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=1.814e^-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

Covariate	p-value	Significance
In_2R_NS	0.02692
In_3R_K	0.04075

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	4.9789	0.083

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2040 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	6690585	2L_6690585_SNP [dm3] 2L_6690585_SNP [dm6]	A	T	3.711e^-7	0.409	INTRON Tsp
2R	1763232	2R_1763232_SNP [dm3] 2R_5875727_SNP [dm6]	T	G	4.892e^-7	0.409	INTERGENIC
X	6123877	X_6123877_SNP [dm3] X_6229844_SNP [dm6]	A	C	6.545e^-7	0.409	SPLICE_SITE_ACCEPTOR CG14446 SPLICE_SITE_REGION CG14446 INTRON CG14446
2L	15177343	2L_15177343_DEL [dm3] 2L_15177343_DEL [dm6]	TCT	AG	1.392e^-6	0.476	INTRON CG4168
3R	26700572	3R_26700572_INS [dm3] 3R_30874850_INS [dm6]	G	GATAG	1.590e^-6	0.476	UTR_3_PRIME CG15546	TF binding site mE1_TFBS_cad
X	18427520	X_18427520_INS [dm3] X_18533487_INS [dm6]	A	AA	1.637e^-6	0.476	INTRON Bx	TF binding site BDTNP1_TFBS_dl
2R	13764194	2R_13764194_SNP [dm3] 2R_17876689_SNP [dm6]	T	C	1.779e^-6	0.476	DOWNSTREAM CG30325 INTRON Elk
3L	20786909	3L_20786909_SNP [dm3] 3L_20793809_SNP [dm6]	C	G	3.437e^-6	0.645	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	11551096	3R_11551096_SNP [dm3] 3R_15725374_SNP [dm6]	C	G	3.452e^-6	0.645	INTERGENIC
3R	27510691	3R_27510691_SNP [dm3] 3R_31684969_SNP [dm6]	G	A	3.552e^-6	0.645	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	6305126	2R_6305126_SNP [dm3] 2R_10417621_SNP [dm6]	G	A	3.783e^-6	0.645	UPSTREAM CG42732 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
X	3464623	X_3464623_SNP [dm3] X_3570590_SNP [dm6]	C	G	4.244e^-6	0.663	DOWNSTREAM CG2875 INTRON CG32791 & 1 other	TF binding site mE1_TFBS_sens
2L	6326078	2L_6326078_SNP [dm3] 2L_6326078_SNP [dm6]	C	T	5.908e^-6	0.795	SYNONYMOUS_CODING PDZ-GEF	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	26700538	3R_26700538_DEL [dm3] 3R_30874816_DEL [dm6]	TT	G	6.176e^-6	0.795	UTR_3_PRIME CG15546	TF binding site mE1_TFBS_cad
3L	2756172	3L_2756172_SNP [dm3] 3L_2756172_SNP [dm6]	G	A	6.815e^-6	0.795	INTRON Mrtf	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	26700569	3R_26700569_SNP [dm3] 3R_30874847_SNP [dm6]	C	A	7.003e^-6	0.795	UTR_3_PRIME CG15546	TF binding site mE1_TFBS_cad
X	3464629	X_3464629_SNP [dm3] X_3570596_SNP [dm6]	C	A	7.555e^-6	0.795	DOWNSTREAM CG2875 INTRON CG32791 & 1 other	TF binding site mE1_TFBS_sens
X	17163604	X_17163604_SNP [dm3] X_17269571_SNP [dm6]	A	T	7.788e^-6	0.795	INTRON f
X	18427514	X_18427514_SNP [dm3] X_18533481_SNP [dm6]	T	C	8.059e^-6	0.795	INTRON Bx	TF binding site BDTNP1_TFBS_dl
2L	8131746	2L_8131746_SNP [dm3] 2L_8131746_SNP [dm6]	G	A	8.573e^-6	0.802	SYNONYMOUS_CODING CG8668	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	4005442	2L_4005442_SNP [dm3] 2L_4005442_SNP [dm6]	G	A	8.981e^-6	0.802	UTR_3_PRIME CG15422 UPSTREAM CG15423 DOWNSTREAM CG34176
2L	13095101	2L_13095101_SNP [dm3] 2L_13095101_SNP [dm6]	T	C	9.631e^-6	0.821	INTERGENIC
X	4207725	X_4207725_SNP [dm3] X_4313692_SNP [dm6]	T	G	1.043e^-5	0.831	DOWNSTREAM mei-9 INTRON CR44957
X	12136186	X_12136186_SNP [dm3] X_12242153_SNP [dm6]	G	T	1.073e^-5	0.831	INTRON Ten-a
X	14048631	X_14048631_SNP [dm3] X_14154598_SNP [dm6]	T	G	1.125e^-5	0.831	INTERGENIC
X	4207737	X_4207737_SNP [dm3] X_4313704_SNP [dm6]	T	A	1.165e^-5	0.831	DOWNSTREAM mei-9 INTRON CR44957
2R	1767538	2R_1767538_SNP [dm3] 2R_5880033_SNP [dm6]	G	A	1.203e^-5	0.831	UTR_5_PRIME CG44438
3R	13394726	3R_13394726_SNP [dm3] 3R_17569004_SNP [dm6]	T	C	1.269e^-5	0.831	UTR_3_PRIME Hmx DOWNSTREAM Hmx
X	12136180	X_12136180_SNP [dm3] X_12242147_SNP [dm6]	T	A	1.292e^-5	0.831	INTRON Ten-a
3R	26700558	3R_26700558_SNP [dm3] 3R_30874836_SNP [dm6]	A	T	1.330e^-5	0.831	UTR_3_PRIME CG15546	TF binding site mE1_TFBS_cad
2R	7061436	2R_7061436_DEL [dm3] 2R_11173931_DEL [dm6]	AA	A	1.589e^-5	0.861	UTR_5_PRIME shn INTRON shn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2R	18733139	2R_18733139_INS [dm3] 2R_22845616_INS [dm6]	T	AGAAATGCA	1.703e^-5	0.861	UPSTREAM CG3649 INTERGENIC
2R	18733145	2R_18733145_SNP [dm3] 2R_22845622_SNP [dm6]	T	A	1.703e^-5	0.861	UPSTREAM CG3649 INTERGENIC
3R	26068611	3R_26068611_SNP [dm3] 3R_30242889_SNP [dm6]	A	G	1.731e^-5	0.861	SYNONYMOUS_CODING CG9737
2L	16711906	2L_16711906_SNP [dm3] 2L_16711906_SNP [dm6]	G	A	1.820e^-5	0.861	INTRON CG31808
X	2767502	X_2767502_SNP [dm3] X_2873469_SNP [dm6]	C	A	1.851e^-5	0.861	UPSTREAM CG14416 INTRON kirre
3R	15081327	3R_15081327_SNP [dm3] 3R_19255605_SNP [dm6]	C	T	1.852e^-5	0.861	INTERGENIC
3L	11204075	3L_11204075_SNP [dm3] 3L_11210975_SNP [dm6]	C	A	1.867e^-5	0.861	SYNONYMOUS_CODING CG7600 UPSTREAM Ube3a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	14061490	X_14061490_DEL [dm3] X_14167457_DEL [dm6]	AAACTTGATCTATTGTTTGG...	A	1.985e^-5	0.861	INTERGENIC
X	12136173	X_12136173_INS [dm3] X_12242140_INS [dm6]	T	TGGTATGCTAGATAACAATT...	2.005e^-5	0.861	INTRON Ten-a
2L	8334626	2L_8334626_SNP [dm3] 2L_8334626_SNP [dm6]	A	C	2.093e^-5	0.861	INTERGENIC
2R	15197886	2R_15197886_SNP [dm3] 2R_19310381_SNP [dm6]	A	C	2.223e^-5	0.861	DOWNSTREAM Rgk1 INTRON EndoB	TF binding site mE1_TFBS_sens
2L	15177339	2L_15177339_SNP [dm3] 2L_15177339_SNP [dm6]	G	A	2.238e^-5	0.861	INTRON CG4168
2L	17431580	2L_17431580_SNP [dm3] 2L_17431580_SNP [dm6]	C	G	2.238e^-5	0.861	INTRON Dif
X	19868563	X_19868563_INS [dm3] X_19974530_INS [dm6]	A	ACACAGTGT	2.293e^-5	0.861	INTERGENIC
3L	2726578	3L_2726578_DEL [dm3] 3L_2726578_DEL [dm6]	AATAGCA	A	2.424e^-5	0.861	INTRON Mrtf
2R	15197839	2R_15197839_SNP [dm3] 2R_19310334_SNP [dm6]	A	G	2.447e^-5	0.861	DOWNSTREAM Rgk1 INTRON EndoB	TF binding site mE1_TFBS_sens
X	13086590	X_13086590_SNP [dm3] X_13192557_SNP [dm6]	T	G	2.536e^-5	0.861	UPSTREAM CG12723 DOWNSTREAM CG2453 INTERGENIC
2L	16028551	2L_16028551_SNP [dm3] 2L_16028551_SNP [dm6]	T	C	2.537e^-5	0.861	INTRON beat-Ic	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	8131748	2L_8131748_SNP [dm3] 2L_8131748_SNP [dm6]	G	A	2.599e^-5	0.861	NON_SYNONYMOUS_CODING CG8668	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	26182355	3R_26182355_SNP [dm3] 3R_30356633_SNP [dm6]	A	G	2.659e^-5	0.861	INTRON hdc
X	8841669	X_8841669_SNP [dm3] X_8947636_SNP [dm6]	A	G	2.743e^-5	0.861	INTRON rdgA
X	12136165	X_12136165_SNP [dm3] X_12242132_SNP [dm6]	T	C	2.806e^-5	0.861	INTRON Ten-a
3R	26649828	3R_26649828_SNP [dm3] 3R_30824106_SNP [dm6]	G	A	2.821e^-5	0.861	INTRON cindr	TF binding site mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA
2L	11872752	2L_11872752_SNP [dm3] 2L_11872752_SNP [dm6]	C	A	2.839e^-5	0.861	INTRON Pde1c
3R	19688846	3R_19688846_SNP [dm3] 3R_23863124_SNP [dm6]	A	C	2.847e^-5	0.861	SYNONYMOUS_CODING Pli	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	12017288	3R_12017288_SNP [dm3] 3R_16191566_SNP [dm6]	A	T	2.882e^-5	0.861	INTRON sra
2L	13537014	2L_13537014_SNP [dm3] 2L_13537014_SNP [dm6]	G	T	2.927e^-5	0.861	INTRON B4
2L	13537039	2L_13537039_SNP [dm3] 2L_13537039_SNP [dm6]	G	A	2.927e^-5	0.861	INTRON B4
2L	10580169	2L_10580169_SNP [dm3] 2L_10580169_SNP [dm6]	G	A	3.017e^-5	0.861	NON_SYNONYMOUS_CODING CG34160 DOWNSTREAM CG34161 INTRON Trim9
3R	20332253	3R_20332253_SNP [dm3] 3R_24506531_SNP [dm6]	C	T	3.063e^-5	0.861	INTERGENIC
3L	4027313	3L_4027313_SNP [dm3] 3L_4027313_SNP [dm6]	G	C	3.080e^-5	0.861	NON_SYNONYMOUS_CODING Gr64a
3L	4027318	3L_4027318_SNP [dm3] 3L_4027318_SNP [dm6]	C	T	3.116e^-5	0.861	SYNONYMOUS_CODING Gr64a
2L	8045319	2L_8045319_SNP [dm3] 2L_8045319_SNP [dm6]	G	A	3.180e^-5	0.861	NON_SYNONYMOUS_CODING CG7466
X	16557862	X_16557862_SNP [dm3] X_16663829_SNP [dm6]	A	T	3.221e^-5	0.861	INTRON r & 1 other	TF binding site mE1_TFBS_chinmo
3L	4027291	3L_4027291_SNP [dm3] 3L_4027291_SNP [dm6]	C	T	3.223e^-5	0.861	SYNONYMOUS_CODING Gr64a
X	11235925	X_11235925_SNP [dm3] X_11341892_SNP [dm6]	G	T	3.227e^-5	0.861	INTRON CG34348	TF binding site BDTNP1_TFBS_dl
3L	4027229	3L_4027229_SNP [dm3] 3L_4027229_SNP [dm6]	G	A	3.281e^-5	0.861	INTRON Gr64a
2L	5841406	2L_5841406_SNP [dm3] 2L_5841406_SNP [dm6]	G	T	3.302e^-5	0.861	INTRON TrissinR
3L	3682683	3L_3682683_SNP [dm3] 3L_3682683_SNP [dm6]	C	T	3.388e^-5	0.861	INTERGENIC
2L	5840493	2L_5840493_SNP [dm3] 2L_5840493_SNP [dm6]	C	T	3.410e^-5	0.861	INTRON TrissinR
3R	15108766	3R_15108766_SNP [dm3] 3R_19283044_SNP [dm6]	A	G	3.426e^-5	0.861	INTERGENIC
3L	20830294	3L_20830294_SNP [dm3] 3L_20837194_SNP [dm6]	T	C	3.455e^-5	0.861	UPSTREAM CG13255 & 1 other DOWNSTREAM CG3288 INTERGENIC
3L	20830715	3L_20830715_SNP [dm3] 3L_20837615_SNP [dm6]	G	A	3.460e^-5	0.861	START_GAINED CG13255 UTR_5_PRIME CG13255 UPSTREAM CG13255 & 1 other DOWNSTREAM CG3288
2R	15197906	2R_15197906_SNP [dm3] 2R_19310401_SNP [dm6]	T	C	3.500e^-5	0.861	DOWNSTREAM Rgk1 INTRON EndoB	TF binding site mE1_TFBS_sens
3R	9731277	3R_9731277_SNP [dm3] 3R_13905555_SNP [dm6]	A	T	3.505e^-5	0.861	DOWNSTREAM ems INTERGENIC
X	4207789	X_4207789_SNP [dm3] X_4313756_SNP [dm6]	G	C	3.622e^-5	0.861	DOWNSTREAM mei-9 EXON CR44957
2L	668623	2L_668623_SNP [dm3] 2L_668623_SNP [dm6]	G	A	3.643e^-5	0.861	INTRON ds	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14048632	X_14048632_SNP [dm3] X_14154599_SNP [dm6]	C	T	3.656e^-5	0.861	INTERGENIC
2L	8183699	2L_8183699_SNP [dm3] 2L_8183699_SNP [dm6]	T	C	3.673e^-5	0.861	SYNONYMOUS_CODING Piezo
2L	6326081	2L_6326081_SNP [dm3] 2L_6326081_SNP [dm6]	A	G	3.736e^-5	0.865	SYNONYMOUS_CODING PDZ-GEF	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	25022067	3R_25022067_SNP [dm3] 3R_29196345_SNP [dm6]	C	T	3.922e^-5	0.888	INTERGENIC
X	9179892	X_9179892_SNP [dm3] X_9285859_SNP [dm6]	C	G	4.083e^-5	0.888	UTR_5_PRIME lz
2R	7060461	2R_7060461_SNP [dm3] 2R_11172956_SNP [dm6]	A	C	4.088e^-5	0.888	UPSTREAM CG13229 & 1 other INTRON shn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_HSA
3L	20830760	3L_20830760_SNP [dm3] 3L_20837660_SNP [dm6]	G	A	4.159e^-5	0.888	UTR_5_PRIME CG13255 UPSTREAM CG13255 & 1 other DOWNSTREAM CG3288
2R	1580839	2R_1580839_SNP [dm3] 2R_5693334_SNP [dm6]	C	T	4.162e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_jumu
X	9929426	X_9929426_SNP [dm3] X_10035393_SNP [dm6]	C	T	4.170e^-5	0.888	NON_SYNONYMOUS_CODING Cht6 INTRON Cht6
2R	16255161	2R_16255161_SNP [dm3] 2R_20367656_SNP [dm6]	C	A	4.229e^-5	0.888	INTERGENIC
3R	21326483	3R_21326483_SNP [dm3] 3R_25500761_SNP [dm6]	C	T	4.326e^-5	0.888	INTERGENIC
3R	21326492	3R_21326492_SNP [dm3] 3R_25500770_SNP [dm6]	T	G	4.326e^-5	0.888	INTERGENIC
3R	26392541	3R_26392541_SNP [dm3] 3R_30566819_SNP [dm6]	G	A	4.345e^-5	0.888	INTRON tmod	TF binding site BDTNP1_TFBS_dl
2R	9236151	2R_9236151_SNP [dm3] 2R_13348646_SNP [dm6]	C	T	4.429e^-5	0.888	INTRON CR44206
2R	20101336	2R_20101336_SNP [dm3] 2R_24213813_SNP [dm6]	T	C	4.614e^-5	0.888	UTR_3_PRIME CG30419
3R	25121905	3R_25121905_SNP [dm3] 3R_29296183_SNP [dm6]	A	T	4.615e^-5	0.888	NON_SYNONYMOUS_CODING CG14506
2R	3518346	2R_3518346_SNP [dm3] 2R_7630841_SNP [dm6]	C	T	4.628e^-5	0.888	DOWNSTREAM CR45131 INTRON CG43340	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	4900998	3L_4900998_SNP [dm3] 3L_4900998_SNP [dm6]	C	G	4.639e^-5	0.888	DOWNSTREAM CG13704 INTERGENIC
2L	15872124	2L_15872124_SNP [dm3] 2L_15872124_SNP [dm6]	C	T	4.648e^-5	0.888	INTERGENIC
2L	15061399	2L_15061399_SNP [dm3] 2L_15061399_SNP [dm6]	T	A	4.715e^-5	0.888	UPSTREAM vas & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
3R	26948426	3R_26948426_SNP [dm3] 3R_31122704_SNP [dm6]	G	A	4.788e^-5	0.888	SYNONYMOUS_CODING Prosalpha3T
X	19008770	X_19008770_SNP [dm3] X_19114737_SNP [dm6]	T	A	4.831e^-5	0.888	INTERGENIC

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By genomic position
Variant impact
Gene name

Vial phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results