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=1.501e^-15)
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_2L_t	0.08346

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

13709 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	10356404	2L_10356404_SNP [dm3] 2L_10356404_SNP [dm6]	G	T	0	0	UTR_5_PRIME CG5367 UPSTREAM CG5045	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	11122621	2L_11122621_SNP [dm3] 2L_11122621_SNP [dm6]	G	T	0	0	UTR_3_PRIME Csl4 UPSTREAM CG14921	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11123623	2L_11123623_SNP [dm3] 2L_11123623_SNP [dm6]	C	T	0	0	UPSTREAM Nup160 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1145086	2L_1145086_SNP [dm3] 2L_1145086_SNP [dm6]	G	A	0	0	INTRON MFS3	TF binding site mE1_TFBS_cad
2L	1145316	2L_1145316_SNP [dm3] 2L_1145316_SNP [dm6]	T	G	0	0	INTRON MFS3	TF binding site mE1_TFBS_cad
2L	1147512	2L_1147512_SNP [dm3] 2L_1147512_SNP [dm6]	C	T	0	0	UPSTREAM CG4749 DOWNSTREAM MFS3 INTERGENIC
2L	1147533	2L_1147533_SNP [dm3] 2L_1147533_SNP [dm6]	C	T	0	0	UPSTREAM CG4749 DOWNSTREAM MFS3 INTERGENIC
2L	1149384	2L_1149384_SNP [dm3] 2L_1149384_SNP [dm6]	A	G	0	0	UTR_3_PRIME CG4749 DOWNSTREAM Tfb4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	1151448	2L_1151448_DEL [dm3] 2L_1151448_DEL [dm6]	CCAACC	C	0	0	UTR_3_PRIME Vps29 UPSTREAM Tfb4 DOWNSTREAM capt	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	1153447	2L_1153447_SNP [dm3] 2L_1153447_SNP [dm6]	G	A	0	0	NON_SYNONYMOUS_CODING capt	TF binding site mE1_TFBS_chinmo
2L	1155396	2L_1155396_SNP [dm3] 2L_1155396_SNP [dm6]	G	A	0	0	INTRON capt
2L	1171061	2L_1171061_SNP [dm3] 2L_1171061_SNP [dm6]	T	C	0	0	SYNONYMOUS_CODING CG5118 UPSTREAM Plap DOWNSTREAM CG31922	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	12923181	2L_12923181_SNP [dm3] 2L_12923181_SNP [dm6]	G	C	0	0	SYNONYMOUS_CODING ACXA UTR_3_PRIME ACXA
2L	12923184	2L_12923184_SNP [dm3] 2L_12923184_SNP [dm6]	G	T	0	0	SYNONYMOUS_CODING ACXA UTR_3_PRIME ACXA
2L	12923201	2L_12923201_SNP [dm3] 2L_12923201_SNP [dm6]	T	C	0	0	INTRON ACXA
2L	16496322	2L_16496322_SNP [dm3] 2L_16496322_SNP [dm6]	C	G	0	0	UPSTREAM Tpr2 INTRON Tpr2	TF binding site mE1_TFBS_bab1
2L	16496323	2L_16496323_INS [dm3] 2L_16496323_INS [dm6]	A	AGGAAGAGTTTGAGCATGCT...	0	0	UPSTREAM Tpr2 INTRON Tpr2	TF binding site mE1_TFBS_bab1
2L	9199454	2L_9199454_SNP [dm3] 2L_9199454_SNP [dm6]	A	G	0	0	INTRON tai
2R	7298565	2R_7298565_INS [dm3] 2R_11411060_INS [dm6]	A	ATA	0	0	UPSTREAM CG34054 DOWNSTREAM Drip INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	12066593	3L_12066593_SNP [dm3] 3L_12073493_SNP [dm6]	C	T	0	0	INTRON Sema-5c
3L	855912	3L_855912_SNP [dm3] 3L_855912_SNP [dm6]	A	C	0	0	INTRON dpr20
3L	855926	3L_855926_DEL [dm3] 3L_855926_DEL [dm6]	AAGAC	A	0	0	INTRON dpr20
X	12529467	X_12529467_SNP [dm3] X_12635434_SNP [dm6]	G	T	0	0	UPSTREAM mir-970 INTRON Tomosyn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	6975779	X_6975779_SNP [dm3] X_7081746_SNP [dm6]	T	C	0	0	INTRON Sxl	TF binding site mE1_TFBS_zfh1
X	6975816	X_6975816_SNP [dm3] X_7081783_SNP [dm6]	T	A	0	0	INTRON Sxl
X	6975987	X_6975987_SNP [dm3] X_7081954_SNP [dm6]	T	G	0	0	DOWNSTREAM Sxl INTRON Sxl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	9787806	X_9787806_SNP [dm3] X_9893773_SNP [dm6]	T	A	1.116e^-67	7.471e^-63	INTRON CG15249
3L	7428020	3L_7428020_SNP [dm3] 3L_7434920_SNP [dm6]	G	C	1.124e^-67	7.471e^-63	UTR_5_PRIME Rac2 INTRON CG42458	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	1112388	3R_1112388_DEL [dm3] 3R_5286666_DEL [dm6]	AT	A	1.155e^-66	7.410e^-62	INTRON mtd
3L	12106191	3L_12106191_INS [dm3] 3L_12113091_INS [dm6]	A	AA	7.548e^-66	4.681e^-61	INTERGENIC
2R	14628234	2R_14628234_INS [dm3] 2R_18740729_INS [dm6]	T	TT	1.832e^-63	1.100e^-58	INTRON Hs3st-A EXON CR30121
2R	13048508	2R_13048508_SNP [dm3] 2R_17161003_SNP [dm6]	G	T	3.194e^-44	1.857e^-39	UPSTREAM CG30457 INTERGENIC
2L	12872319	2L_12872319_SNP [dm3] 2L_12872319_SNP [dm6]	C	T	7.848e^-28	4.424e^-23	INTERGENIC
2L	4021953	2L_4021953_SNP [dm3] 2L_4021953_SNP [dm6]	A	T	5.295e^-27	2.897e^-22	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_jumu
2L	10144109	2L_10144109_SNP [dm3] 2L_10144109_SNP [dm6]	A	T	3.311e^-26	1.760e^-21	UPSTREAM CG4839 INTRON CG44153
3L	7141174	3L_7141174_SNP [dm3] 3L_7148074_SNP [dm6]	G	A	1.209e^-22	6.249e^-18	INTRON corn	TF binding site mE1_TFBS_cad
2L	2256670	2L_2256670_SNP [dm3] 2L_2256670_SNP [dm6]	C	T	2.669e^-22	1.342e^-17	DOWNSTREAM CR44787 INTERGENIC
2L	11812107	2L_11812107_SNP [dm3] 2L_11812107_SNP [dm6]	G	A	5.733e^-21	2.807e^-16	SYNONYMOUS_CODING CycY	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15992170	3L_15992170_SNP [dm3] 3L_15999070_SNP [dm6]	A	C	2.057e^-20	9.569e^-16	INTRON CG5830
3L	15992172	3L_15992172_SNP [dm3] 3L_15999072_SNP [dm6]	A	C	2.057e^-20	9.569e^-16	INTRON CG5830
3L	20603952	3L_20603952_SNP [dm3] 3L_20610852_SNP [dm6]	G	T	6.838e^-18	3.103e^-13	INTRON knrl
X	2620098	X_2620098_SNP [dm3] X_2726065_SNP [dm6]	T	A	8.218e^-18	3.640e^-13	NON_SYNONYMOUS_CODING fs_1_Ya UPSTREAM CG2709	TF binding site BDTNP1_TFBS_Mad BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12419949	3L_12419949_SNP [dm3] 3L_12426849_SNP [dm6]	G	C	9.275e^-18	3.751e^-13	INTRON toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	12420994	3L_12420994_SNP [dm3] 3L_12427894_SNP [dm6]	G	C	9.275e^-18	3.751e^-13	INTRON toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	12421028	3L_12421028_DEL [dm3] 3L_12427928_DEL [dm6]	AA	T	9.275e^-18	3.751e^-13	INTRON toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	12422198	3L_12422198_SNP [dm3] 3L_12429098_SNP [dm6]	A	C	9.275e^-18	3.751e^-13	INTRON toe
2R	18055581	2R_18055581_SNP [dm3] 2R_22168076_SNP [dm6]	G	T	1.667e^-17	6.120e^-13	INTRON a	TF binding site mE1_TFBS_chinmo
3L	12417379	3L_12417379_SNP [dm3] 3L_12424279_SNP [dm6]	T	A	1.676e^-17	6.120e^-13	INTRON toe	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12417409	3L_12417409_SNP [dm3] 3L_12424309_SNP [dm6]	T	A	1.676e^-17	6.120e^-13	INTRON toe	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12420844	3L_12420844_SNP [dm3] 3L_12427744_SNP [dm6]	C	G	1.676e^-17	6.120e^-13	NON_SYNONYMOUS_CODING toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	12422478	3L_12422478_SNP [dm3] 3L_12429378_SNP [dm6]	C	T	1.842e^-17	6.120e^-13	INTRON toe
3L	12422479	3L_12422479_SNP [dm3] 3L_12429379_SNP [dm6]	C	A	1.842e^-17	6.120e^-13	INTRON toe
3L	12422483	3L_12422483_SNP [dm3] 3L_12429383_SNP [dm6]	C	A	1.842e^-17	6.120e^-13	INTRON toe
3L	12422485	3L_12422485_DEL [dm3] 3L_12429385_DEL [dm6]	TT	T	1.842e^-17	6.120e^-13	INTRON toe
3L	12422491	3L_12422491_DEL [dm3] 3L_12429391_DEL [dm6]	GAGTGT	A	1.842e^-17	6.120e^-13	INTRON toe
3L	12422501	3L_12422501_INS [dm3] 3L_12429401_INS [dm6]	A	AT	1.842e^-17	6.120e^-13	INTRON toe
3L	20637862	3L_20637862_SNP [dm3] 3L_20644762_SNP [dm6]	C	A	2.358e^-17	7.695e^-13	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9868581	3R_9868581_SNP [dm3] 3R_14042859_SNP [dm6]	T	G	2.999e^-17	9.500e^-13	INTERGENIC
3R	8923237	3R_8923237_SNP [dm3] 3R_13097515_SNP [dm6]	A	C	3.013e^-17	9.500e^-13	INTRON timeout
3L	12422505	3L_12422505_SNP [dm3] 3L_12429405_SNP [dm6]	G	T	3.306e^-17	1.013e^-12	INTRON toe
3L	12420847	3L_12420847_SNP [dm3] 3L_12427747_SNP [dm6]	C	G	3.322e^-17	1.013e^-12	NON_SYNONYMOUS_CODING toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	14698655	2R_14698655_SNP [dm3] 2R_18811150_SNP [dm6]	G	A	4.592e^-17	1.378e^-12	INTRON CG15096
3R	8923074	3R_8923074_SNP [dm3] 3R_13097352_SNP [dm6]	G	C	5.447e^-17	1.609e^-12	INTRON timeout
3L	12422408	3L_12422408_DEL [dm3] 3L_12429308_DEL [dm6]	TT	T	5.949e^-17	1.729e^-12	INTRON toe
3L	18642501	3L_18642501_SNP [dm3] 3L_18649401_SNP [dm6]	A	C	6.102e^-17	1.747e^-12	INTRON MYPT-75D
3L	8798510	3L_8798510_SNP [dm3] 3L_8805410_SNP [dm6]	G	A	7.019e^-17	1.979e^-12	NON_SYNONYMOUS_CODING CG34427 DOWNSTREAM CG13312	TF binding site mE1_TFBS_chinmo
3L	3894156	3L_3894156_SNP [dm3] 3L_3894156_SNP [dm6]	T	C	7.848e^-17	2.179e^-12	UPSTREAM snRNA:U11 DOWNSTREAM Gr63a INTRON Fie
2R	14701040	2R_14701040_SNP [dm3] 2R_18813535_SNP [dm6]	A	G	8.811e^-17	2.411e^-12	INTRON CG15096
2R	14698633	2R_14698633_SNP [dm3] 2R_18811128_SNP [dm6]	T	C	1.029e^-16	2.774e^-12	INTRON CG15096
3L	12420645	3L_12420645_DEL [dm3] 3L_12427545_DEL [dm6]	TT	T	1.668e^-16	4.433e^-12	INTRON toe	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	8796429	3L_8796429_SNP [dm3] 3L_8803329_SNP [dm6]	T	C	1.771e^-16	4.579e^-12	DOWNSTREAM CG32023 INTRON CG34426
3L	1063223	3L_1063223_SNP [dm3] 3L_1063223_SNP [dm6]	A	G	1.772e^-16	4.579e^-12	INTRON bab1
3L	1064235	3L_1064235_SNP [dm3] 3L_1064235_SNP [dm6]	C	G	1.801e^-16	4.591e^-12	INTRON bab1
2R	14563334	2R_14563334_SNP [dm3] 2R_18675829_SNP [dm6]	A	C	2.689e^-16	6.413e^-12	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	7892242	2R_7892242_SNP [dm3] 2R_12004737_SNP [dm6]	G	C	2.689e^-16	6.413e^-12	INTRON otk
2R	7893002	2R_7893002_SNP [dm3] 2R_12005497_SNP [dm6]	T	A	2.689e^-16	6.413e^-12	NON_SYNONYMOUS_CODING otk	TF binding site mE1_TFBS_chinmo
3L	12101249	3L_12101249_SNP [dm3] 3L_12108149_SNP [dm6]	A	G	2.689e^-16	6.413e^-12	INTERGENIC
3L	7425643	3L_7425643_SNP [dm3] 3L_7432543_SNP [dm6]	T	A	2.689e^-16	6.413e^-12	INTRON CG42458
3L	7057760	3L_7057760_INS [dm3] 3L_7064660_INS [dm6]	G	GTTT	3.808e^-16	8.967e^-12	INTRON CG8641
3L	14054813	3L_14054813_SNP [dm3] 3L_14061713_SNP [dm6]	G	A	4.400e^-16	9.985e^-12	INTRON CG32138
3L	12408841	3L_12408841_SNP [dm3] 3L_12415741_SNP [dm6]	A	G	4.508e^-16	9.985e^-12	SYNONYMOUS_CODING ArfGAP1 UPSTREAM CG32103	TF binding site mE1_TFBS_chinmo
3L	12413971	3L_12413971_SNP [dm3] 3L_12420871_SNP [dm6]	C	T	4.508e^-16	9.985e^-12	INTERGENIC
3L	12417385	3L_12417385_SNP [dm3] 3L_12424285_SNP [dm6]	G	A	4.508e^-16	9.985e^-12	INTRON toe	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12417521	3L_12417521_SNP [dm3] 3L_12424421_SNP [dm6]	T	C	4.508e^-16	9.985e^-12	INTRON toe	TF binding site mE1_TFBS_cad
2R	14742947	2R_14742947_SNP [dm3] 2R_18855442_SNP [dm6]	A	T	4.595e^-16	1.006e^-11	UPSTREAM Jheh1 DOWNSTREAM Jheh2 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_cnc
3L	12099886	3L_12099886_SNP [dm3] 3L_12106786_SNP [dm6]	T	A	4.726e^-16	1.022e^-11	INTERGENIC
2R	8689524	2R_8689524_SNP [dm3] 2R_12802019_SNP [dm6]	A	G	4.989e^-16	1.067e^-11	DOWNSTREAM sca INTERGENIC
3L	1139664	3L_1139664_INS [dm3] 3L_1139664_INS [dm6]	T	TT	6.550e^-16	1.345e^-11	DOWNSTREAM bab2 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	12106921	3L_12106921_DEL [dm3] 3L_12113821_DEL [dm6]	TAAGCAAAAATAAAGTTTTG...	T	6.918e^-16	1.345e^-11	INTERGENIC
3L	15222709	3L_15222709_SNP [dm3] 3L_15229609_SNP [dm6]	T	G	7.122e^-16	1.345e^-11	INTERGENIC	TF binding site BDTNP1_TFBS_z
3R	1060052	3R_1060052_SNP [dm3] 3R_5234330_SNP [dm6]	G	A	7.156e^-16	1.345e^-11	NON_SYNONYMOUS_CODING Mms19	TF binding site mE1_TFBS_sens
3R	1088729	3R_1088729_SNP [dm3] 3R_5263007_SNP [dm6]	T	A	7.156e^-16	1.345e^-11	UPSTREAM Tim17a2 INTRON Hph	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	1129679	3R_1129679_SNP [dm3] 3R_5303957_SNP [dm6]	A	G	7.156e^-16	1.345e^-11	INTRON mtd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	1146541	3R_1146541_SNP [dm3] 3R_5320819_SNP [dm6]	G	T	7.156e^-16	1.345e^-11	INTRON mtd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	1149523	3R_1149523_SNP [dm3] 3R_5323801_SNP [dm6]	G	C	7.156e^-16	1.345e^-11	UTR_5_PRIME mtd INTRON mtd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3R	1193278	3R_1193278_SNP [dm3] 3R_5367556_SNP [dm6]	A	G	7.156e^-16	1.345e^-11	UPSTREAM CR44103 INTRON Cerk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	1198149	3R_1198149_SNP [dm3] 3R_5372427_SNP [dm6]	C	A	7.156e^-16	1.345e^-11	DOWNSTREAM hd & 3 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	1203766	3R_1203766_SNP [dm3] 3R_5378044_SNP [dm6]	T	A	7.156e^-16	1.345e^-11	DOWNSTREAM kkv & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
3R	1205981	3R_1205981_SNP [dm3] 3R_5380259_SNP [dm6]	G	A	7.156e^-16	1.345e^-11	INTRON kkv	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	7894078	2R_7894078_SNP [dm3] 2R_12006573_SNP [dm6]	C	G	7.822e^-16	1.426e^-11	INTRON otk

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By genomic position
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Microbiota_OTU023 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results