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=1.539e^-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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	3.5401	0.0599

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2403 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	18851129	X_18851129_INS [dm3] X_18957096_INS [dm6]	A	ACAAATATTG	1.113e^-6	0.669	INTRON CG43759
2R	12379912	2R_12379912_SNP [dm3] 2R_16492407_SNP [dm6]	T	C	1.891e^-6	0.669	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2866098	2L_2866098_SNP [dm3] 2L_2866098_SNP [dm6]	A	G	2.144e^-6	0.669	INTRON CG2991
3L	16037490	3L_16037490_SNP [dm3] 3L_16044390_SNP [dm6]	T	C	2.167e^-6	0.669	INTRON th	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_Trl
2L	6105874	2L_6105874_SNP [dm3] 2L_6105874_SNP [dm6]	T	C	2.233e^-6	0.669	INTRON stai
2L	1561541	2L_1561541_SNP [dm3] 2L_1561541_SNP [dm6]	T	A	2.462e^-6	0.669	INTRON haf
X	20396880	X_20396880_SNP [dm3] X_20525853_SNP [dm6]	G	A	3.762e^-6	0.669	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
3L	3499847	3L_3499847_SNP [dm3] 3L_3499847_SNP [dm6]	G	T	5.327e^-6	0.669	INTRON CG42324
2L	4261013	2L_4261013_SNP [dm3] 2L_4261013_SNP [dm6]	T	C	5.776e^-6	0.669	INTRON CR44080
3L	12705144	3L_12705144_INS [dm3] 3L_12712044_INS [dm6]	T	TGAAATATA	6.159e^-6	0.669	INTERGENIC	TF binding site mE1_TFBS_D
3L	12705165	3L_12705165_DEL [dm3] 3L_12712065_DEL [dm6]	AG	A	6.159e^-6	0.669	INTERGENIC	TF binding site mE1_TFBS_D
3L	12705307	3L_12705307_SNP [dm3] 3L_12712207_SNP [dm6]	T	G	6.159e^-6	0.669	INTERGENIC
3L	12705308	3L_12705308_SNP [dm3] 3L_12712208_SNP [dm6]	T	A	6.159e^-6	0.669	INTERGENIC
2R	2397947	2R_2397947_SNP [dm3] 2R_6510442_SNP [dm6]	G	T	7.359e^-6	0.669	UPSTREAM CR45127 INTRON jing	TF binding site BDTNP1_TFBS_dl
3R	19211784	3R_19211784_SNP [dm3] 3R_23386062_SNP [dm6]	T	C	8.313e^-6	0.669	INTERGENIC	TF binding site mE1_TFBS_Trl
3L	4635922	3L_4635922_SNP [dm3] 3L_4635922_SNP [dm6]	C	A	8.524e^-6	0.669	DOWNSTREAM axo INTRON axo	TF binding site mE1_TFBS_hkb
3L	2105093	3L_2105093_SNP [dm3] 3L_2105093_SNP [dm6]	G	C	9.361e^-6	0.669	INTRON sls	TF binding site mE1_TFBS_chinmo
2L	8583625	2L_8583625_SNP [dm3] 2L_8583625_SNP [dm6]	C	T	9.415e^-6	0.669	INTRON Sema-1a
3L	12705303	3L_12705303_INS [dm3] 3L_12712203_INS [dm6]	C	CCTT	9.651e^-6	0.669	INTERGENIC
3L	12705141	3L_12705141_INS [dm3] 3L_12712041_INS [dm6]	T	TA	9.854e^-6	0.669	INTERGENIC	TF binding site mE1_TFBS_D mE1_TFBS_HSA
3L	12705146	3L_12705146_SNP [dm3] 3L_12712046_SNP [dm6]	G	A	9.854e^-6	0.669	INTERGENIC	TF binding site mE1_TFBS_D
3R	19250659	3R_19250659_SNP [dm3] 3R_23424937_SNP [dm6]	C	T	9.987e^-6	0.669	DOWNSTREAM CG43694 INTRON CG4374
2L	9087754	2L_9087754_SNP [dm3] 2L_9087754_SNP [dm6]	T	C	1.081e^-5	0.669	SYNONYMOUS_CODING Toll-4	TF binding site BDTNP1_TFBS_twi
2L	563223	2L_563223_SNP [dm3] 2L_563223_SNP [dm6]	T	C	1.118e^-5	0.669	START_GAINED CG11835 UTR_5_PRIME CG11835 UPSTREAM CG2794 INTRON CG11835	TF binding site mE1_TFBS_chinmo
2R	15208408	2R_15208408_SNP [dm3] 2R_19320903_SNP [dm6]	G	A	1.211e^-5	0.669	INTRON Rgk1
X	18842174	X_18842174_SNP [dm3] X_18948141_SNP [dm6]	C	G	1.244e^-5	0.669	INTRON CG43759	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2R	2348113	2R_2348113_SNP [dm3] 2R_6460608_SNP [dm6]	C	A	1.318e^-5	0.669	INTERGENIC
X	12813552	X_12813552_SNP [dm3] X_12919519_SNP [dm6]	G	A	1.341e^-5	0.669	UTR_5_PRIME fne
2R	13552926	2R_13552926_SNP [dm3] 2R_17665421_SNP [dm6]	G	T	1.348e^-5	0.669	UPSTREAM eIF3-S8 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_run mE1_TFBS_Trl mE1_TFBS_Ubx
2L	22931363	2L_22931363_SNP [dm3] 2L_23038631_SNP [dm6]	T	G	1.364e^-5	0.669	INTERGENIC
2L	22446523	2L_22446523_DEL [dm3] 2L_22553791_DEL [dm6]	ATAGCCTGG	A	1.393e^-5	0.669	UTR_3_PRIME CG17493	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	2797921	2L_2797921_SNP [dm3] 2L_2797921_SNP [dm6]	T	G	1.412e^-5	0.669	INTRON Syt1 EXON CR43821	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	16037555	3L_16037555_SNP [dm3] 3L_16044455_SNP [dm6]	A	G	1.417e^-5	0.669	INTRON th	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_Trl
3L	3792170	3L_3792170_SNP [dm3] 3L_3792170_SNP [dm6]	A	G	1.531e^-5	0.669	DOWNSTREAM CG32266 INTRON CG32264
2R	6746413	2R_6746413_SNP [dm3] 2R_10858908_SNP [dm6]	A	G	1.619e^-5	0.669	UPSTREAM CR44302 INTRON CG30015
3L	12705311	3L_12705311_SNP [dm3] 3L_12712211_SNP [dm6]	A	G	1.625e^-5	0.669	INTERGENIC
3L	12705369	3L_12705369_SNP [dm3] 3L_12712269_SNP [dm6]	G	C	1.710e^-5	0.669	INTERGENIC
2L	9079208	2L_9079208_SNP [dm3] 2L_9079208_SNP [dm6]	T	A	1.730e^-5	0.669	INTERGENIC
2L	9079278	2L_9079278_SNP [dm3] 2L_9079278_SNP [dm6]	A	T	1.730e^-5	0.669	INTERGENIC
2L	9079121	2L_9079121_SNP [dm3] 2L_9079121_SNP [dm6]	C	T	1.790e^-5	0.669	INTERGENIC
X	16071254	X_16071254_SNP [dm3] X_16177221_SNP [dm6]	A	C	1.892e^-5	0.669	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	17877171	2R_17877171_SNP [dm3] 2R_21989666_SNP [dm6]	C	T	1.938e^-5	0.669	SYNONYMOUS_CODING CG34370	TF binding site mE1_TFBS_cad
2L	554505	2L_554505_SNP [dm3] 2L_554505_SNP [dm6]	T	C	1.972e^-5	0.669	SYNONYMOUS_CODING rempA
3L	3499962	3L_3499962_SNP [dm3] 3L_3499962_SNP [dm6]	C	T	2.043e^-5	0.669	INTRON CG42324
2R	1922669	2R_1922669_SNP [dm3] 2R_6035164_SNP [dm6]	T	C	2.067e^-5	0.669	INTRON SCAP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	18604425	3R_18604425_SNP [dm3] 3R_22778703_SNP [dm6]	A	C	2.078e^-5	0.669	INTRON CG7029 EXON CR43654	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	6106168	2L_6106168_INS [dm3] 2L_6106168_INS [dm6]	G	CT	2.118e^-5	0.669	INTRON stai
2L	6106172	2L_6106172_INS [dm3] 2L_6106172_INS [dm6]	T	TAAGCTA	2.118e^-5	0.669	INTRON stai
X	20396870	X_20396870_SNP [dm3] X_20525843_SNP [dm6]	G	A	2.133e^-5	0.669	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
X	20396871	X_20396871_SNP [dm3] X_20525844_SNP [dm6]	G	A	2.133e^-5	0.669	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
3L	1759415	3L_1759415_SNP [dm3] 3L_1759415_SNP [dm6]	G	A	2.229e^-5	0.669	SYNONYMOUS_CODING Dhc62B DOWNSTREAM CG8001	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	13693541	2R_13693541_SNP [dm3] 2R_17806036_SNP [dm6]	A	T	2.310e^-5	0.669	INTRON grh	TF binding site BDTNP1_TFBS_dl
3R	8517999	3R_8517999_SNP [dm3] 3R_12692277_SNP [dm6]	G	T	2.447e^-5	0.669	SYNONYMOUS_CODING CG31347 UPSTREAM Su_fu_ INTRON Arp1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	9235815	2L_9235815_SNP [dm3] 2L_9235815_SNP [dm6]	T	A	2.477e^-5	0.669	DOWNSTREAM tRNA:CR31885 INTRON tai
2R	1922700	2R_1922700_SNP [dm3] 2R_6035195_SNP [dm6]	T	C	2.486e^-5	0.669	INTRON SCAP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12474432	2R_12474432_INS [dm3] 2R_16586927_INS [dm6]	T	TT	2.493e^-5	0.669	DOWNSTREAM CG8311 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	9074778	2L_9074778_SNP [dm3] 2L_9074778_SNP [dm6]	C	T	2.525e^-5	0.669	INTERGENIC
2R	1928321	2R_1928321_SNP [dm3] 2R_6040816_SNP [dm6]	T	A	2.546e^-5	0.669	UPSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	1928456	2R_1928456_SNP [dm3] 2R_6040951_SNP [dm6]	C	G	2.546e^-5	0.669	UPSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	15274440	2L_15274440_SNP [dm3] 2L_15274440_SNP [dm6]	A	T	2.564e^-5	0.669	INTRON UK114	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14107422	2L_14107422_SNP [dm3] 2L_14107422_SNP [dm6]	T	C	2.565e^-5	0.669	UTR_3_PRIME CG16879 DOWNSTREAM CG16879 & 1 other
3L	12705191	3L_12705191_DEL [dm3] 3L_12712091_DEL [dm6]	AAATATCCTA	A	2.603e^-5	0.669	INTERGENIC
2L	9985299	2L_9985299_SNP [dm3] 2L_9985299_SNP [dm6]	T	A	2.663e^-5	0.669	UPSTREAM CR13130 INTRON bib	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	800295	2R_800295_SNP [dm3] 2R_4912790_SNP [dm6]	G	A	2.685e^-5	0.669	INTERGENIC	transposable element FlyBase
2L	22450549	2L_22450549_SNP [dm3] 2L_22557817_SNP [dm6]	G	A	2.716e^-5	0.669	INTERGENIC
2R	18444112	2R_18444112_SNP [dm3] 2R_22556607_SNP [dm6]	T	C	2.905e^-5	0.669	SYNONYMOUS_CODING px	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13656806	3L_13656806_SNP [dm3] 3L_13663706_SNP [dm6]	T	C	2.926e^-5	0.669	INTRON bru-3
X	11164903	X_11164903_SNP [dm3] X_11270870_SNP [dm6]	T	C	2.994e^-5	0.669	INTRON CG44422
X	18859778	X_18859778_SNP [dm3] X_18965745_SNP [dm6]	C	G	2.995e^-5	0.669	INTRON CG43759
3R	26659694	3R_26659694_SNP [dm3] 3R_30833972_SNP [dm6]	C	A	3.013e^-5	0.669	INTRON CG15544
2L	827721	2L_827721_SNP [dm3] 2L_827721_SNP [dm6]	G	A	3.086e^-5	0.669	INTRON dock	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	18011462	2L_18011462_SNP [dm3] 2L_18011462_SNP [dm6]	C	G	3.129e^-5	0.669	UTR_5_PRIME elfless UPSTREAM rdo
3R	16067745	3R_16067745_SNP [dm3] 3R_20242023_SNP [dm6]	A	C	3.131e^-5	0.669	INTRON Nlg4
2L	4478083	2L_4478083_SNP [dm3] 2L_4478083_SNP [dm6]	T	C	3.131e^-5	0.669	UTR_3_PRIME dp
2L	554520	2L_554520_SNP [dm3] 2L_554520_SNP [dm6]	A	G	3.178e^-5	0.669	SYNONYMOUS_CODING rempA
2R	9641336	2R_9641336_SNP [dm3] 2R_13753831_SNP [dm6]	A	C	3.184e^-5	0.669	UPSTREAM CG6280 INTERGENIC
2R	2035245	2R_2035245_SNP [dm3] 2R_6147740_SNP [dm6]	C	G	3.295e^-5	0.669	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	3.295e^-5	0.669	INTRON EcR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	2105215	3L_2105215_SNP [dm3] 3L_2105215_SNP [dm6]	T	C	3.350e^-5	0.669	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3R	9442936	3R_9442936_SNP [dm3] 3R_13617214_SNP [dm6]	G	A	3.415e^-5	0.669	DOWNSTREAM CG9269 & 1 other INTERGENIC
X	16510329	X_16510329_SNP [dm3] X_16616296_SNP [dm6]	A	G	3.473e^-5	0.669	SYNONYMOUS_CODING CG9782	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	2397231	X_2397231_SNP [dm3] X_2503198_SNP [dm6]	T	A	3.641e^-5	0.669	INTRON trol
2L	7333251	2L_7333251_SNP [dm3] 2L_7333251_SNP [dm6]	T	A	3.727e^-5	0.669	UPSTREAM Wnt6 INTERGENIC
X	2397230	X_2397230_SNP [dm3] X_2503197_SNP [dm6]	T	A	3.831e^-5	0.669	INTRON trol
X	2397235	X_2397235_SNP [dm3] X_2503202_SNP [dm6]	G	T	3.831e^-5	0.669	INTRON trol
2L	22427226	2L_22427226_SNP [dm3] 2L_22534494_SNP [dm6]	T	C	3.999e^-5	0.669	UTR_3_PRIME RpL5 DOWNSTREAM RpL5 & 1 other
X	4706947	X_4706947_SNP [dm3] X_4812914_SNP [dm6]	A	T	4.074e^-5	0.669	INTERGENIC
2R	13341748	2R_13341748_SNP [dm3] 2R_17454243_SNP [dm6]	T	A	4.099e^-5	0.669	SYNONYMOUS_CODING CG10764
2L	4721535	2L_4721535_SNP [dm3] 2L_4721535_SNP [dm6]	G	A	4.149e^-5	0.669	UTR_3_PRIME CG34351
2L	14425051	2L_14425051_SNP [dm3] 2L_14425051_SNP [dm6]	T	A	4.188e^-5	0.669	NON_SYNONYMOUS_CODING Cpr35B	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	14425102	2L_14425102_SNP [dm3] 2L_14425102_SNP [dm6]	C	A	4.188e^-5	0.669	INTRON Cpr35B	TF binding site mE1_TFBS_chinmo
2L	14425108	2L_14425108_SNP [dm3] 2L_14425108_SNP [dm6]	T	G	4.188e^-5	0.669	INTRON Cpr35B	TF binding site mE1_TFBS_chinmo
2L	14425121	2L_14425121_SNP [dm3] 2L_14425121_SNP [dm6]	T	A	4.188e^-5	0.669	NON_SYNONYMOUS_CODING Cpr35B SPLICE_SITE_REGION Cpr35B	TF binding site mE1_TFBS_chinmo
2R	1877446	2R_1877446_SNP [dm3] 2R_5989941_SNP [dm6]	T	A	4.211e^-5	0.669	INTRON Src42A
2R	1883462	2R_1883462_SNP [dm3] 2R_5995957_SNP [dm6]	A	C	4.211e^-5	0.669	INTRON Src42A
3L	13968410	3L_13968410_SNP [dm3] 3L_13975310_SNP [dm6]	A	G	4.241e^-5	0.669	INTRON Hsc70-1
3L	2105204	3L_2105204_SNP [dm3] 3L_2105204_SNP [dm6]	T	C	4.247e^-5	0.669	NON_SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2R	1923988	2R_1923988_SNP [dm3] 2R_6036483_SNP [dm6]	G	A	4.262e^-5	0.669	UPSTREAM SCAP DOWNSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Ubx
2L	2797927	2L_2797927_SNP [dm3] 2L_2797927_SNP [dm6]	T	G	4.433e^-5	0.669	INTRON Syt1 EXON CR43821	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	9079277	2L_9079277_SNP [dm3] 2L_9079277_SNP [dm6]	C	A	4.448e^-5	0.669	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

CN_Hobo_TEMP_W phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results