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=8.115e^-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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2162 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
3L	13883106	3L_13883106_SNP [dm3] 3L_13890006_SNP [dm6]	A	T	8.163e^-7	0.866	INTRON dysc
3L	12641204	3L_12641204_DEL [dm3] 3L_12648104_DEL [dm6]	TT	T	1.220e^-6	0.866	DOWNSTREAM CR43431 EXON CR32111	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13277556	3L_13277556_SNP [dm3] 3L_13284456_SNP [dm6]	T	A	5.227e^-6	0.866	DOWNSTREAM CR45752 EXON CR43913
2R	4068556	2R_4068556_SNP [dm3] 2R_8181051_SNP [dm6]	C	T	6.002e^-6	0.866	INTRON LRP1
3L	8993631	3L_8993631_SNP [dm3] 3L_9000531_SNP [dm6]	A	T	6.073e^-6	0.866	INTRON CG5087
3L	17848047	3L_17848047_SNP [dm3] 3L_17854947_SNP [dm6]	G	T	8.482e^-6	0.866	INTRON CG5535	TF binding site mE1_TFBS_HSA
3R	14560988	3R_14560988_SNP [dm3] 3R_18735266_SNP [dm6]	T	C	8.585e^-6	0.866	SYNONYMOUS_CODING Mekk1	TF binding site mE1_TFBS_cad
3R	5118268	3R_5118268_SNP [dm3] 3R_9292546_SNP [dm6]	A	T	1.012e^-5	0.866	INTERGENIC
2R	12577928	2R_12577928_SNP [dm3] 2R_16690423_SNP [dm6]	A	T	1.143e^-5	0.866	UPSTREAM CG5210 INTRON CG30463
2R	8733169	2R_8733169_SNP [dm3] 2R_12845664_SNP [dm6]	A	G	1.173e^-5	0.866	SYNONYMOUS_CODING CG17575 DOWNSTREAM Or49b	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	20126550	2L_20126550_DEL [dm3] 2L_20126550_DEL [dm6]	CAAAATGGTGTAGC...	C	1.339e^-5	0.866	INTERGENIC
3R	5118235	3R_5118235_SNP [dm3] 3R_9292513_SNP [dm6]	T	C	1.374e^-5	0.866	INTERGENIC
3R	15566725	3R_15566725_SNP [dm3] 3R_19741003_SNP [dm6]	A	G	1.382e^-5	0.866	INTRON GluClalpha	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	17025724	2R_17025724_SNP [dm3] 2R_21138219_SNP [dm6]	G	C	1.387e^-5	0.866	SPLICE_SITE_REGION Magi INTRON Magi	TF binding site mE1_TFBS_chinmo
X	3482356	X_3482356_SNP [dm3] X_3588323_SNP [dm6]	G	C	1.404e^-5	0.866	INTRON AstA-R1
2R	12577927	2R_12577927_SNP [dm3] 2R_16690422_SNP [dm6]	C	T	1.480e^-5	0.866	UPSTREAM CG5210 INTRON CG30463
2R	8007438	2R_8007438_SNP [dm3] 2R_12119933_SNP [dm6]	A	G	1.525e^-5	0.866	UPSTREAM jeb INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	7369138	2R_7369138_SNP [dm3] 2R_11481633_SNP [dm6]	T	G	1.701e^-5	0.866	INTRON inv
2L	16609427	2L_16609427_SNP [dm3] 2L_16609427_SNP [dm6]	T	G	1.746e^-5	0.866	SYNONYMOUS_CODING CG4631 INTRON CG42389
3L	13184451	3L_13184451_SNP [dm3] 3L_13191351_SNP [dm6]	A	G	1.758e^-5	0.866	INTERGENIC
2R	18074268	2R_18074268_SNP [dm3] 2R_22186763_SNP [dm6]	C	T	1.760e^-5	0.866	SPLICE_SITE_REGION Vps35 DOWNSTREAM MED16 INTRON Vps35	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3L	17836055	3L_17836055_SNP [dm3] 3L_17842955_SNP [dm6]	A	G	1.768e^-5	0.866	DOWNSTREAM CR45175 & 1 other INTRON CG5567
3L	13207434	3L_13207434_SNP [dm3] 3L_13214334_SNP [dm6]	A	T	1.894e^-5	0.866	DOWNSTREAM tRNA:CR32127 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3R	14559283	3R_14559283_SNP [dm3] 3R_18733561_SNP [dm6]	C	A	1.922e^-5	0.866	SYNONYMOUS_CODING Mekk1 DOWNSTREAM CG14302	TF binding site mE1_TFBS_chinmo
2R	8733032	2R_8733032_INS [dm3] 2R_12845527_INS [dm6]	A	ATT	1.925e^-5	0.866	DOWNSTREAM CG17575 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9647455	3L_9647455_SNP [dm3] 3L_9654355_SNP [dm6]	C	T	1.937e^-5	0.866	INTRON fry & 1 other
2L	4969233	2L_4969233_SNP [dm3] 2L_4969233_SNP [dm6]	C	T	1.955e^-5	0.866	UPSTREAM Scox DOWNSTREAM l_2_05714 INTRON CG3756	TF binding site mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
3L	17840685	3L_17840685_SNP [dm3] 3L_17847585_SNP [dm6]	C	A	2.026e^-5	0.866	SYNONYMOUS_CODING CG7430	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	12641209	3L_12641209_SNP [dm3] 3L_12648109_SNP [dm6]	T	G	2.029e^-5	0.866	DOWNSTREAM CR43431 EXON CR32111	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12862379	X_12862379_SNP [dm3] X_12968346_SNP [dm6]	C	T	2.032e^-5	0.866	NON_SYNONYMOUS_CODING Mur11Da
3L	12525958	3L_12525958_SNP [dm3] 3L_12532858_SNP [dm6]	T	C	2.071e^-5	0.866	SYNONYMOUS_CODING Tsf2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	7369159	2R_7369159_SNP [dm3] 2R_11481654_SNP [dm6]	G	C	2.202e^-5	0.866	INTRON inv
2L	8720582	2L_8720582_SNP [dm3] 2L_8720582_SNP [dm6]	T	G	2.295e^-5	0.866	INTRON raw
3L	3842551	3L_3842551_SNP [dm3] 3L_3842551_SNP [dm6]	T	C	2.361e^-5	0.866	DOWNSTREAM enc INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	5130321	2R_5130321_SNP [dm3] 2R_9242816_SNP [dm6]	G	A	2.381e^-5	0.866	SYNONYMOUS_CODING Cyp4p3 DOWNSTREAM Cyp4p1 INTRON hig
3L	20780981	3L_20780981_SNP [dm3] 3L_20787881_SNP [dm6]	G	T	2.440e^-5	0.866	SYNONYMOUS_CODING CG11396	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2R	11024955	2R_11024955_SNP [dm3] 2R_15137450_SNP [dm6]	C	T	2.442e^-5	0.866	INTRON chn	TF binding site mE1_TFBS_inv
3L	14512745	3L_14512745_SNP [dm3] 3L_14519645_SNP [dm6]	G	T	2.459e^-5	0.866	DOWNSTREAM CG4613 INTRON bbg
2R	12266130	2R_12266130_SNP [dm3] 2R_16378625_SNP [dm6]	A	G	2.535e^-5	0.866	UPSTREAM CR45316 DOWNSTREAM CR45317 INTERGENIC
X	3481763	X_3481763_SNP [dm3] X_3587730_SNP [dm6]	C	G	2.709e^-5	0.866	INTRON AstA-R1
3R	15116874	3R_15116874_SNP [dm3] 3R_19291152_SNP [dm6]	C	G	2.709e^-5	0.866	INTERGENIC
3R	15116883	3R_15116883_SNP [dm3] 3R_19291161_SNP [dm6]	G	A	2.730e^-5	0.866	INTERGENIC
2R	8760056	2R_8760056_SNP [dm3] 2R_12872551_SNP [dm6]	G	A	2.763e^-5	0.866	UPSTREAM CR43469 DOWNSTREAM CG3790 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	12265994	2R_12265994_SNP [dm3] 2R_16378489_SNP [dm6]	A	C	2.854e^-5	0.866	UPSTREAM CR45316 DOWNSTREAM CR45317 INTERGENIC
3L	13207633	3L_13207633_SNP [dm3] 3L_13214533_SNP [dm6]	A	T	2.981e^-5	0.866	DOWNSTREAM tRNA:CR32127 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	17835682	3L_17835682_SNP [dm3] 3L_17842582_SNP [dm6]	T	A	3.056e^-5	0.866	INTRON CG5567 EXON CR45175
3R	15562185	3R_15562185_SNP [dm3] 3R_19736463_SNP [dm6]	G	T	3.106e^-5	0.866	INTRON GluClalpha
3R	14557301	3R_14557301_SNP [dm3] 3R_18731579_SNP [dm6]	C	T	3.111e^-5	0.866	UTR_3_PRIME Cha DOWNSTREAM Cha
2L	551691	2L_551691_SNP [dm3] 2L_551691_SNP [dm6]	G	T	3.170e^-5	0.866	NON_SYNONYMOUS_CODING Ets21C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	14256920	3R_14256920_SNP [dm3] 3R_18431198_SNP [dm6]	C	G	3.184e^-5	0.866	DOWNSTREAM fru INTRON fru
3L	17835680	3L_17835680_SNP [dm3] 3L_17842580_SNP [dm6]	T	G	3.234e^-5	0.866	INTRON CG5567 EXON CR45175
2R	18074274	2R_18074274_SNP [dm3] 2R_22186769_SNP [dm6]	C	T	3.269e^-5	0.866	SPLICE_SITE_REGION Vps35 SYNONYMOUS_CODING Vps35 DOWNSTREAM MED16	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	13539924	2L_13539924_SNP [dm3] 2L_13539924_SNP [dm6]	T	C	3.282e^-5	0.866	UPSTREAM CG16852 INTRON B4
2L	3446484	2L_3446484_SNP [dm3] 2L_3446484_SNP [dm6]	G	T	3.354e^-5	0.866	NON_SYNONYMOUS_CODING CG2772	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13206226	3L_13206226_SNP [dm3] 3L_13213126_SNP [dm6]	T	C	3.422e^-5	0.866	UPSTREAM tRNA:CR32127 DOWNSTREAM tRNA:CR32126 INTERGENIC
3R	18155172	3R_18155172_SNP [dm3] 3R_22329450_SNP [dm6]	A	C	3.479e^-5	0.866	INTRON CG7080	TF binding site mE1_TFBS_cad
3R	18155177	3R_18155177_SNP [dm3] 3R_22329455_SNP [dm6]	C	T	3.479e^-5	0.866	INTRON CG7080	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	10205268	2R_10205268_SNP [dm3] 2R_14317763_SNP [dm6]	C	T	3.507e^-5	0.866	INTRON Shroom
3L	13207655	3L_13207655_SNP [dm3] 3L_13214555_SNP [dm6]	A	G	3.569e^-5	0.866	DOWNSTREAM tRNA:CR32127 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	5862859	3R_5862859_SNP [dm3] 3R_10037137_SNP [dm6]	A	G	3.573e^-5	0.866	INTRON Mical
2R	18748479	2R_18748479_SNP [dm3] 2R_22860956_SNP [dm6]	C	T	3.607e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	11024907	2R_11024907_SNP [dm3] 2R_15137402_SNP [dm6]	T	G	3.671e^-5	0.866	INTRON chn	TF binding site mE1_TFBS_inv
3L	12641214	3L_12641214_SNP [dm3] 3L_12648114_SNP [dm6]	C	T	3.682e^-5	0.866	DOWNSTREAM CR43431 EXON CR32111	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	18748480	2R_18748480_SNP [dm3] 2R_22860957_SNP [dm6]	T	A	3.729e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	18748481	2R_18748481_INS [dm3] 2R_22860958_INS [dm6]	T	TATATA	3.729e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	10540924	2L_10540924_DEL [dm3] 2L_10540924_DEL [dm6]	CATCTCTGCCACCCAAAAGT...	A	3.742e^-5	0.866	INTERGENIC
3L	17834574	3L_17834574_SNP [dm3] 3L_17841474_SNP [dm6]	A	G	3.825e^-5	0.866	UPSTREAM CR45175 & 1 other DOWNSTREAM CG5567 INTERGENIC
2L	17613796	2L_17613796_SNP [dm3] 2L_17613796_SNP [dm6]	G	C	4.146e^-5	0.866	INTERGENIC
3L	13207665	3L_13207665_SNP [dm3] 3L_13214565_SNP [dm6]	G	A	4.164e^-5	0.866	DOWNSTREAM tRNA:CR32127 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	1893128	2L_1893128_SNP [dm3] 2L_1893128_SNP [dm6]	G	C	4.165e^-5	0.866	INTRON CG7337
X	5005160	X_5005160_SNP [dm3] X_5111127_SNP [dm6]	C	G	4.237e^-5	0.866	INTRON rg & 1 other
3R	5348342	3R_5348342_SNP [dm3] 3R_9522620_SNP [dm6]	A	G	4.261e^-5	0.866	SYNONYMOUS_CODING CG8176
3R	18155170	3R_18155170_SNP [dm3] 3R_22329448_SNP [dm6]	T	C	4.296e^-5	0.866	INTRON CG7080	TF binding site mE1_TFBS_cad
2R	11024935	2R_11024935_SNP [dm3] 2R_15137430_SNP [dm6]	G	C	4.373e^-5	0.866	INTRON chn	TF binding site mE1_TFBS_inv
3R	5321156	3R_5321156_SNP [dm3] 3R_9495434_SNP [dm6]	G	T	4.387e^-5	0.866	SYNONYMOUS_CODING CG8147	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	27226467	3R_27226467_SNP [dm3] 3R_31400745_SNP [dm6]	A	G	4.390e^-5	0.866	SYNONYMOUS_CODING Gcn2 DOWNSTREAM CG11337	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	551692	2L_551692_SNP [dm3] 2L_551692_SNP [dm6]	T	C	4.455e^-5	0.866	NON_SYNONYMOUS_CODING Ets21C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	19255810	3L_19255810_SNP [dm3] 3L_19262710_SNP [dm6]	T	C	4.484e^-5	0.866	UTR_3_PRIME Max DOWNSTREAM Bet1	TF binding site mE1_TFBS_cad
2L	371772	2L_371772_SNP [dm3] 2L_371772_SNP [dm6]	T	G	4.489e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	16551173	3L_16551173_SNP [dm3] 3L_16558073_SNP [dm6]	A	G	4.543e^-5	0.866	DOWNSTREAM CG4229 INTERGENIC
2L	5268825	2L_5268825_SNP [dm3] 2L_5268825_SNP [dm6]	G	A	4.570e^-5	0.866	SYNONYMOUS_CODING Cyp4ac3 DOWNSTREAM Cyp4ac2 INTRON tkv
3L	13206924	3L_13206924_SNP [dm3] 3L_13213824_SNP [dm6]	A	G	4.689e^-5	0.866	UPSTREAM tRNA:CR32127 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	1893110	2L_1893110_SNP [dm3] 2L_1893110_SNP [dm6]	C	T	4.748e^-5	0.866	INTRON CG7337
2L	7063939	2L_7063939_SNP [dm3] 2L_7063939_SNP [dm6]	G	A	4.755e^-5	0.866	UPSTREAM Sem1 DOWNSTREAM Nuf2 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA
3L	17835669	3L_17835669_SNP [dm3] 3L_17842569_SNP [dm6]	A	G	4.786e^-5	0.866	INTRON CG5567 EXON CR45175
3L	17835676	3L_17835676_SNP [dm3] 3L_17842576_SNP [dm6]	T	A	4.786e^-5	0.866	INTRON CG5567 EXON CR45175
3R	5332065	3R_5332065_SNP [dm3] 3R_9506343_SNP [dm6]	G	A	4.839e^-5	0.866	SYNONYMOUS_CODING rump UTR_3_PRIME rump DOWNSTREAM CG8149
3L	17874501	3L_17874501_SNP [dm3] 3L_17881401_SNP [dm6]	T	C	4.972e^-5	0.866	SYNONYMOUS_CODING CG7408
2R	4326241	2R_4326241_INS [dm3] 2R_8438736_INS [dm6]	A	AA	5.029e^-5	0.866	DOWNSTREAM Lcp4 & 1 other INTERGENIC
2L	5268777	2L_5268777_SNP [dm3] 2L_5268777_SNP [dm6]	A	C	5.082e^-5	0.866	DOWNSTREAM Cyp4ac2 INTRON tkv & 1 other
3R	5862858	3R_5862858_SNP [dm3] 3R_10037136_SNP [dm6]	A	T	5.082e^-5	0.866	INTRON Mical
2L	7411527	2L_7411527_SNP [dm3] 2L_7411527_SNP [dm6]	C	A	5.194e^-5	0.866	SYNONYMOUS_CODING CG15818 UPSTREAM chm	TF binding site BDTNP1_TFBS_dl
3L	17871483	3L_17871483_SNP [dm3] 3L_17878383_SNP [dm6]	C	A	5.198e^-5	0.866	UPSTREAM CG7408 INTERGENIC
2R	5131848	2R_5131848_SNP [dm3] 2R_9244343_SNP [dm6]	C	A	5.201e^-5	0.866	UTR_3_PRIME Cyp4p3 INTRON hig
2R	16053352	2R_16053352_SNP [dm3] 2R_20165847_SNP [dm6]	C	T	5.224e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5268843	2L_5268843_SNP [dm3] 2L_5268843_SNP [dm6]	T	A	5.275e^-5	0.866	NON_SYNONYMOUS_CODING Cyp4ac3 DOWNSTREAM Cyp4ac2 INTRON tkv
3L	13185081	3L_13185081_SNP [dm3] 3L_13191981_SNP [dm6]	T	C	5.322e^-5	0.866	INTERGENIC
3L	17835684	3L_17835684_SNP [dm3] 3L_17842584_SNP [dm6]	G	T	5.372e^-5	0.866	INTRON CG5567 EXON CR45175
3R	5399431	3R_5399431_SNP [dm3] 3R_9573709_SNP [dm6]	G	A	5.453e^-5	0.866	UPSTREAM CG9399 DOWNSTREAM Kap-alpha3 INTRON CG9399	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
X	5407285	X_5407285_SNP [dm3] X_5513252_SNP [dm6]	G	A	5.486e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

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Missing results

By genomic position
Variant impact
Gene name

Fecal_PH_PAeruginosa phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results