6]	G	C	4.176e^-6	0.09	INTRON dve
3L	6293755	3L_6293755_SNP [dm3] 3L_6300655_SNP [dm6]	G	A	4.176e^-6	0.09	INTERGENIC	TF binding site mE1_TFBS_HSA
X	13692169	X_13692169_INS [dm3] X_13798136_INS [dm6]	A	AA	4.239e^-6	0.09	UPSTREAM CG10996 INTRON inaE
3R	20051147	3R_20051147_DEL [dm3] 3R_24225425_DEL [dm6]	GCTG	G	4.245e^-6	0.09	CODON_DELETION Spps	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	16895812	X_16895812_INS [dm3] X_17001779_INS [dm6]	T	TTTACCCTT	4.477e^-6	0.093	INTRON CG45002
3L	6293688	3L_6293688_SNP [dm3] 3L_6300588_SNP [dm6]	A	T	4.496e^-6	0.093	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	11769496	2R_11769496_DEL [dm3] 2R_15881991_DEL [dm6]	TATTC	T	4.507e^-6	0.093	INTRON sli
3R	15892073	3R_15892073_SNP [dm3] 3R_20066351_SNP [dm6]	C	G	4.771e^-6	0.097	INTERGENIC
2R	18122805	2R_18122805_SNP [dm3] 2R_22235300_SNP [dm6]	G	T	4.830e^-6	0.097	DOWNSTREAM CR44755 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	12107227	3L_12107227_SNP [dm3] 3L_12114127_SNP [dm6]	G	A	4.902e^-6	0.097	INTERGENIC
X	17636382	X_17636382_INS [dm3] X_17742349_INS [dm6]	C	CCTTGATTCTGC...	4.936e^-6	0.097	INTRON CG42684	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_Trl
3L	14675527	3L_14675527_DEL [dm3] 3L_14682427_DEL [dm6]	ATTTTTCA	A	4.965e^-6	0.097	INTRON ome
3R	15711541	3R_15711541_SNP [dm3] 3R_19885819_SNP [dm6]	G	A	5.240e^-6	0.101	UTR_3_PRIME Pk92B DOWNSTREAM ninaE
3R	15886276	3R_15886276_SNP [dm3] 3R_20060554_SNP [dm6]	A	G	5.791e^-6	0.11	UPSTREAM CG4390 INTERGENIC
2R	5201035	2R_5201035_INS [dm3] 2R_9313530_INS [dm6]	C	CC	5.794e^-6	0.11	UPSTREAM mir-987 INTRON CG13739 & 1 other
3R	15890913	3R_15890913_SNP [dm3] 3R_20065191_SNP [dm6]	T	C	5.868e^-6	0.11	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

SegregVariants_X phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results