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=1.507e^-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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1567 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
2L	9824945	2L_9824945_SNP [dm3] 2L_9824945_SNP [dm6]	A	G	3.640e^-7	0.661	INTRON nAChRalpha6
2R	12392094	2R_12392094_INS [dm3] 2R_16504589_INS [dm6]	C	CACCCCCCA	9.041e^-6	0.957	INTRON Sema-2a
3R	26963749	3R_26963749_SNP [dm3] 3R_31138027_SNP [dm6]	T	C	1.113e^-5	0.957	INTRON Gycbeta100B
2L	10216987	2L_10216987_SNP [dm3] 2L_10216987_SNP [dm6]	C	T	1.164e^-5	0.957	SYNONYMOUS_CODING Npc1a	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	10091948	2L_10091948_SNP [dm3] 2L_10091948_SNP [dm6]	A	G	1.218e^-5	0.957	SYNONYMOUS_CODING CG13133 INTRON CG44153	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12392088	2R_12392088_SNP [dm3] 2R_16504583_SNP [dm6]	A	C	1.285e^-5	0.957	INTRON Sema-2a
X	4850023	X_4850023_SNP [dm3] X_4955990_SNP [dm6]	C	A	1.473e^-5	0.957	DOWNSTREAM Ptp4E & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_kn
2R	3040600	2R_3040600_SNP [dm3] 2R_7153095_SNP [dm6]	A	T	1.609e^-5	0.957	SYNONYMOUS_CODING Spn43Ab DOWNSTREAM Spn43Ad INTRON pk	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	7051350	2L_7051350_SNP [dm3] 2L_7051350_SNP [dm6]	C	T	1.656e^-5	0.957	INTRON milt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad
2L	10029121	2L_10029121_SNP [dm3] 2L_10029121_SNP [dm6]	C	G	1.664e^-5	0.957	UTR_3_PRIME CG13127
2L	14894113	2L_14894113_SNP [dm3] 2L_14894113_SNP [dm6]	G	C	1.711e^-5	0.957	INTERGENIC
3R	24882287	3R_24882287_SNP [dm3] 3R_29056565_SNP [dm6]	A	T	1.715e^-5	0.957	NON_SYNONYMOUS_CODING Sirt7 DOWNSTREAM CG11843
3R	4585151	3R_4585151_SNP [dm3] 3R_8759429_SNP [dm6]	C	G	1.765e^-5	0.957	INTRON CG11768 & 1 other
2L	8975274	2L_8975274_SNP [dm3] 2L_8975274_SNP [dm6]	T	A	1.776e^-5	0.957	UTR_5_PRIME CG9541 UPSTREAM CG9541	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
X	2666078	X_2666078_SNP [dm3] X_2772045_SNP [dm6]	G	C	1.906e^-5	0.957	INTRON kirre
X	2284680	X_2284680_SNP [dm3] X_2390647_SNP [dm6]	T	A	1.940e^-5	0.957	INTERGENIC
2L	702221	2L_702221_SNP [dm3] 2L_702221_SNP [dm6]	G	A	2.124e^-5	0.957	INTRON ds	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl
X	2399609	X_2399609_SNP [dm3] X_2505576_SNP [dm6]	T	G	2.225e^-5	0.957	UPSTREAM trol INTRON trol	TF binding site mE1_TFBS_cad
3R	14175778	3R_14175778_DEL [dm3] 3R_18350056_DEL [dm6]	CTAAGTATAT	C	2.283e^-5	0.957	INTRON CG15803
2R	14227947	2R_14227947_SNP [dm3] 2R_18340442_SNP [dm6]	C	G	2.390e^-5	0.957	INTRON sbb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18276415	2R_18276415_SNP [dm3] 2R_22388910_SNP [dm6]	G	A	2.543e^-5	0.957	INTRON CG13506
3L	1614702	3L_1614702_SNP [dm3] 3L_1614702_SNP [dm6]	C	T	2.947e^-5	0.957	NON_SYNONYMOUS_CODING CG12105 UPSTREAM CG12105 INTRON CG33791 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	26963771	3R_26963771_SNP [dm3] 3R_31138049_SNP [dm6]	A	T	3.042e^-5	0.957	INTRON Gycbeta100B
3L	1188053	3L_1188053_SNP [dm3] 3L_1188053_SNP [dm6]	G	A	3.144e^-5	0.957	INTERGENIC
2L	11166476	2L_11166476_SNP [dm3] 2L_11166476_SNP [dm6]	G	A	3.302e^-5	0.957	INTRON Ca-beta
2L	19789025	2L_19789025_SNP [dm3] 2L_19789025_SNP [dm6]	G	A	3.314e^-5	0.957	INTRON CdGAPr
X	15560909	X_15560909_SNP [dm3] X_15666876_SNP [dm6]	C	T	3.450e^-5	0.957	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	15560914	X_15560914_SNP [dm3] X_15666881_SNP [dm6]	T	C	3.450e^-5	0.957	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	24881038	3R_24881038_SNP [dm3] 3R_29055316_SNP [dm6]	C	T	3.452e^-5	0.957	NON_SYNONYMOUS_CODING CG11843 UPSTREAM Sirt7	TF binding site BDTNP1_TFBS_dl
3R	24881063	3R_24881063_SNP [dm3] 3R_29055341_SNP [dm6]	G	C	3.452e^-5	0.957	SYNONYMOUS_CODING CG11843 UPSTREAM Sirt7	TF binding site BDTNP1_TFBS_dl
3R	20929533	3R_20929533_SNP [dm3] 3R_25103811_SNP [dm6]	C	T	3.729e^-5	0.957	NON_SYNONYMOUS_CODING CG34027 DOWNSTREAM CG45095
3R	13611718	3R_13611718_SNP [dm3] 3R_17785996_SNP [dm6]	C	T	3.785e^-5	0.957	INTRON CG43102
3R	24880829	3R_24880829_SNP [dm3] 3R_29055107_SNP [dm6]	G	T	3.838e^-5	0.957	NON_SYNONYMOUS_CODING CG11843 UPSTREAM Sirt7	TF binding site BDTNP1_TFBS_dl
3L	12349162	3L_12349162_SNP [dm3] 3L_12356062_SNP [dm6]	G	A	3.933e^-5	0.957	INTERGENIC
3L	11193198	3L_11193198_SNP [dm3] 3L_11200098_SNP [dm6]	A	G	3.989e^-5	0.957	INTRON Plod & 1 other
3L	3633461	3L_3633461_SNP [dm3] 3L_3633461_SNP [dm6]	A	G	4.022e^-5	0.957	INTRON dar1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3L	1189002	3L_1189002_SNP [dm3] 3L_1189002_SNP [dm6]	G	A	4.159e^-5	0.957	UPSTREAM CG13912 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
3L	9509103	3L_9509103_SNP [dm3] 3L_9516003_SNP [dm6]	C	A	4.455e^-5	0.957	INTRON CG33700
3L	4289564	3L_4289564_SNP [dm3] 3L_4289564_SNP [dm6]	T	C	4.476e^-5	0.957	SYNONYMOUS_CODING Hexo1	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	9633603	2L_9633603_SNP [dm3] 2L_9633603_SNP [dm6]	T	A	4.509e^-5	0.957	UPSTREAM Apoltp INTERGENIC
3L	11907388	3L_11907388_SNP [dm3] 3L_11914288_SNP [dm6]	C	A	4.524e^-5	0.957	INTRON CG44837
3R	26963840	3R_26963840_INS [dm3] 3R_31138118_INS [dm6]	A	AA	4.739e^-5	0.957	INTRON Gycbeta100B
3R	26963842	3R_26963842_SNP [dm3] 3R_31138120_SNP [dm6]	G	A	4.739e^-5	0.957	INTRON Gycbeta100B
2L	7903161	2L_7903161_SNP [dm3] 2L_7903161_SNP [dm6]	C	T	4.746e^-5	0.957	INTRON Snoo
2L	7903205	2L_7903205_SNP [dm3] 2L_7903205_SNP [dm6]	T	A	4.746e^-5	0.957	INTRON Snoo
2L	7903434	2L_7903434_SNP [dm3] 2L_7903434_SNP [dm6]	T	C	4.746e^-5	0.957	INTRON Snoo
2L	7904122	2L_7904122_SNP [dm3] 2L_7904122_SNP [dm6]	G	A	4.746e^-5	0.957	INTRON Snoo
2L	7904259	2L_7904259_SNP [dm3] 2L_7904259_SNP [dm6]	C	T	4.746e^-5	0.957	INTRON Snoo
2L	10514949	2L_10514949_SNP [dm3] 2L_10514949_SNP [dm6]	C	T	4.831e^-5	0.957	INTRON Fatp & 1 other
3L	427841	3L_427841_SNP [dm3] 3L_427841_SNP [dm6]	C	T	4.894e^-5	0.957	INTERGENIC
2L	7904690	2L_7904690_SNP [dm3] 2L_7904690_SNP [dm6]	C	G	5.067e^-5	0.957	INTRON Snoo	TF binding site mE1_TFBS_chinmo
2L	19789027	2L_19789027_SNP [dm3] 2L_19789027_SNP [dm6]	T	A	5.070e^-5	0.957	INTRON CdGAPr
2L	19789033	2L_19789033_SNP [dm3] 2L_19789033_SNP [dm6]	A	G	5.070e^-5	0.957	INTRON CdGAPr
2L	1318084	2L_1318084_SNP [dm3] 2L_1318084_SNP [dm6]	C	A	5.099e^-5	0.957	INTERGENIC
2L	1318088	2L_1318088_SNP [dm3] 2L_1318088_SNP [dm6]	G	T	5.099e^-5	0.957	INTERGENIC
2R	11663155	2R_11663155_SNP [dm3] 2R_15775650_SNP [dm6]	G	A	5.132e^-5	0.957	INTRON Zasp52	TF binding site mE1_TFBS_chinmo
2R	14413756	2R_14413756_DEL [dm3] 2R_18526251_DEL [dm6]	ACTATAAATA	A	5.273e^-5	0.957	UTR_3_PRIME CG43066 DOWNSTREAM CG43066
2L	9968121	2L_9968121_SNP [dm3] 2L_9968121_SNP [dm6]	G	A	5.456e^-5	0.957	SYNONYMOUS_CODING RpL13 UPSTREAM Dref	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens
3R	24883928	3R_24883928_SNP [dm3] 3R_29058206_SNP [dm6]	A	G	5.469e^-5	0.957	NON_SYNONYMOUS_CODING Sirt7	TF binding site mE1_TFBS_sens
3R	14175882	3R_14175882_SNP [dm3] 3R_18350160_SNP [dm6]	A	T	5.515e^-5	0.957	INTRON CG15803
3R	14175884	3R_14175884_SNP [dm3] 3R_18350162_SNP [dm6]	G	C	5.515e^-5	0.957	INTRON CG15803
2R	14531475	2R_14531475_SNP [dm3] 2R_18643970_SNP [dm6]	C	T	5.619e^-5	0.957	INTRON SP2637
2R	9854889	2R_9854889_SNP [dm3] 2R_13967384_SNP [dm6]	T	C	5.644e^-5	0.957	SYNONYMOUS_CODING Cp1 UPSTREAM Aats-phe	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	11843564	X_11843564_SNP [dm3] X_11949531_SNP [dm6]	A	T	5.691e^-5	0.957	INTRON cac	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	3823285	3R_3823285_SNP [dm3] 3R_7997563_SNP [dm6]	C	A	5.920e^-5	0.957	INTERGENIC
3R	3824488	3R_3824488_SNP [dm3] 3R_7998766_SNP [dm6]	C	T	5.920e^-5	0.957	INTERGENIC
2L	7333427	2L_7333427_SNP [dm3] 2L_7333427_SNP [dm6]	A	C	5.929e^-5	0.957	UPSTREAM Wnt6 INTERGENIC
X	5868727	X_5868727_SNP [dm3] X_5974694_SNP [dm6]	G	A	5.944e^-5	0.957	INTRON Grip
2R	6058432	2R_6058432_SNP [dm3] 2R_10170927_SNP [dm6]	A	G	5.958e^-5	0.957	INTRON KCNQ
3L	13204182	3L_13204182_SNP [dm3] 3L_13211082_SNP [dm6]	G	C	6.101e^-5	0.957	UPSTREAM tRNA:CR32129 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	19909992	3R_19909992_SNP [dm3] 3R_24084270_SNP [dm6]	G	A	6.233e^-5	0.957	INTRON 4EHP
2L	7906844	2L_7906844_SNP [dm3] 2L_7906844_SNP [dm6]	T	A	6.323e^-5	0.957	INTRON Snoo
2L	7907494	2L_7907494_SNP [dm3] 2L_7907494_SNP [dm6]	T	A	6.323e^-5	0.957	INTRON Snoo	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	2922495	3L_2922495_SNP [dm3] 3L_2922495_SNP [dm6]	T	C	6.324e^-5	0.957	INTRON Shab
2R	13779380	2R_13779380_SNP [dm3] 2R_17891875_SNP [dm6]	A	G	6.342e^-5	0.957	INTRON Elk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	25520527	3R_25520527_SNP [dm3] 3R_29694805_SNP [dm6]	G	T	6.351e^-5	0.957	INTRON dmrt99B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd
2L	11607832	2L_11607832_SNP [dm3] 2L_11607832_SNP [dm6]	C	T	6.448e^-5	0.957	INTRON kek2	TF binding site mE1_TFBS_Ubx
2L	5965903	2L_5965903_SNP [dm3] 2L_5965903_SNP [dm6]	G	A	6.555e^-5	0.957	SYNONYMOUS_CODING CG13992 UPSTREAM psd	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	8973595	3L_8973595_SNP [dm3] 3L_8980495_SNP [dm6]	T	C	6.615e^-5	0.957	UPSTREAM CG5644 INTERGENIC
3R	26338099	3R_26338099_SNP [dm3] 3R_30512377_SNP [dm6]	T	G	6.642e^-5	0.957	UTR_3_PRIME CG31524 UPSTREAM PH4alphaNE2
2R	14606616	2R_14606616_SNP [dm3] 2R_18719111_SNP [dm6]	G	A	6.649e^-5	0.957	INTRON Hs3st-A
3L	13204177	3L_13204177_SNP [dm3] 3L_13211077_SNP [dm6]	G	T	6.722e^-5	0.957	UPSTREAM tRNA:CR32129 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15273213	2R_15273213_SNP [dm3] 2R_19385708_SNP [dm6]	T	A	6.824e^-5	0.957	UPSTREAM CG10081 DOWNSTREAM CG10073 INTERGENIC
3R	14174865	3R_14174865_SNP [dm3] 3R_18349143_SNP [dm6]	T	C	6.911e^-5	0.957	INTRON CG15803
2L	5965921	2L_5965921_SNP [dm3] 2L_5965921_SNP [dm6]	G	A	6.924e^-5	0.957	SYNONYMOUS_CODING CG13992 UPSTREAM psd	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	19102584	2R_19102584_SNP [dm3] 2R_23215061_SNP [dm6]	G	A	7.023e^-5	0.957	INTERGENIC
3L	2963716	3L_2963716_INS [dm3] 3L_2963716_INS [dm6]	G	TGCACACTAAAAGA...	7.037e^-5	0.957	UTR_3_PRIME Or63a
3L	16540819	3L_16540819_SNP [dm3] 3L_16547719_SNP [dm6]	G	A	7.062e^-5	0.957	INTERGENIC
3L	15896021	3L_15896021_INS [dm3] 3L_15902921_INS [dm6]	T	TCTT	7.081e^-5	0.957	UTR_3_PRIME sff
X	16410025	X_16410025_SNP [dm3] X_16515992_SNP [dm6]	A	G	7.186e^-5	0.957	INTRON para
X	8878169	X_8878169_SNP [dm3] X_8984136_SNP [dm6]	C	G	7.199e^-5	0.957	SYNONYMOUS_CODING CG12662 INTRON rdgA & 1 other
2L	7906722	2L_7906722_SNP [dm3] 2L_7906722_SNP [dm6]	T	C	7.263e^-5	0.957	INTRON Snoo
3R	24884393	3R_24884393_SNP [dm3] 3R_29058671_SNP [dm6]	A	C	7.352e^-5	0.957	SYNONYMOUS_CODING Sirt7 DOWNSTREAM Cul5
2L	1318102	2L_1318102_SNP [dm3] 2L_1318102_SNP [dm6]	G	T	7.385e^-5	0.957	INTERGENIC
3L	1266401	3L_1266401_SNP [dm3] 3L_1266401_SNP [dm6]	C	T	7.556e^-5	0.957	INTRON CG9134
2L	19290339	2L_19290339_SNP [dm3] 2L_19290339_SNP [dm6]	A	T	7.558e^-5	0.957	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	5463019	2L_5463019_SNP [dm3] 2L_5463019_SNP [dm6]	G	A	7.690e^-5	0.957	INTRON mid
2L	10096892	2L_10096892_SNP [dm3] 2L_10096892_SNP [dm6]	T	C	7.849e^-5	0.957	INTRON CG44153 & 1 other
2R	2035245	2R_2035245_SNP [dm3] 2R_6147740_SNP [dm6]	C	G	7.897e^-5	0.957	INTRON EcR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	2035267	2R_2035267_SNP [dm3] 2R_6147762_SNP [dm6]	T	C	7.897e^-5	0.957	INTRON EcR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

CN_Hobo_TIDAL_W phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results