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=3.551e^-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

Covariate	p-value	Significance
In_3R_K	0.04816
In_3R_Mo	0.06657

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2166 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
3R	2287353	3R_2287353_DEL [dm3] 3R_6461631_DEL [dm6]	ACTTAATGCCTAACAACAAC...	A	8.192e^-8	0.13	INTERGENIC
2R	2882279	2R_2882279_SNP [dm3] 2R_6994774_SNP [dm6]	T	C	1.402e^-7	0.13	DOWNSTREAM CG30159 INTRON Tsp42Ea	TF binding site mE1_TFBS_Trl
3R	12210089	3R_12210089_SNP [dm3] 3R_16384367_SNP [dm6]	C	T	8.976e^-7	0.31	INTRON ss	regulatory region REDfly_CRMs
3R	2287402	3R_2287402_INS [dm3] 3R_6461680_INS [dm6]	A	AA	1.016e^-6	0.31	INTERGENIC
2L	2735023	2L_2735023_INS [dm3] 2L_2735023_INS [dm6]	G	TA	1.146e^-6	0.31	UPSTREAM CG31689 INTRON CG31689
X	19877188	X_19877188_SNP [dm3] X_19983155_SNP [dm6]	C	G	1.324e^-6	0.31	INTERGENIC
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	1.442e^-6	0.31	INTERGENIC
3R	11341833	3R_11341833_SNP [dm3] 3R_15516111_SNP [dm6]	T	C	1.456e^-6	0.31	INTERGENIC
3R	10849873	3R_10849873_SNP [dm3] 3R_15024151_SNP [dm6]	T	G	1.554e^-6	0.31	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	12896174	3R_12896174_SNP [dm3] 3R_17070452_SNP [dm6]	A	G	1.664e^-6	0.31	DOWNSTREAM Ns1 & 1 other INTERGENIC
2L	13998264	2L_13998264_INS [dm3] 2L_13998264_INS [dm6]	T	TTAGAAAGT	2.151e^-6	0.333	INTRON rk
2L	21009759	2L_21009759_SNP [dm3] 2L_21009759_SNP [dm6]	C	G	2.186e^-6	0.333	INTRON CG42238	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3R	11342771	3R_11342771_DEL [dm3] 3R_15517049_DEL [dm6]	TCTCCACAGACT...	T	2.717e^-6	0.333	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	2285727	3R_2285727_SNP [dm3] 3R_6460005_SNP [dm6]	T	C	2.880e^-6	0.333	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	17937590	2L_17937590_SNP [dm3] 2L_17937590_SNP [dm6]	T	C	2.929e^-6	0.333	INTERGENIC
2L	12779647	2L_12779647_SNP [dm3] 2L_12779647_SNP [dm6]	G	A	3.054e^-6	0.333	INTERGENIC
2L	2735028	2L_2735028_SNP [dm3] 2L_2735028_SNP [dm6]	C	G	3.237e^-6	0.333	UPSTREAM CG31689 INTRON CG31689
2L	16063746	2L_16063746_SNP [dm3] 2L_16063746_SNP [dm6]	G	C	3.345e^-6	0.333	INTRON beat-Ia	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	5444829	3L_5444829_SNP [dm3] 3L_5451729_SNP [dm6]	T	C	3.540e^-6	0.333	INTERGENIC
X	6624836	X_6624836_DEL [dm3] X_6730803_DEL [dm6]	CATTTTTCCTC...	C	3.834e^-6	0.333	UPSTREAM CG3168 INTRON CG3168
2L	17937581	2L_17937581_SNP [dm3] 2L_17937581_SNP [dm6]	A	C	3.839e^-6	0.333	INTERGENIC
3L	15790682	3L_15790682_DEL [dm3] 3L_15797582_DEL [dm6]	TA	T	3.978e^-6	0.333	INTERGENIC
X	12823916	X_12823916_SNP [dm3] X_12929883_SNP [dm6]	T	C	4.180e^-6	0.333	INTRON fne	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	4.298e^-6	0.333	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	16063742	2L_16063742_SNP [dm3] 2L_16063742_SNP [dm6]	T	C	4.898e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	19877187	X_19877187_SNP [dm3] X_19983154_SNP [dm6]	C	T	5.280e^-6	0.35	INTERGENIC
3R	11342215	3R_11342215_SNP [dm3] 3R_15516493_SNP [dm6]	C	T	5.613e^-6	0.35	INTERGENIC
2L	20359648	2L_20359648_SNP [dm3] 2L_20359648_SNP [dm6]	G	A	5.646e^-6	0.35	DOWNSTREAM RtGEF INTRON RtGEF
3R	11342729	3R_11342729_SNP [dm3] 3R_15517007_SNP [dm6]	A	C	5.690e^-6	0.35	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	11342118	3R_11342118_SNP [dm3] 3R_15516396_SNP [dm6]	C	A	5.848e^-6	0.35	INTERGENIC
2L	16063704	2L_16063704_SNP [dm3] 2L_16063704_SNP [dm6]	A	G	6.436e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
2L	16063710	2L_16063710_SNP [dm3] 2L_16063710_SNP [dm6]	A	G	6.507e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
2L	20331677	2L_20331677_SNP [dm3] 2L_20331677_SNP [dm6]	A	G	6.556e^-6	0.35	INTRON spir
2L	16063744	2L_16063744_SNP [dm3] 2L_16063744_SNP [dm6]	T	C	6.669e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	14943493	3R_14943493_SNP [dm3] 3R_19117771_SNP [dm6]	T	C	6.727e^-6	0.35	INTRON CG6040
2R	4682739	2R_4682739_SNP [dm3] 2R_8795234_SNP [dm6]	G	A	6.920e^-6	0.35	INTERGENIC
2L	17937597	2L_17937597_SNP [dm3] 2L_17937597_SNP [dm6]	C	A	7.367e^-6	0.35	INTERGENIC
2L	16063671	2L_16063671_SNP [dm3] 2L_16063671_SNP [dm6]	G	A	7.497e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
2L	16063676	2L_16063676_INS [dm3] 2L_16063676_INS [dm6]	C	AT	7.497e^-6	0.35	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
3L	8895277	3L_8895277_SNP [dm3] 3L_8902177_SNP [dm6]	G	A	7.534e^-6	0.35	UPSTREAM TrpA1 INTRON TrpA1
3R	12896178	3R_12896178_SNP [dm3] 3R_17070456_SNP [dm6]	G	A	7.867e^-6	0.357	DOWNSTREAM Ns1 & 1 other INTERGENIC
3R	25451580	3R_25451580_SNP [dm3] 3R_29625858_SNP [dm6]	C	A	8.451e^-6	0.365	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25451581	3R_25451581_SNP [dm3] 3R_29625859_SNP [dm6]	C	A	8.451e^-6	0.365	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	12169749	2L_12169749_SNP [dm3] 2L_12169749_SNP [dm6]	T	C	8.637e^-6	0.365	UTR_3_PRIME CG31760 UPSTREAM CG17217	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	12210079	3R_12210079_SNP [dm3] 3R_16384357_SNP [dm6]	T	A	1.001e^-5	0.414	INTRON ss	regulatory region REDfly_CRMs
2L	20075713	2L_20075713_SNP [dm3] 2L_20075713_SNP [dm6]	C	G	1.078e^-5	0.436	UPSTREAM neb & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
2L	12724112	2L_12724112_SNP [dm3] 2L_12724112_SNP [dm6]	T	C	1.159e^-5	0.449	INTRON MRP	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	12724133	2L_12724133_SNP [dm3] 2L_12724133_SNP [dm6]	T	C	1.159e^-5	0.449	INTRON MRP	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	15051899	3R_15051899_SNP [dm3] 3R_19226177_SNP [dm6]	T	G	1.268e^-5	0.474	DOWNSTREAM CG11703 INTRON vib	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	1.274e^-5	0.474	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	20334426	2L_20334426_SNP [dm3] 2L_20334426_SNP [dm6]	G	T	1.331e^-5	0.476	INTRON spir
X	3528653	X_3528653_SNP [dm3] X_3634620_SNP [dm6]	A	G	1.345e^-5	0.476	INTRON AstA-R1
3R	11342086	3R_11342086_SNP [dm3] 3R_15516364_SNP [dm6]	A	T	1.356e^-5	0.476	INTERGENIC
3R	14896155	3R_14896155_DEL [dm3] 3R_19070433_DEL [dm6]	CC	C	1.442e^-5	0.497	INTRON cdi
2L	10478277	2L_10478277_SNP [dm3] 2L_10478277_SNP [dm6]	T	A	1.470e^-5	0.497	INTRON RluA-2
X	5493581	X_5493581_SNP [dm3] X_5599548_SNP [dm6]	G	A	1.513e^-5	0.503	INTRON Vsx1
3R	2282359	3R_2282359_SNP [dm3] 3R_6456637_SNP [dm6]	C	T	1.599e^-5	0.522	UTR_5_PRIME CG9727 UPSTREAM Zif & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
2L	17937588	2L_17937588_SNP [dm3] 2L_17937588_SNP [dm6]	C	T	1.762e^-5	0.557	INTERGENIC
2R	15058720	2R_15058720_SNP [dm3] 2R_19171215_SNP [dm6]	T	G	1.767e^-5	0.557	INTRON CG10737
2L	12779642	2L_12779642_SNP [dm3] 2L_12779642_SNP [dm6]	G	A	1.940e^-5	0.602	INTERGENIC
2L	8000295	2L_8000295_SNP [dm3] 2L_8000295_SNP [dm6]	A	G	1.990e^-5	0.607	DOWNSTREAM Sirup INTRON Wwox	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	18209327	3L_18209327_SNP [dm3] 3L_18216227_SNP [dm6]	T	A	2.083e^-5	0.625	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20336420	2L_20336420_SNP [dm3] 2L_20336420_SNP [dm6]	G	A	2.185e^-5	0.633	INTRON spir
3R	9855212	3R_9855212_SNP [dm3] 3R_14029490_SNP [dm6]	T	A	2.266e^-5	0.633	SYNONYMOUS_CODING Cyp6d5 INTRON rdx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
3R	26074742	3R_26074742_SNP [dm3] 3R_30249020_SNP [dm6]	G	A	2.280e^-5	0.633	UPSTREAM tRNA:CR31383 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2L	18995624	2L_18995624_SNP [dm3] 2L_18995624_SNP [dm6]	T	C	2.300e^-5	0.633	SYNONYMOUS_CODING CG10650
3L	8901978	3L_8901978_SNP [dm3] 3L_8908878_SNP [dm6]	G	T	2.318e^-5	0.633	SYNONYMOUS_CODING mfr UTR_5_PRIME mfr UTR_3_PRIME mfr	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	19398092	X_19398092_SNP [dm3] X_19504059_SNP [dm6]	G	T	2.324e^-5	0.633	UPSTREAM Pfrx INTRON Pfrx & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	736383	2L_736383_SNP [dm3] 2L_736383_SNP [dm6]	G	A	2.349e^-5	0.633	DOWNSTREAM Eaat2 INTERGENIC
3R	14853539	3R_14853539_SNP [dm3] 3R_19027817_SNP [dm6]	T	C	2.439e^-5	0.645	SYNONYMOUS_CODING NP15.6 INTRON gatA	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	16136747	2L_16136747_DEL [dm3] 2L_16136747_DEL [dm6]	TT	T	2.487e^-5	0.645	UPSTREAM CR44871 INTERGENIC
2L	21725536	2L_21725536_SNP [dm3] 2L_21725536_SNP [dm6]	A	G	2.574e^-5	0.645	INTRON CG31619	transposable element FlyBase
2L	5669821	2L_5669821_SNP [dm3] 2L_5669821_SNP [dm6]	A	G	2.574e^-5	0.645	SYNONYMOUS_CODING Hsp60C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	13433604	2L_13433604_SNP [dm3] 2L_13433604_SNP [dm6]	G	C	2.605e^-5	0.645	INTRON CG42784
2L	20324587	2L_20324587_SNP [dm3] 2L_20324587_SNP [dm6]	C	T	2.609e^-5	0.645	INTRON spir
2L	9465933	2L_9465933_SNP [dm3] 2L_9465933_SNP [dm6]	A	G	2.650e^-5	0.645	INTERGENIC
2L	16063726	2L_16063726_SNP [dm3] 2L_16063726_SNP [dm6]	T	C	2.670e^-5	0.645	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
2L	19724017	2L_19724017_SNP [dm3] 2L_19724017_SNP [dm6]	A	T	2.808e^-5	0.651	INTRON Lar
3L	7395804	3L_7395804_SNP [dm3] 3L_7402704_SNP [dm6]	C	A	2.865e^-5	0.651	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	21882791	2L_21882791_SNP [dm3] 2L_21882791_SNP [dm6]	G	C	2.867e^-5	0.651	INTERGENIC
3R	10849828	3R_10849828_SNP [dm3] 3R_15024106_SNP [dm6]	G	A	2.938e^-5	0.651	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	10849852	3R_10849852_SNP [dm3] 3R_15024130_SNP [dm6]	T	C	2.938e^-5	0.651	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	10849874	3R_10849874_SNP [dm3] 3R_15024152_SNP [dm6]	T	A	2.938e^-5	0.651	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	16063667	2L_16063667_SNP [dm3] 2L_16063667_SNP [dm6]	A	C	3.018e^-5	0.651	INTRON beat-Ia	TF binding site BDTNP1_TFBS_twi
X	11186139	X_11186139_SNP [dm3] X_11292106_SNP [dm6]	G	A	3.055e^-5	0.651	INTRON CG44422
3L	1463180	3L_1463180_SNP [dm3] 3L_1463180_SNP [dm6]	C	T	3.095e^-5	0.651	UPSTREAM CR44842 & 1 other INTRON Ptp61F	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	10254359	2R_10254359_DEL [dm3] 2R_14366854_DEL [dm6]	TT	T	3.117e^-5	0.651	UTR_5_PRIME CG34442 DOWNSTREAM CG34184
X	17313287	X_17313287_SNP [dm3] X_17419254_SNP [dm6]	C	G	3.195e^-5	0.651	INTRON CG8611
3L	7220792	3L_7220792_SNP [dm3] 3L_7227692_SNP [dm6]	A	T	3.197e^-5	0.651	INTERGENIC
3L	8724603	3L_8724603_SNP [dm3] 3L_8731503_SNP [dm6]	C	T	3.209e^-5	0.651	UPSTREAM Cp16 DOWNSTREAM Cp19 INTERGENIC
2L	1082268	2L_1082268_SNP [dm3] 2L_1082268_SNP [dm6]	A	G	3.214e^-5	0.651	SYNONYMOUS_CODING Atg4a DOWNSTREAM CG4629	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	1868790	3L_1868790_SNP [dm3] 3L_1868790_SNP [dm6]	A	C	3.298e^-5	0.651	UTR_3_PRIME CG12025 DOWNSTREAM CG12025
2L	16042709	2L_16042709_SNP [dm3] 2L_16042709_SNP [dm6]	G	A	3.346e^-5	0.651	UPSTREAM BicC & 1 other INTRON BicC & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5444814	3L_5444814_SNP [dm3] 3L_5451714_SNP [dm6]	C	T	3.367e^-5	0.651	INTERGENIC
3R	9749922	3R_9749922_INS [dm3] 3R_13924200_INS [dm6]	A	AA	3.377e^-5	0.651	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	13433592	2L_13433592_SNP [dm3] 2L_13433592_SNP [dm6]	A	C	3.377e^-5	0.651	INTRON CG42784
2L	10895326	2L_10895326_SNP [dm3] 2L_10895326_SNP [dm6]	A	C	3.392e^-5	0.651	EXON CR44491
2L	10487588	2L_10487588_SNP [dm3] 2L_10487588_SNP [dm6]	T	C	3.526e^-5	0.655	INTRON CG7456	TF binding site mE1_TFBS_inv
2L	8098939	2L_8098939_SNP [dm3] 2L_8098939_SNP [dm6]	T	C	3.584e^-5	0.655	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3R	18450177	3R_18450177_SNP [dm3] 3R_22624455_SNP [dm6]	T	G	3.614e^-5	0.655	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

Microbiota_OTU013 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results