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=1.774e^-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
wolba	0.03062
In_2R_NS	0.09065
In_3R_Mo	0.07937

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3037 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
X	13823869	X_13823869_DEL [dm3] X_13929836_DEL [dm6]	TAT	T	2.315e^-7	0.119	INTRON mamo
3R	20561238	3R_20561238_SNP [dm3] 3R_24735516_SNP [dm6]	A	T	3.449e^-7	0.119	INTRON tok
2L	17998195	2L_17998195_DEL [dm3] 2L_17998195_DEL [dm6]	GG	G	3.661e^-7	0.119	INTERGENIC
3R	25830791	3R_25830791_SNP [dm3] 3R_30005069_SNP [dm6]	A	C	4.061e^-7	0.119	UPSTREAM CG7911 DOWNSTREAM CG7912 INTRON Nlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	25830813	3R_25830813_SNP [dm3] 3R_30005091_SNP [dm6]	C	T	4.061e^-7	0.119	UPSTREAM CG7911 DOWNSTREAM CG7912 INTRON Nlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	17998191	2L_17998191_SNP [dm3] 2L_17998191_SNP [dm6]	G	C	4.496e^-7	0.119	INTERGENIC
3R	23413844	3R_23413844_SNP [dm3] 3R_27588122_SNP [dm6]	G	A	5.198e^-7	0.119	SYNONYMOUS_CODING CG5639	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23413737	3R_23413737_SNP [dm3] 3R_27588015_SNP [dm6]	G	T	5.211e^-7	0.119	INTRON CG5639	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	9700174	X_9700174_SNP [dm3] X_9806141_SNP [dm6]	T	A	6.875e^-7	0.14	INTRON CG32698
X	15673263	X_15673263_INS [dm3] X_15779230_INS [dm6]	G	GAAAGAAGATCATTGGATTA...	8.645e^-7	0.144	DOWNSTREAM CG43672 INTRON CG43673
X	15673302	X_15673302_SNP [dm3] X_15779269_SNP [dm6]	A	C	8.645e^-7	0.144	DOWNSTREAM CG43672 INTRON CG43673
3L	14950589	3L_14950589_SNP [dm3] 3L_14957489_SNP [dm6]	G	A	1.091e^-6	0.156	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
X	15673303	X_15673303_SNP [dm3] X_15779270_SNP [dm6]	A	C	1.104e^-6	0.156	DOWNSTREAM CG43672 INTRON CG43673
2R	16399869	2R_16399869_SNP [dm3] 2R_20512364_SNP [dm6]	G	A	1.291e^-6	0.169	DOWNSTREAM CR44648 & 2 others INTERGENIC
3L	5999215	3L_5999215_SNP [dm3] 3L_6006115_SNP [dm6]	A	G	2.615e^-6	0.292	INTRON PVRAP
2R	16399680	2R_16399680_SNP [dm3] 2R_20512175_SNP [dm6]	A	T	2.724e^-6	0.292	DOWNSTREAM CR44648 & 2 others INTERGENIC
3R	13673489	3R_13673489_INS [dm3] 3R_17847767_INS [dm6]	G	GGTCGCACAG	2.797e^-6	0.292	INTRON tinc
3L	14752954	3L_14752954_SNP [dm3] 3L_14759854_SNP [dm6]	T	C	2.961e^-6	0.292	DOWNSTREAM CG33260 INTRON Trl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	1525834	3L_1525834_DEL [dm3] 3L_1525834_DEL [dm6]	AA	A	3.032e^-6	0.292	INTRON CG12090
3R	18476760	3R_18476760_SNP [dm3] 3R_22651038_SNP [dm6]	C	A	3.406e^-6	0.297	INTRON CG45058
3L	16685212	3L_16685212_SNP [dm3] 3L_16692112_SNP [dm6]	G	A	3.441e^-6	0.297	INTRON Lasp & 2 others
2R	12508133	2R_12508133_SNP [dm3] 2R_16620628_SNP [dm6]	A	G	4.377e^-6	0.297	INTRON CG5065
2R	12508219	2R_12508219_SNP [dm3] 2R_16620714_SNP [dm6]	T	G	4.377e^-6	0.297	INTRON CG5065
2R	12508381	2R_12508381_SNP [dm3] 2R_16620876_SNP [dm6]	T	A	4.377e^-6	0.297	INTRON CG5065	TF binding site mE1_TFBS_cad
2R	12508390	2R_12508390_DEL [dm3] 2R_16620885_DEL [dm6]	CG	C	4.377e^-6	0.297	INTRON CG5065	TF binding site mE1_TFBS_cad
3L	14040244	3L_14040244_SNP [dm3] 3L_14047144_SNP [dm6]	A	G	4.377e^-6	0.297	SYNONYMOUS_CODING blue	TF binding site mE1_TFBS_cad
3R	26463923	3R_26463923_SNP [dm3] 3R_30638201_SNP [dm6]	C	T	4.377e^-6	0.297	INTERGENIC
2L	9941063	2L_9941063_SNP [dm3] 2L_9941063_SNP [dm6]	A	G	4.890e^-6	0.32	UTR_3_PRIME CG4619 DOWNSTREAM CG4619 INTRON CG5853
2R	16399798	2R_16399798_SNP [dm3] 2R_20512293_SNP [dm6]	A	T	5.324e^-6	0.326	DOWNSTREAM CR44648 & 2 others INTERGENIC
3L	5426181	3L_5426181_SNP [dm3] 3L_5433081_SNP [dm6]	A	G	5.542e^-6	0.326	SYNONYMOUS_CODING CG34391
3L	13319350	3L_13319350_SNP [dm3] 3L_13326250_SNP [dm6]	T	A	5.804e^-6	0.326	INTERGENIC
2L	12959436	2L_12959436_SNP [dm3] 2L_12959436_SNP [dm6]	T	A	6.078e^-6	0.326	INTERGENIC
3R	27873606	3R_27873606_SNP [dm3] 3R_32047884_SNP [dm6]	T	C	6.340e^-6	0.326	UTR_3_PRIME krz DOWNSTREAM krz
3R	26464186	3R_26464186_SNP [dm3] 3R_30638464_SNP [dm6]	C	T	6.609e^-6	0.326	INTERGENIC
2R	18738294	2R_18738294_SNP [dm3] 2R_22850771_SNP [dm6]	A	G	6.715e^-6	0.326	SYNONYMOUS_CODING CG13531	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	4942971	2R_4942971_SNP [dm3] 2R_9055466_SNP [dm6]	G	T	6.807e^-6	0.326	INTRON CG13743	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1404204	2L_1404204_SNP [dm3] 2L_1404204_SNP [dm6]	A	G	6.820e^-6	0.326	INTRON lea	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_kn
3L	7953752	3L_7953752_INS [dm3] 3L_7960652_INS [dm6]	A	AAA	7.338e^-6	0.326	INTERGENIC	TF binding site mE1_TFBS_cad
3R	14103515	3R_14103515_SNP [dm3] 3R_18277793_SNP [dm6]	T	A	7.570e^-6	0.326	DOWNSTREAM CG7142 INTRON eIF-1A
2L	12965318	2L_12965318_SNP [dm3] 2L_12965318_SNP [dm6]	G	T	7.829e^-6	0.326	INTERGENIC
3R	25831122	3R_25831122_SNP [dm3] 3R_30005400_SNP [dm6]	G	A	7.996e^-6	0.326	SYNONYMOUS_CODING Nlp UPSTREAM CG7911 DOWNSTREAM CG7912	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	19048886	2L_19048886_SNP [dm3] 2L_19048886_SNP [dm6]	T	G	8.425e^-6	0.326	UPSTREAM CG10470 DOWNSTREAM Acn & 1 other INTERGENIC
3R	19066475	3R_19066475_SNP [dm3] 3R_23240753_SNP [dm6]	G	A	8.598e^-6	0.326	UPSTREAM CG4467 INTRON CG4467
X	12204737	X_12204737_SNP [dm3] X_12310704_SNP [dm6]	A	G	8.884e^-6	0.326	INTRON Ten-a
2L	6512070	2L_6512070_SNP [dm3] 2L_6512070_SNP [dm6]	C	T	9.029e^-6	0.326	INTRON CG31637
3L	18685820	3L_18685820_SNP [dm3] 3L_18692720_SNP [dm6]	C	A	9.085e^-6	0.326	DOWNSTREAM CR43987 INTERGENIC
3R	25814112	3R_25814112_SNP [dm3] 3R_29988390_SNP [dm6]	G	A	9.358e^-6	0.326	SYNONYMOUS_CODING CG7896	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	19490716	3R_19490716_SNP [dm3] 3R_23664994_SNP [dm6]	G	A	9.634e^-6	0.326	INTRON CG31145
3R	19490790	3R_19490790_SNP [dm3] 3R_23665068_SNP [dm6]	G	A	9.634e^-6	0.326	INTRON CG31145
2L	9811486	2L_9811486_SNP [dm3] 2L_9811486_SNP [dm6]	A	T	1.014e^-5	0.326	INTRON nAChRalpha6
3R	25814100	3R_25814100_SNP [dm3] 3R_29988378_SNP [dm6]	A	T	1.070e^-5	0.326	SYNONYMOUS_CODING CG7896	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	23251726	3R_23251726_SNP [dm3] 3R_27426004_SNP [dm6]	G	A	1.109e^-5	0.326	INTRON side	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	13319356	3L_13319356_SNP [dm3] 3L_13326256_SNP [dm6]	A	G	1.115e^-5	0.326	INTERGENIC
3L	2620140	3L_2620140_INS [dm3] 3L_2620140_INS [dm6]	T	TTGGTTTGGTTTGGGTT...	1.160e^-5	0.326	INTRON Pxn
3L	2469524	3L_2469524_SNP [dm3] 3L_2469524_SNP [dm6]	A	G	1.176e^-5	0.326	INTRON CG45186	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	13638071	3R_13638071_SNP [dm3] 3R_17812349_SNP [dm6]	C	T	1.176e^-5	0.326	INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA
3R	13638090	3R_13638090_SNP [dm3] 3R_17812368_SNP [dm6]	G	C	1.176e^-5	0.326	INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	13638141	3R_13638141_SNP [dm3] 3R_17812419_SNP [dm6]	A	T	1.176e^-5	0.326	INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	14103948	3R_14103948_SNP [dm3] 3R_18278226_SNP [dm6]	G	A	1.176e^-5	0.326	UTR_3_PRIME CG7142 INTRON eIF-1A	TF binding site mE1_TFBS_chinmo
3R	14104221	3R_14104221_SNP [dm3] 3R_18278499_SNP [dm6]	G	A	1.176e^-5	0.326	SYNONYMOUS_CODING CG7142 INTRON eIF-1A	TF binding site mE1_TFBS_chinmo
3R	14108499	3R_14108499_SNP [dm3] 3R_18282777_SNP [dm6]	C	T	1.176e^-5	0.326	UTR_3_PRIME eIF-1A UPSTREAM CG8064 DOWNSTREAM CG14312 & 1 other	TF binding site mE1_TFBS_inv
3R	18806015	3R_18806015_SNP [dm3] 3R_22980293_SNP [dm6]	G	A	1.176e^-5	0.326	INTERGENIC
3R	26605221	3R_26605221_SNP [dm3] 3R_30779499_SNP [dm6]	A	T	1.176e^-5	0.326	INTRON zfh1
X	19020662	X_19020662_SNP [dm3] X_19126629_SNP [dm6]	A	C	1.176e^-5	0.326	INTRON tgy
X	4199794	X_4199794_SNP [dm3] X_4305761_SNP [dm6]	T	C	1.176e^-5	0.326	INTERGENIC
X	4199799	X_4199799_SNP [dm3] X_4305766_SNP [dm6]	C	G	1.176e^-5	0.326	INTERGENIC
3L	21639920	3L_21639920_SNP [dm3] 3L_21646820_SNP [dm6]	G	C	1.191e^-5	0.326	INTRON CG43980
2L	16383541	2L_16383541_SNP [dm3] 2L_16383541_SNP [dm6]	C	T	1.239e^-5	0.334	INTERGENIC
2R	16662939	2R_16662939_SNP [dm3] 2R_20775434_SNP [dm6]	T	A	1.264e^-5	0.336	DOWNSTREAM CG43709 & 1 other INTERGENIC
2L	6792436	2L_6792436_SNP [dm3] 2L_6792436_SNP [dm6]	G	T	1.377e^-5	0.338	INTRON nrv2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	14965687	3L_14965687_SNP [dm3] 3L_14972587_SNP [dm6]	T	C	1.382e^-5	0.338	UPSTREAM Brd INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	10369254	2L_10369254_SNP [dm3] 2L_10369254_SNP [dm6]	T	A	1.388e^-5	0.338	INTRON rho-5	TF binding site mE1_TFBS_cad
2L	1962577	2L_1962577_SNP [dm3] 2L_1962577_SNP [dm6]	T	A	1.401e^-5	0.338	INTRON erm	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	24119987	3R_24119987_SNP [dm3] 3R_28294265_SNP [dm6]	A	G	1.411e^-5	0.338	SYNONYMOUS_CODING CG17856 DOWNSTREAM CR44229 & 1 other
2R	14832655	2R_14832655_SNP [dm3] 2R_18945150_SNP [dm6]	A	G	1.438e^-5	0.338	INTRON sano
3L	17188547	3L_17188547_SNP [dm3] 3L_17195447_SNP [dm6]	A	T	1.438e^-5	0.338	INTRON Rbp6	TF binding site mE1_TFBS_inv
3L	18685843	3L_18685843_DEL [dm3] 3L_18692743_DEL [dm6]	TAGGGGCTACGCAAGTTTAA...	T	1.438e^-5	0.338	DOWNSTREAM CR43987 INTERGENIC
2R	3858717	2R_3858717_DEL [dm3] 2R_7971212_DEL [dm6]	GG	C	1.442e^-5	0.338	UPSTREAM CSN4 INTRON CG8726	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	19582206	X_19582206_SNP [dm3] X_19688173_SNP [dm6]	T	C	1.465e^-5	0.338	NON_SYNONYMOUS_CODING CG14227 DOWNSTREAM Ubqn	TF binding site mE1_TFBS_sens
3R	19116275	3R_19116275_SNP [dm3] 3R_23290553_SNP [dm6]	C	T	1.510e^-5	0.338	UTR_3_PRIME pnt UPSTREAM CG4434 DOWNSTREAM pnt
2R	17122918	2R_17122918_SNP [dm3] 2R_21235413_SNP [dm6]	A	G	1.542e^-5	0.338	INTRON ASPP
3R	25814061	3R_25814061_SNP [dm3] 3R_29988339_SNP [dm6]	C	T	1.568e^-5	0.338	SYNONYMOUS_CODING CG7896	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3L	18848471	3L_18848471_SNP [dm3] 3L_18855371_SNP [dm6]	T	A	1.578e^-5	0.338	DOWNSTREAM CR45387 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	2536461	X_2536461_SNP [dm3] X_2642428_SNP [dm6]	A	T	1.611e^-5	0.338	UPSTREAM sgg INTRON sgg	TF binding site BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	12959936	2L_12959936_SNP [dm3] 2L_12959936_SNP [dm6]	G	A	1.625e^-5	0.338	INTERGENIC
3R	25842766	3R_25842766_SNP [dm3] 3R_30017044_SNP [dm6]	C	A	1.652e^-5	0.338	INTRON Mgat2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	19361203	3R_19361203_SNP [dm3] 3R_23535481_SNP [dm6]	T	A	1.655e^-5	0.338	SYNONYMOUS_CODING CG16732 UPSTREAM CG10170
3L	5426205	3L_5426205_SNP [dm3] 3L_5433105_SNP [dm6]	A	C	1.712e^-5	0.338	SYNONYMOUS_CODING CG34391
3R	25297708	3R_25297708_SNP [dm3] 3R_29471986_SNP [dm6]	G	T	1.713e^-5	0.338	INTRON Ptp99A
2R	17346019	2R_17346019_SNP [dm3] 2R_21458514_SNP [dm6]	G	A	1.715e^-5	0.338	INTRON Sdc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13882654	2R_13882654_DEL [dm3] 2R_17995149_DEL [dm6]	TGTAAGG	T	1.717e^-5	0.338	INTRON dpr13
2R	13882663	2R_13882663_SNP [dm3] 2R_17995158_SNP [dm6]	A	G	1.717e^-5	0.338	INTRON dpr13
2R	13882671	2R_13882671_SNP [dm3] 2R_17995166_SNP [dm6]	T	A	1.717e^-5	0.338	INTRON dpr13
2L	12958066	2L_12958066_SNP [dm3] 2L_12958066_SNP [dm6]	C	A	1.754e^-5	0.342	INTERGENIC
X	17344151	X_17344151_SNP [dm3] X_17450118_SNP [dm6]	A	G	1.826e^-5	0.347	NON_SYNONYMOUS_CODING CG8568
3R	19066390	3R_19066390_SNP [dm3] 3R_23240668_SNP [dm6]	G	A	1.874e^-5	0.347	UPSTREAM CG4467 INTRON CG4467
3R	19066555	3R_19066555_SNP [dm3] 3R_23240833_SNP [dm6]	A	G	1.874e^-5	0.347	UPSTREAM CG4467 INTRON CG4467
3R	19066565	3R_19066565_SNP [dm3] 3R_23240843_SNP [dm6]	G	A	1.874e^-5	0.347	UPSTREAM CG4467 INTRON CG4467
3R	19066566	3R_19066566_SNP [dm3] 3R_23240844_SNP [dm6]	G	A	1.874e^-5	0.347	UPSTREAM CG4467 INTRON CG4467
2R	18678157	2R_18678157_SNP [dm3] 2R_22790652_SNP [dm6]	G	A	1.927e^-5	0.352	INTRON CG42260

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Phenotype distribution and association to known covariates

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GWAS results