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=3.452e^-7)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1309 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	8809578	3L_8809578_SNP [dm3] 3L_8816478_SNP [dm6]	T	A	6.525e^-6	0.929	INTERGENIC
3R	10249200	3R_10249200_SNP [dm3] 3R_14423478_SNP [dm6]	A	G	7.103e^-6	0.929	UPSTREAM CR44176 INTRON cv-c
2L	4442692	2L_4442692_SNP [dm3] 2L_4442692_SNP [dm6]	C	A	1.196e^-5	0.929	SYNONYMOUS_CODING CG15432 UPSTREAM Sfp24F DOWNSTREAM morgue	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
3R	10249771	3R_10249771_SNP [dm3] 3R_14424049_SNP [dm6]	G	A	1.341e^-5	0.929	INTRON cv-c
2R	7070027	2R_7070027_SNP [dm3] 2R_11182522_SNP [dm6]	T	G	2.071e^-5	0.929	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	7070036	2R_7070036_SNP [dm3] 2R_11182531_SNP [dm6]	G	C	2.071e^-5	0.929	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	13577007	X_13577007_SNP [dm3] X_13682974_SNP [dm6]	A	G	2.438e^-5	0.929	UTR_5_PRIME CG11158
X	13866409	X_13866409_SNP [dm3] X_13972376_SNP [dm6]	T	G	2.466e^-5	0.929	INTRON mamo
2L	7012816	2L_7012816_SNP [dm3] 2L_7012816_SNP [dm6]	C	G	2.891e^-5	0.929	UPSTREAM CG43322 DOWNSTREAM CG43321 INTERGENIC
2R	9610105	2R_9610105_DEL [dm3] 2R_13722600_DEL [dm6]	GG	G	3.029e^-5	0.929	INTRON fas
3R	10249290	3R_10249290_SNP [dm3] 3R_14423568_SNP [dm6]	C	T	3.157e^-5	0.929	INTRON cv-c
X	17274549	X_17274549_SNP [dm3] X_17380516_SNP [dm6]	G	T	3.170e^-5	0.929	INTERGENIC
3L	17740227	3L_17740227_SNP [dm3] 3L_17747127_SNP [dm6]	G	A	3.631e^-5	0.929	UPSTREAM CG6034 INTRON Ccn
3L	17740673	3L_17740673_SNP [dm3] 3L_17747573_SNP [dm6]	C	T	3.631e^-5	0.929	UPSTREAM CG6034 INTRON Ccn
2L	4349985	2L_4349985_SNP [dm3] 2L_4349985_SNP [dm6]	C	G	3.684e^-5	0.929	DOWNSTREAM CR44699 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
3R	9886678	3R_9886678_SNP [dm3] 3R_14060956_SNP [dm6]	A	T	3.882e^-5	0.929	INTRON foxo	TF binding site mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
3R	18593697	3R_18593697_INS [dm3] 3R_22767975_INS [dm6]	A	AA	3.927e^-5	0.929	UPSTREAM CG13841 DOWNSTREAM CG43091 & 1 other INTRON Usp12-46 & 1 other
2L	16665677	2L_16665677_SNP [dm3] 2L_16665677_SNP [dm6]	G	C	3.937e^-5	0.929	INTRON Trpgamma	transposable element FlyBase
X	3153646	X_3153646_SNP [dm3] X_3259613_SNP [dm6]	G	C	4.295e^-5	0.929	INTRON dnc
2R	18538508	2R_18538508_SNP [dm3] 2R_22651003_SNP [dm6]	A	C	4.419e^-5	0.929	INTRON nsr	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16122919	2R_16122919_SNP [dm3] 2R_20235414_SNP [dm6]	C	G	4.502e^-5	0.929	UPSTREAM CG44625 & 1 other DOWNSTREAM CG11044 & 1 other INTERGENIC
3L	12606182	3L_12606182_SNP [dm3] 3L_12613082_SNP [dm6]	A	G	4.774e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
3L	8472576	3L_8472576_SNP [dm3] 3L_8479476_SNP [dm6]	A	C	4.792e^-5	0.929	SYNONYMOUS_CODING CG43163	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
3R	25897263	3R_25897263_SNP [dm3] 3R_30071541_SNP [dm6]	C	T	5.014e^-5	0.929	INTRON sima
3L	12606207	3L_12606207_SNP [dm3] 3L_12613107_SNP [dm6]	T	A	5.443e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
3L	12606208	3L_12606208_SNP [dm3] 3L_12613108_SNP [dm6]	T	A	5.443e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
3L	2365224	3L_2365224_SNP [dm3] 3L_2365224_SNP [dm6]	G	A	5.557e^-5	0.929	INTERGENIC
3L	2365246	3L_2365246_INS [dm3] 3L_2365246_INS [dm6]	T	TGGTT	5.557e^-5	0.929	INTERGENIC
2R	4709932	2R_4709932_SNP [dm3] 2R_8822427_SNP [dm6]	C	G	5.649e^-5	0.929	INTRON sns	TF binding site mE1_TFBS_chinmo
2L	19951553	2L_19951553_DEL [dm3] 2L_19951553_DEL [dm6]	TA	G	5.677e^-5	0.929	INTRON sick	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	15030639	2R_15030639_SNP [dm3] 2R_19143134_SNP [dm6]	C	T	5.786e^-5	0.929	INTRON ena	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Trl
3R	26580162	3R_26580162_SNP [dm3] 3R_30754440_SNP [dm6]	G	C	5.887e^-5	0.929	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	6329796	2L_6329796_SNP [dm3] 2L_6329796_SNP [dm6]	T	G	5.913e^-5	0.929	INTRON PDZ-GEF	TF binding site mE1_TFBS_cad
3L	17739962	3L_17739962_SNP [dm3] 3L_17746862_SNP [dm6]	G	A	5.963e^-5	0.929	UPSTREAM CG6034 INTRON Ccn
3L	17738232	3L_17738232_SNP [dm3] 3L_17745132_SNP [dm6]	G	A	5.988e^-5	0.929	DOWNSTREAM CG6034 INTRON Ccn
2R	16122527	2R_16122527_SNP [dm3] 2R_20235022_SNP [dm6]	A	T	6.039e^-5	0.929	START_GAINED CG44624 UTR_5_PRIME CG44624 UPSTREAM CG44625 DOWNSTREAM CG11044
2R	16122529	2R_16122529_SNP [dm3] 2R_20235024_SNP [dm6]	G	C	6.039e^-5	0.929	UTR_5_PRIME CG44624 UPSTREAM CG44625 DOWNSTREAM CG11044
3L	12606423	3L_12606423_INS [dm3] 3L_12613323_INS [dm6]	A	AT	6.099e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
3L	17740457	3L_17740457_SNP [dm3] 3L_17747357_SNP [dm6]	G	C	6.110e^-5	0.929	UPSTREAM CG6034 INTRON Ccn
X	18886862	X_18886862_SNP [dm3] X_18992829_SNP [dm6]	T	C	6.129e^-5	0.929	INTRON CG43759	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	10249699	3R_10249699_SNP [dm3] 3R_14423977_SNP [dm6]	C	A	6.345e^-5	0.929	INTRON cv-c
2R	12044760	2R_12044760_SNP [dm3] 2R_16157255_SNP [dm6]	A	C	6.356e^-5	0.929	DOWNSTREAM CG10734 INTRON lbk
2L	5849965	2L_5849965_SNP [dm3] 2L_5849965_SNP [dm6]	G	A	6.375e^-5	0.929	INTRON TrissinR
3L	12606235	3L_12606235_SNP [dm3] 3L_12613135_SNP [dm6]	G	A	6.393e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
X	18945107	X_18945107_SNP [dm3] X_19051074_SNP [dm6]	A	T	6.503e^-5	0.929	UTR_3_PRIME Diedel3 DOWNSTREAM Diedel3
2L	7390125	2L_7390125_SNP [dm3] 2L_7390125_SNP [dm6]	G	A	6.529e^-5	0.929	SYNONYMOUS_CODING gudu DOWNSTREAM CG5160	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2259386	2L_2259386_SNP [dm3] 2L_2259386_SNP [dm6]	C	T	6.593e^-5	0.929	DOWNSTREAM CR44788 INTERGENIC
2L	2259404	2L_2259404_SNP [dm3] 2L_2259404_SNP [dm6]	T	C	6.593e^-5	0.929	EXON CR44788
2L	2259406	2L_2259406_SNP [dm3] 2L_2259406_SNP [dm6]	C	T	6.593e^-5	0.929	EXON CR44788
2L	2259407	2L_2259407_SNP [dm3] 2L_2259407_SNP [dm6]	T	C	6.593e^-5	0.929	EXON CR44788
2R	8891260	2R_8891260_SNP [dm3] 2R_13003755_SNP [dm6]	C	T	6.593e^-5	0.929	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	12605689	3L_12605689_SNP [dm3] 3L_12612589_SNP [dm6]	C	G	6.593e^-5	0.929	INTRON caup
3L	12606083	3L_12606083_SNP [dm3] 3L_12612983_SNP [dm6]	C	T	6.593e^-5	0.929	INTRON caup	silencer mE1_HDAC_PRE
2R	7070095	2R_7070095_SNP [dm3] 2R_11182590_SNP [dm6]	A	G	6.828e^-5	0.929	UPSTREAM shn INTRON shn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	18876662	X_18876662_SNP [dm3] X_18982629_SNP [dm6]	G	A	7.039e^-5	0.929	INTRON CG43759
X	18876806	X_18876806_SNP [dm3] X_18982773_SNP [dm6]	T	A	7.039e^-5	0.929	INTRON CG43759
X	18876808	X_18876808_SNP [dm3] X_18982775_SNP [dm6]	C	T	7.039e^-5	0.929	INTRON CG43759
3L	6361188	3L_6361188_SNP [dm3] 3L_6368088_SNP [dm6]	T	C	7.192e^-5	0.929	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
2R	18775847	2R_18775847_SNP [dm3] 2R_22888324_SNP [dm6]	T	G	7.366e^-5	0.929	SYNONYMOUS_CODING Gmer UPSTREAM MED23 DOWNSTREAM asrij	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	8082053	X_8082053_SNP [dm3] X_8188020_SNP [dm6]	C	T	7.446e^-5	0.929	INTRON sdt
2R	19518925	2R_19518925_SNP [dm3] 2R_23631402_SNP [dm6]	A	G	7.476e^-5	0.929	INTERGENIC	silencer mE1_HDAC_PRE
2L	8324558	2L_8324558_INS [dm3] 2L_8324558_INS [dm6]	C	CTCCTGCT	7.568e^-5	0.929	INTRON CG7781
3L	17739865	3L_17739865_SNP [dm3] 3L_17746765_SNP [dm6]	C	T	7.620e^-5	0.929	SYNONYMOUS_CODING CG6034 INTRON Ccn
3L	6649799	3L_6649799_SNP [dm3] 3L_6656699_SNP [dm6]	T	C	7.643e^-5	0.929	INTERGENIC
3L	3145251	3L_3145251_SNP [dm3] 3L_3145251_SNP [dm6]	T	C	7.778e^-5	0.929	SYNONYMOUS_CODING CG1291 DOWNSTREAM CG12082	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	7160096	2R_7160096_SNP [dm3] 2R_11272591_SNP [dm6]	A	G	7.789e^-5	0.929	UPSTREAM Cpr47Ef INTERGENIC	TF binding site mE1_TFBS_cad
3L	12605508	3L_12605508_SNP [dm3] 3L_12612408_SNP [dm6]	T	C	7.805e^-5	0.929	INTRON caup
3L	17744152	3L_17744152_SNP [dm3] 3L_17751052_SNP [dm6]	T	A	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744158	3L_17744158_SNP [dm3] 3L_17751058_SNP [dm6]	G	C	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744163	3L_17744163_SNP [dm3] 3L_17751063_SNP [dm6]	C	T	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744164	3L_17744164_SNP [dm3] 3L_17751064_SNP [dm6]	C	T	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744170	3L_17744170_SNP [dm3] 3L_17751070_SNP [dm6]	A	T	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744173	3L_17744173_SNP [dm3] 3L_17751073_SNP [dm6]	A	G	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744175	3L_17744175_SNP [dm3] 3L_17751075_SNP [dm6]	T	A	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744179	3L_17744179_MNP [dm3] 3L_17751079_MNP [dm6]	GAA	TTC	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744188	3L_17744188_SNP [dm3] 3L_17751088_SNP [dm6]	T	C	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
3L	17744189	3L_17744189_SNP [dm3] 3L_17751089_SNP [dm6]	A	T	7.895e^-5	0.929	UPSTREAM Adgf-B DOWNSTREAM Adgf-A INTERGENIC
X	16234624	X_16234624_SNP [dm3] X_16340591_SNP [dm6]	G	C	7.909e^-5	0.929	UTR_3_PRIME Dsp1 DOWNSTREAM Dsp1
2L	13030083	2L_13030083_SNP [dm3] 2L_13030083_SNP [dm6]	T	C	7.911e^-5	0.929	SYNONYMOUS_CODING CG9932	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	13060154	2R_13060154_SNP [dm3] 2R_17172649_SNP [dm6]	T	A	8.261e^-5	0.929	INTERGENIC
3L	5649597	3L_5649597_SNP [dm3] 3L_5656497_SNP [dm6]	A	G	8.404e^-5	0.929	INTRON lin-28	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	5649600	3L_5649600_SNP [dm3] 3L_5656500_SNP [dm6]	G	A	8.404e^-5	0.929	INTRON lin-28	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	9901605	2R_9901605_SNP [dm3] 2R_14014100_SNP [dm6]	A	T	8.463e^-5	0.929	INTRON mam
2L	16082151	2L_16082151_SNP [dm3] 2L_16082151_SNP [dm6]	G	A	8.469e^-5	0.929	DOWNSTREAM beat-Ia INTERGENIC
2L	4141699	2L_4141699_SNP [dm3] 2L_4141699_SNP [dm6]	A	G	8.484e^-5	0.929	INTERGENIC
3L	2920501	3L_2920501_SNP [dm3] 3L_2920501_SNP [dm6]	G	A	8.517e^-5	0.929	INTRON Shab
2L	5248343	2L_5248343_SNP [dm3] 2L_5248343_SNP [dm6]	A	C	8.857e^-5	0.929	INTRON tkv
2L	5248349	2L_5248349_SNP [dm3] 2L_5248349_SNP [dm6]	G	A	8.857e^-5	0.929	INTRON tkv
3L	2920465	3L_2920465_INS [dm3] 3L_2920465_INS [dm6]	C	CTATGTATTTGTATTATTC...	9.207e^-5	0.929	INTRON Shab
3L	2920472	3L_2920472_SNP [dm3] 3L_2920472_SNP [dm6]	A	G	9.207e^-5	0.929	INTRON Shab
3L	17934912	3L_17934912_SNP [dm3] 3L_17941812_SNP [dm6]	T	C	9.263e^-5	0.929	INTRON CG43174
2R	8888926	2R_8888926_SNP [dm3] 2R_13001421_SNP [dm6]	G	A	9.321e^-5	0.929	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8888932	2R_8888932_SNP [dm3] 2R_13001427_SNP [dm6]	G	A	9.321e^-5	0.929	SYNONYMOUS_CODING Su_z_2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	17709429	3L_17709429_SNP [dm3] 3L_17716329_SNP [dm6]	C	T	9.345e^-5	0.929	INTRON Ccn	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	9273151	X_9273151_SNP [dm3] X_9379118_SNP [dm6]	G	C	9.375e^-5	0.929	INTRON mgl
X	9273193	X_9273193_SNP [dm3] X_9379160_SNP [dm6]	T	A	9.375e^-5	0.929	INTRON mgl
3R	26456440	3R_26456440_DEL [dm3] 3R_30630718_DEL [dm6]	ACTA	A	9.386e^-5	0.929	INTERGENIC	TF binding site mE1_TFBS_cad
3L	4056711	3L_4056711_SNP [dm3] 3L_4056711_SNP [dm6]	T	G	9.440e^-5	0.929	INTRON CG1136	TF binding site mE1_TFBS_cad
3R	18004542	3R_18004542_DEL [dm3] 3R_22178820_DEL [dm6]	TT	T	9.487e^-5	0.929	INTRON SKIP
3R	18004547	3R_18004547_SNP [dm3] 3R_22178825_SNP [dm6]	G	T	9.487e^-5	0.929	INTRON SKIP

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By genomic position
Variant impact
Gene name

daughters3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results