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=5.909e^-18)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

25154 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	10135596	2L_10135596_SNP [dm3] 2L_10135596_SNP [dm6]	G	T	0	0	INTRON CG44153
2L	10471736	2L_10471736_SNP [dm3] 2L_10471736_SNP [dm6]	G	A	0	0	SYNONYMOUS_CODING RluA-1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12112219	2L_12112219_SNP [dm3] 2L_12112219_SNP [dm6]	G	A	0	0	UTR_3_PRIME Phae2 DOWNSTREAM Phae2
2L	12178908	2L_12178908_SNP [dm3] 2L_12178908_SNP [dm6]	T	A	0	0	INTRON aret
2L	12583516	2L_12583516_SNP [dm3] 2L_12583516_SNP [dm6]	C	G	0	0	DOWNSTREAM CR44596 EXON CR44595
2L	14968124	2L_14968124_SNP [dm3] 2L_14968124_SNP [dm6]	C	T	0	0	INTRON CG42313
2L	16689277	2L_16689277_SNP [dm3] 2L_16689277_SNP [dm6]	A	T	0	0	INTRON grp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	19105596	2L_19105596_SNP [dm3] 2L_19105596_SNP [dm6]	T	C	0	0	INTRON Lim3
2L	20657493	2L_20657493_SNP [dm3] 2L_20657493_SNP [dm6]	C	G	0	0	INTRON CG2614	TF binding site mE1_TFBS_sens
2L	22028653	2L_22028653_SNP [dm3] 2L_22028653_SNP [dm6]	T	A	0	0	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3804620	2L_3804620_SNP [dm3] 2L_3804620_SNP [dm6]	T	C	0	0	INTRON Reph	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	5515293	2L_5515293_SNP [dm3] 2L_5515293_SNP [dm6]	C	A	0	0	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7524301	2L_7524301_SNP [dm3] 2L_7524301_SNP [dm6]	G	C	0	0	INTRON RapGAP1
2L	7964285	2L_7964285_SNP [dm3] 2L_7964285_SNP [dm6]	T	C	0	0	INTRON Snoo	TF binding site mE1_TFBS_inv
2L	9725968	2L_9725968_SNP [dm3] 2L_9725968_SNP [dm6]	C	T	0	0	INTRON Nckx30C
2R	12325869	2R_12325869_SNP [dm3] 2R_16438364_SNP [dm6]	T	A	0	0	INTERGENIC
2R	1438916	2R_1438916_INS [dm3] 2R_5551411_INS [dm6]	A	AAGATT	0	0	INTERGENIC	transposable element FlyBase
2R	282651	2R_282651_DEL [dm3] 2R_4395146_DEL [dm6]	TCTTAAATAGAGGAAAAGGA...	T	0	0	INTRON Gprk1
2R	293709	2R_293709_SNP [dm3] 2R_4406204_SNP [dm6]	T	A	0	0	INTRON Gprk1
3L	10320987	3L_10320987_SNP [dm3] 3L_10327887_SNP [dm6]	C	T	0	0	DOWNSTREAM CR45244 INTERGENIC
3L	18207549	3L_18207549_SNP [dm3] 3L_18214449_SNP [dm6]	T	G	0	0	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3L	4608219	3L_4608219_SNP [dm3] 3L_4608219_SNP [dm6]	A	T	0	0	INTRON Src64B
3L	5160870	3L_5160870_SNP [dm3] 3L_5167770_SNP [dm6]	A	T	0	0	INTRON shep
3L	5281993	3L_5281993_INS [dm3] 3L_5288893_INS [dm6]	T	TT	0	0	INTERGENIC
3R	10875254	3R_10875254_SNP [dm3] 3R_15049532_SNP [dm6]	C	T	0	0	INTERGENIC
3R	12672504	3R_12672504_SNP [dm3] 3R_16846782_SNP [dm6]	T	C	0	0	INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3R	14923581	3R_14923581_SNP [dm3] 3R_19097859_SNP [dm6]	T	A	0	0	INTRON CG6040
3R	16205267	3R_16205267_SNP [dm3] 3R_20379545_SNP [dm6]	T	C	0	0	UTR_3_PRIME Gfrl
3R	17251163	3R_17251163_SNP [dm3] 3R_21425441_SNP [dm6]	G	A	0	0	DOWNSTREAM lbl INTRON lbl
3R	18194884	3R_18194884_SNP [dm3] 3R_22369162_SNP [dm6]	C	G	0	0	UPSTREAM PyK INTRON PyK	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	5537209	3R_5537209_SNP [dm3] 3R_9711487_SNP [dm6]	A	C	0	0	NON_SYNONYMOUS_CODING dmt UPSTREAM trbd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	8928025	X_8928025_SNP [dm3] X_9033992_SNP [dm6]	C	T	0	0	INTRON CR43836 & 1 other
2R	13745844	2R_13745844_SNP [dm3] 2R_17858339_SNP [dm6]	T	C	2.585e^-40	1.419e^-35	INTRON olf186-F
2R	13746320	2R_13746320_SNP [dm3] 2R_17858815_SNP [dm6]	C	T	4.111e^-40	2.191e^-35	INTRON olf186-F
2R	14751213	2R_14751213_SNP [dm3] 2R_18863708_SNP [dm6]	C	A	7.649e^-39	3.850e^-34	UPSTREAM CG43070 DOWNSTREAM CG43069 & 1 other INTERGENIC
2R	14751231	2R_14751231_SNP [dm3] 2R_18863726_SNP [dm6]	T	A	7.649e^-39	3.850e^-34	UPSTREAM CG43070 DOWNSTREAM CG43069 & 1 other INTERGENIC
2R	14705624	2R_14705624_SNP [dm3] 2R_18818119_SNP [dm6]	G	C	3.580e^-34	1.753e^-29	INTERGENIC
2R	14885370	2R_14885370_SNP [dm3] 2R_18997865_SNP [dm6]	G	T	9.587e^-34	4.571e^-29	SYNONYMOUS_CODING tn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2648918	2L_2648918_SNP [dm3] 2L_2648918_SNP [dm6]	C	G	1.647e^-23	7.651e^-19	NON_SYNONYMOUS_CODING CG33125 UTR_3_PRIME CG33125 DOWNSTREAM CG43851
2L	3934783	2L_3934783_SNP [dm3] 2L_3934783_SNP [dm6]	A	T	3.577e^-23	1.620e^-18	INTRON fred
3R	10225115	3R_10225115_SNP [dm3] 3R_14399393_SNP [dm6]	T	G	3.941e^-20	1.742e^-15	INTRON cv-c
3R	5553123	3R_5553123_SNP [dm3] 3R_9727401_SNP [dm6]	A	T	7.843e^-20	3.384e^-15	UTR_3_PRIME FoxP INTRON FoxP	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	2267840	2L_2267840_SNP [dm3] 2L_2267840_SNP [dm6]	T	G	2.895e^-19	1.029e^-14	DOWNSTREAM CG17242 INTERGENIC
2L	5605983	2L_5605983_SNP [dm3] 2L_5605983_SNP [dm6]	G	A	2.895e^-19	1.029e^-14	SPLICE_SITE_REGION CG14010 INTRON CG14010
2L	5607141	2L_5607141_SNP [dm3] 2L_5607141_SNP [dm6]	A	C	2.895e^-19	1.029e^-14	INTRON CG14010	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	5607168	2L_5607168_DEL [dm3] 2L_5607168_DEL [dm6]	ATTTCTTACTTGTCGTAATT...	A	2.895e^-19	1.029e^-14	INTRON CG14010	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	5607253	2L_5607253_DEL [dm3] 2L_5607253_DEL [dm6]	TATCT	T	2.895e^-19	1.029e^-14	INTRON CG14010
2L	5607607	2L_5607607_SNP [dm3] 2L_5607607_SNP [dm6]	A	G	2.895e^-19	1.029e^-14	INTRON CG14010
2L	5608463	2L_5608463_SNP [dm3] 2L_5608463_SNP [dm6]	T	C	2.895e^-19	1.029e^-14	INTRON CG14010
2L	5608729	2L_5608729_SNP [dm3] 2L_5608729_SNP [dm6]	A	T	2.895e^-19	1.029e^-14	INTRON CG14010
2L	5609887	2L_5609887_SNP [dm3] 2L_5609887_SNP [dm6]	C	A	2.895e^-19	1.029e^-14	INTRON CG14010
2L	5701609	2L_5701609_SNP [dm3] 2L_5701609_SNP [dm6]	T	C	5.497e^-19	1.642e^-14	INTERGENIC
2L	5611132	2L_5611132_SNP [dm3] 2L_5611132_SNP [dm6]	T	C	5.503e^-19	1.642e^-14	INTRON CG14010
3L	11063969	3L_11063969_SNP [dm3] 3L_11070869_SNP [dm6]	G	A	5.505e^-19	1.642e^-14	NON_SYNONYMOUS_CODING Mocs1
3R	10224629	3R_10224629_SNP [dm3] 3R_14398907_SNP [dm6]	G	C	5.508e^-19	1.642e^-14	INTRON cv-c
2L	5608645	2L_5608645_SNP [dm3] 2L_5608645_SNP [dm6]	C	T	5.511e^-19	1.642e^-14	INTRON CG14010	transposable element FlyBase
3L	2740914	3L_2740914_SNP [dm3] 3L_2740914_SNP [dm6]	C	T	5.518e^-19	1.642e^-14	DOWNSTREAM Acp62F INTRON Mrtf
3R	14604373	3R_14604373_SNP [dm3] 3R_18778651_SNP [dm6]	A	C	5.521e^-19	1.642e^-14	INTRON CG7720
3L	7556209	3L_7556209_SNP [dm3] 3L_7563109_SNP [dm6]	C	A	5.549e^-19	1.642e^-14	NON_SYNONYMOUS_CODING frac	TF binding site BDTNP1_TFBS_twi
2R	16604924	2R_16604924_SNP [dm3] 2R_20717419_SNP [dm6]	T	A	5.573e^-19	1.642e^-14	INTRON dpr
X	5240326	X_5240326_SNP [dm3] X_5346293_SNP [dm6]	A	G	5.618e^-19	1.642e^-14	INTRON SK
X	5240327	X_5240327_SNP [dm3] X_5346294_SNP [dm6]	A	C	5.618e^-19	1.642e^-14	INTRON SK
3R	5551616	3R_5551616_SNP [dm3] 3R_9725894_SNP [dm6]	C	T	6.239e^-19	1.794e^-14	UPSTREAM hyd DOWNSTREAM FoxP INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
3L	14364207	3L_14364207_SNP [dm3] 3L_14371107_SNP [dm6]	C	T	1.049e^-18	2.870e^-14	INTERGENIC
3R	16335812	3R_16335812_SNP [dm3] 3R_20510090_SNP [dm6]	G	A	1.050e^-18	2.870e^-14	UTR_5_PRIME CG4288
3R	10999334	3R_10999334_SNP [dm3] 3R_15173612_SNP [dm6]	T	C	1.062e^-18	2.870e^-14	DOWNSTREAM Mf INTRON Mf & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	12339207	2R_12339207_SNP [dm3] 2R_16451702_SNP [dm6]	G	T	1.070e^-18	2.870e^-14	INTERGENIC
3L	20673887	3L_20673887_SNP [dm3] 3L_20680787_SNP [dm6]	T	C	1.077e^-18	2.870e^-14	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10465069	3R_10465069_SNP [dm3] 3R_14639347_SNP [dm6]	G	A	2.011e^-18	5.133e^-14	SYNONYMOUS_CODING Cad88C INTRON CG7886
3R	13280622	3R_13280622_SNP [dm3] 3R_17454900_SNP [dm6]	G	A	2.011e^-18	5.133e^-14	DOWNSTREAM CG14330 INTERGENIC
3R	9436081	3R_9436081_SNP [dm3] 3R_13610359_SNP [dm6]	T	A	2.011e^-18	5.133e^-14	INTERGENIC
3R	13821733	3R_13821733_DEL [dm3] 3R_17996011_DEL [dm6]	CT	C	2.054e^-18	5.168e^-14	INTRON cpo
3R	14604372	3R_14604372_SNP [dm3] 3R_18778650_SNP [dm6]	G	A	3.793e^-18	9.414e^-14	INTRON CG7720
X	5610591	X_5610591_SNP [dm3] X_5716558_SNP [dm6]	T	G	4.000e^-18	9.795e^-14	INTRON CG33080
3L	11061880	3L_11061880_SNP [dm3] 3L_11068780_SNP [dm6]	T	C	7.411e^-18	1.791e^-13	UTR_3_PRIME CG45101 & 1 other DOWNSTREAM CG6310
3R	23127878	3R_23127878_SNP [dm3] 3R_27302156_SNP [dm6]	C	T	9.270e^-18	2.210e^-13	INTRON CG3339
2L	3726827	2L_3726827_SNP [dm3] 2L_3726827_SNP [dm6]	C	G	1.955e^-17	4.601e^-13	SYNONYMOUS_CODING Shaw UTR_3_PRIME Shaw
2L	8189380	2L_8189380_SNP [dm3] 2L_8189380_SNP [dm6]	T	G	2.654e^-17	6.164e^-13	UTR_3_PRIME Piezo DOWNSTREAM CG34134
3L	1754062	3L_1754062_SNP [dm3] 3L_1754062_SNP [dm6]	G	A	4.294e^-17	8.944e^-13	SYNONYMOUS_CODING Cht2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3L	19031888	3L_19031888_SNP [dm3] 3L_19038788_SNP [dm6]	A	G	4.294e^-17	8.944e^-13	INTRON nkd	TF binding site mE1_TFBS_cad
3L	8311874	3L_8311874_SNP [dm3] 3L_8318774_SNP [dm6]	A	T	4.294e^-17	8.944e^-13	INTRON CG43059
3R	10246331	3R_10246331_SNP [dm3] 3R_14420609_SNP [dm6]	G	A	4.294e^-17	8.944e^-13	NON_SYNONYMOUS_CODING natalisin INTRON cv-c	TF binding site mE1_TFBS_cad
3R	10246537	3R_10246537_SNP [dm3] 3R_14420815_SNP [dm6]	G	A	4.294e^-17	8.944e^-13	SYNONYMOUS_CODING natalisin DOWNSTREAM CR44176 INTRON cv-c	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	10246628	3R_10246628_SNP [dm3] 3R_14420906_SNP [dm6]	G	A	4.294e^-17	8.944e^-13	SPLICE_SITE_REGION natalisin DOWNSTREAM CR44176 INTRON cv-c & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	5752356	3R_5752356_SNP [dm3] 3R_9926634_SNP [dm6]	G	T	4.294e^-17	8.944e^-13	INTRON Glut4EF	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	5752417	3R_5752417_SNP [dm3] 3R_9926695_SNP [dm6]	C	T	4.294e^-17	8.944e^-13	INTRON Glut4EF	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	9504058	X_9504058_SNP [dm3] X_9610025_SNP [dm6]	C	T	4.294e^-17	8.944e^-13	SYNONYMOUS_CODING CG42797	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	5605716	2L_5605716_SNP [dm3] 2L_5605716_SNP [dm6]	G	T	5.139e^-17	1.046e^-12	INTRON CG14010
2L	5605739	2L_5605739_SNP [dm3] 2L_5605739_SNP [dm6]	A	G	5.139e^-17	1.046e^-12	INTRON CG14010
2R	17899543	2R_17899543_SNP [dm3] 2R_22012038_SNP [dm6]	T	C	7.446e^-17	1.377e^-12	INTRON CG34370
2L	441144	2L_441144_SNP [dm3] 2L_441144_SNP [dm6]	C	G	7.489e^-17	1.377e^-12	INTRON ex	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	8176731	2R_8176731_SNP [dm3] 2R_12289226_SNP [dm6]	C	T	7.489e^-17	1.377e^-12	INTRON CG42700
3L	8283154	3L_8283154_SNP [dm3] 3L_8290054_SNP [dm6]	T	A	7.489e^-17	1.377e^-12	UPSTREAM cert DOWNSTREAM CG7201 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Ubx
X	21321224	X_21321224_SNP [dm3] X_21450197_SNP [dm6]	G	A	7.508e^-17	1.377e^-12	INTRON CG42343	TF binding site mE1_TFBS_HSA
2L	3421318	2L_3421318_SNP [dm3] 2L_3421318_SNP [dm6]	A	G	7.522e^-17	1.377e^-12	INTRON pgant2
2L	3421319	2L_3421319_SNP [dm3] 2L_3421319_SNP [dm6]	A	G	7.522e^-17	1.377e^-12	INTRON pgant2
2L	3421320	2L_3421320_DEL [dm3] 2L_3421320_DEL [dm6]	TGA	T	7.522e^-17	1.377e^-12	INTRON pgant2
2L	3421324	2L_3421324_SNP [dm3] 2L_3421324_SNP [dm6]	A	C	7.522e^-17	1.377e^-12	INTRON pgant2
2L	3421327	2L_3421327_DEL [dm3] 2L_3421327_DEL [dm6]	GAGCAG	ATA	7.522e^-17	1.377e^-12	INTRON pgant2
3L	24296231	3L_24296231_SNP [dm3] 3L_24303131_SNP [dm6]	G	A	2.260e^-16	4.020e^-12	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU077 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results