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=3.288e^-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

Covariate	p-value	Significance
In_3R_Mo	0.08418

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1861 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	11508784	3L_11508784_SNP [dm3] 3L_11515684_SNP [dm6]	C	A	9.554e^-8	0.179	INTRON CG7512
3L	11509003	3L_11509003_SNP [dm3] 3L_11515903_SNP [dm6]	A	C	3.796e^-7	0.299	INTRON CG7512
X	8927791	X_8927791_SNP [dm3] X_9033758_SNP [dm6]	A	G	5.798e^-7	0.299	INTRON CR43836 & 1 other
X	8927781	X_8927781_SNP [dm3] X_9033748_SNP [dm6]	T	A	1.180e^-6	0.299	INTRON CR43836 & 1 other
3L	11508520	3L_11508520_SNP [dm3] 3L_11515420_SNP [dm6]	T	C	1.284e^-6	0.299	INTRON CG7512
X	8927813	X_8927813_SNP [dm3] X_9033780_SNP [dm6]	A	C	1.298e^-6	0.299	INTRON CR43836 & 1 other
3L	11508979	3L_11508979_SNP [dm3] 3L_11515879_SNP [dm6]	G	A	1.309e^-6	0.299	INTRON CG7512
3L	11508999	3L_11508999_SNP [dm3] 3L_11515899_SNP [dm6]	C	G	1.338e^-6	0.299	INTRON CG7512
X	8927776	X_8927776_SNP [dm3] X_9033743_SNP [dm6]	G	T	1.436e^-6	0.299	INTRON CR43836 & 1 other
2L	307423	2L_307423_SNP [dm3] 2L_307423_SNP [dm6]	A	G	1.764e^-6	0.311	INTRON Plc21C	TF binding site mE1_TFBS_Trl
2R	13843155	2R_13843155_SNP [dm3] 2R_17955650_SNP [dm6]	C	T	1.826e^-6	0.311	NON_SYNONYMOUS_CODING PpY-55A DOWNSTREAM CR44418
X	12653734	X_12653734_SNP [dm3] X_12759701_SNP [dm6]	T	A	2.195e^-6	0.343	DOWNSTREAM CG12717 INTRON ade5	TF binding site mE1_TFBS_inv
X	8927745	X_8927745_DEL [dm3] X_9033712_DEL [dm6]	TTTTTCC	T	2.712e^-6	0.365	INTRON CR43836 & 1 other
2R	16931871	2R_16931871_SNP [dm3] 2R_21044366_SNP [dm6]	T	C	2.817e^-6	0.365	INTERGENIC
2R	5217280	2R_5217280_SNP [dm3] 2R_9329775_SNP [dm6]	T	C	3.280e^-6	0.365	INTRON CG13954 & 1 other
X	8927741	X_8927741_DEL [dm3] X_9033708_DEL [dm6]	CCA	C	3.368e^-6	0.365	INTRON CR43836 & 1 other
3L	12852441	3L_12852441_SNP [dm3] 3L_12859341_SNP [dm6]	C	T	3.373e^-6	0.365	NON_SYNONYMOUS_CODING CG32107
X	8927823	X_8927823_SNP [dm3] X_9033790_SNP [dm6]	G	T	3.574e^-6	0.365	INTRON CR43836 & 1 other
2L	12064109	2L_12064109_SNP [dm3] 2L_12064109_SNP [dm6]	G	T	3.752e^-6	0.365	SYNONYMOUS_CODING CG14946 UPSTREAM Rab3-GAP	TF binding site mE1_TFBS_sens
3L	5231686	3L_5231686_DEL [dm3] 3L_5238586_DEL [dm6]	GCC	G	4.094e^-6	0.365	INTRON shep
3L	5231689	3L_5231689_DEL [dm3] 3L_5238589_DEL [dm6]	GTAAAAATGCGA...	G	4.094e^-6	0.365	INTRON shep
2L	284303	2L_284303_SNP [dm3] 2L_284303_SNP [dm6]	T	C	4.476e^-6	0.381	INTRON CG3625	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5231642	3L_5231642_DEL [dm3] 3L_5238542_DEL [dm6]	TGGCG	T	5.552e^-6	0.427	INTRON shep
3L	5231662	3L_5231662_SNP [dm3] 3L_5238562_SNP [dm6]	T	C	5.552e^-6	0.427	INTRON shep
X	8927778	X_8927778_SNP [dm3] X_9033745_SNP [dm6]	C	A	5.805e^-6	0.427	INTRON CR43836 & 1 other
X	8931352	X_8931352_SNP [dm3] X_9037319_SNP [dm6]	T	C	5.920e^-6	0.427	INTRON CR43836 & 1 other
2R	9075508	2R_9075508_SNP [dm3] 2R_13188003_SNP [dm6]	A	G	6.409e^-6	0.437	INTRON seq & 2 others	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	5231661	3L_5231661_SNP [dm3] 3L_5238561_SNP [dm6]	C	T	6.891e^-6	0.437	INTRON shep
3L	10632868	3L_10632868_SNP [dm3] 3L_10639768_SNP [dm6]	C	T	7.059e^-6	0.437	UTR_5_PRIME CG18628 DOWNSTREAM CG32066 & 1 other
2R	16989542	2R_16989542_SNP [dm3] 2R_21102037_SNP [dm6]	A	G	7.220e^-6	0.437	UTR_5_PRIME ktub DOWNSTREAM CG34396	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	5231649	3L_5231649_SNP [dm3] 3L_5238549_SNP [dm6]	C	A	7.233e^-6	0.437	INTRON shep
2L	20790060	2L_20790060_SNP [dm3] 2L_20790060_SNP [dm6]	G	T	7.592e^-6	0.441	SPLICE_SITE_REGION vari DOWNSTREAM Pomp INTRON vari	TF binding site mE1_TFBS_sens
3R	14453825	3R_14453825_SNP [dm3] 3R_18628103_SNP [dm6]	A	C	7.796e^-6	0.441	DOWNSTREAM tRNA:CR31228 INTRON qin	TF binding site BDTNP1_TFBS_twi
X	8927814	X_8927814_SNP [dm3] X_9033781_SNP [dm6]	A	T	8.024e^-6	0.441	INTRON CR43836 & 1 other
X	8927786	X_8927786_SNP [dm3] X_9033753_SNP [dm6]	A	G	8.347e^-6	0.441	INTRON CR43836 & 1 other
2L	13844347	2L_13844347_SNP [dm3] 2L_13844347_SNP [dm6]	T	A	8.470e^-6	0.441	UTR_3_PRIME CG8997 UPSTREAM CG33306 DOWNSTREAM CG8997 INTRON CenG1A	TF binding site mE1_TFBS_cad
3L	5231602	3L_5231602_DEL [dm3] 3L_5238502_DEL [dm6]	GGACTCAATACAATCCTGTA...	G	8.790e^-6	0.444	INTRON shep
2R	16686787	2R_16686787_SNP [dm3] 2R_20799282_SNP [dm6]	C	T	9.006e^-6	0.444	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16987601	2R_16987601_SNP [dm3] 2R_21100096_SNP [dm6]	C	T	9.608e^-6	0.462	INTRON CG34396	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	16985709	2R_16985709_SNP [dm3] 2R_21098204_SNP [dm6]	C	A	1.265e^-5	0.591	SYNONYMOUS_CODING CG34396 UPSTREAM CG4038 INTRON CG34396	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5228425	2R_5228425_SNP [dm3] 2R_9340920_SNP [dm6]	A	G	1.328e^-5	0.591	INTRON CG13954 & 1 other
2R	6735422	2R_6735422_SNP [dm3] 2R_10847917_SNP [dm6]	T	C	1.345e^-5	0.591	INTRON CG30015
3L	13058142	3L_13058142_SNP [dm3] 3L_13065042_SNP [dm6]	C	A	1.391e^-5	0.591	INTERGENIC
3L	6052400	3L_6052400_SNP [dm3] 3L_6059300_SNP [dm6]	T	G	1.397e^-5	0.591	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
3L	5231716	3L_5231716_SNP [dm3] 3L_5238616_SNP [dm6]	G	T	1.450e^-5	0.591	INTRON shep
2R	16987557	2R_16987557_SNP [dm3] 2R_21100052_SNP [dm6]	G	A	1.451e^-5	0.591	SYNONYMOUS_CODING CG34396 INTRON CG34396	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
X	8927826	X_8927826_SNP [dm3] X_9033793_SNP [dm6]	G	A	1.496e^-5	0.594	INTRON CR43836 & 1 other
2L	5773907	2L_5773907_DEL [dm3] 2L_5773907_DEL [dm6]	AAT	C	1.522e^-5	0.594	UPSTREAM CG9171 INTRON CG9171	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3L	10632892	3L_10632892_SNP [dm3] 3L_10639792_SNP [dm6]	C	T	1.616e^-5	0.618	UTR_5_PRIME CG18628 DOWNSTREAM CG32066 & 1 other
2L	13641318	2L_13641318_SNP [dm3] 2L_13641318_SNP [dm6]	A	G	1.817e^-5	0.681	UPSTREAM ics INTRON ics	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12470353	2R_12470353_SNP [dm3] 2R_16582848_SNP [dm6]	T	G	1.875e^-5	0.686	INTRON Cdk4 EXON CR44375	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	12852638	3L_12852638_SNP [dm3] 3L_12859538_SNP [dm6]	T	G	1.905e^-5	0.686	NON_SYNONYMOUS_CODING CG32107
2L	333077	2L_333077_SNP [dm3] 2L_333077_SNP [dm6]	A	C	1.980e^-5	0.687	UPSTREAM CG31921 INTRON Plc21C	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	13844768	2R_13844768_SNP [dm3] 2R_17957263_SNP [dm6]	G	A	1.980e^-5	0.687	UPSTREAM PpY-55A INTERGENIC
3L	10835024	3L_10835024_SNP [dm3] 3L_10841924_SNP [dm6]	T	C	2.025e^-5	0.69	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	4905095	3R_4905095_SNP [dm3] 3R_9079373_SNP [dm6]	C	A	2.164e^-5	0.702	INTRON pum
3L	12852622	3L_12852622_SNP [dm3] 3L_12859522_SNP [dm6]	T	A	2.220e^-5	0.702	SYNONYMOUS_CODING CG32107
3L	2626348	3L_2626348_SNP [dm3] 3L_2626348_SNP [dm6]	A	T	2.224e^-5	0.702	INTRON Pxn
3L	11509025	3L_11509025_SNP [dm3] 3L_11515925_SNP [dm6]	T	C	2.275e^-5	0.702	INTRON CG7512
2R	15434782	2R_15434782_SNP [dm3] 2R_19547277_SNP [dm6]	C	A	2.277e^-5	0.702	UPSTREAM sm INTRON sm
3L	11509052	3L_11509052_SNP [dm3] 3L_11515952_SNP [dm6]	A	T	2.328e^-5	0.702	INTRON CG7512
2L	13821812	2L_13821812_SNP [dm3] 2L_13821812_SNP [dm6]	G	C	2.337e^-5	0.702	NON_SYNONYMOUS_CODING b	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3393589	2L_3393589_SNP [dm3] 2L_3393589_SNP [dm6]	G	A	2.379e^-5	0.702	INTERGENIC
2R	5228436	2R_5228436_SNP [dm3] 2R_9340931_SNP [dm6]	C	T	2.396e^-5	0.702	INTRON CG13954 & 1 other
X	6541215	X_6541215_SNP [dm3] X_6647182_SNP [dm6]	G	A	2.475e^-5	0.706	INTRON pigs	TF binding site mE1_TFBS_chinmo
2L	14014158	2L_14014158_SNP [dm3] 2L_14014158_SNP [dm6]	A	G	2.486e^-5	0.706	INTRON bgm	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2R	5901558	2R_5901558_SNP [dm3] 2R_10014053_SNP [dm6]	A	T	2.576e^-5	0.721	INTRON Pka-R2
X	6806993	X_6806993_SNP [dm3] X_6912960_SNP [dm6]	T	C	2.618e^-5	0.722	INTRON CG14431
X	15173297	X_15173297_SNP [dm3] X_15279264_SNP [dm6]	G	T	2.711e^-5	0.736	INTERGENIC
2L	3720935	2L_3720935_SNP [dm3] 2L_3720935_SNP [dm6]	G	A	2.813e^-5	0.753	UPSTREAM Shaw INTRON Shaw
2L	19856691	2L_19856691_SNP [dm3] 2L_19856691_SNP [dm6]	G	A	2.958e^-5	0.769	INTRON sick
3L	10893565	3L_10893565_DEL [dm3] 3L_10900465_DEL [dm6]	GG	G	3.029e^-5	0.769	INTERGENIC
2R	13840994	2R_13840994_SNP [dm3] 2R_17953489_SNP [dm6]	G	A	3.040e^-5	0.769	INTERGENIC
3L	12852427	3L_12852427_SNP [dm3] 3L_12859327_SNP [dm6]	T	G	3.079e^-5	0.769	NON_SYNONYMOUS_CODING CG32107
2L	1856218	2L_1856218_SNP [dm3] 2L_1856218_SNP [dm6]	A	G	3.093e^-5	0.769	INTRON wry
3L	6052492	3L_6052492_SNP [dm3] 3L_6059392_SNP [dm6]	T	G	3.147e^-5	0.769	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
3L	6052716	3L_6052716_SNP [dm3] 3L_6059616_SNP [dm6]	T	A	3.180e^-5	0.769	UPSTREAM CG6592 DOWNSTREAM CR45441 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv mE1_TFBS_run
2L	7929503	2L_7929503_SNP [dm3] 2L_7929503_SNP [dm6]	A	T	3.200e^-5	0.769	INTRON Snoo
3R	14453686	3R_14453686_SNP [dm3] 3R_18627964_SNP [dm6]	A	T	3.318e^-5	0.779	DOWNSTREAM tRNA:CR31228 INTRON qin
2L	13844337	2L_13844337_SNP [dm3] 2L_13844337_SNP [dm6]	C	T	3.325e^-5	0.779	UTR_3_PRIME CG8997 UPSTREAM CG33306 DOWNSTREAM CG8997 INTRON CenG1A	TF binding site mE1_TFBS_cad
2R	16985281	2R_16985281_SNP [dm3] 2R_21097776_SNP [dm6]	G	A	3.522e^-5	0.815	UTR_5_PRIME CG34396 UPSTREAM CG4038 INTRON CG34396	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	6806997	X_6806997_SNP [dm3] X_6912964_SNP [dm6]	C	G	3.694e^-5	0.84	INTRON CG14431
X	12654109	X_12654109_SNP [dm3] X_12760076_SNP [dm6]	C	A	3.738e^-5	0.84	DOWNSTREAM CG12717 INTRON ade5	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
2L	5773918	2L_5773918_SNP [dm3] 2L_5773918_SNP [dm6]	C	T	3.766e^-5	0.84	UPSTREAM CG9171 INTRON CG9171	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	6540246	X_6540246_SNP [dm3] X_6646213_SNP [dm6]	A	G	3.840e^-5	0.845	INTRON pigs	TF binding site mE1_TFBS_chinmo
2R	5900874	2R_5900874_SNP [dm3] 2R_10013369_SNP [dm6]	T	G	3.897e^-5	0.845	INTRON Pka-R2
2R	6735556	2R_6735556_SNP [dm3] 2R_10848051_SNP [dm6]	A	T	3.921e^-5	0.845	INTRON CG30015
X	5250117	X_5250117_SNP [dm3] X_5356084_SNP [dm6]	T	C	3.988e^-5	0.847	INTRON SK
3L	11508941	3L_11508941_SNP [dm3] 3L_11515841_SNP [dm6]	G	A	4.054e^-5	0.847	INTRON CG7512
2R	17501493	2R_17501493_SNP [dm3] 2R_21613988_SNP [dm6]	T	G	4.141e^-5	0.847	UTR_3_PRIME CG18870 UPSTREAM CG15673 DOWNSTREAM CG18870
2L	13641515	2L_13641515_SNP [dm3] 2L_13641515_SNP [dm6]	T	C	4.232e^-5	0.847	UPSTREAM ics INTRON ics	TF binding site BDTNP1_TFBS_dl
2L	12263756	2L_12263756_SNP [dm3] 2L_12263756_SNP [dm6]	A	G	4.256e^-5	0.847	INTRON aret
3L	6052459	3L_6052459_SNP [dm3] 3L_6059359_SNP [dm6]	T	C	4.284e^-5	0.847	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
2L	8071926	2L_8071926_SNP [dm3] 2L_8071926_SNP [dm6]	T	A	4.289e^-5	0.847	UTR_3_PRIME MED20 UPSTREAM poe & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	11383656	3L_11383656_SNP [dm3] 3L_11390556_SNP [dm6]	T	A	4.293e^-5	0.847	INTERGENIC
3L	5231658	3L_5231658_SNP [dm3] 3L_5238558_SNP [dm6]	T	A	4.460e^-5	0.864	INTRON shep
2R	6672439	2R_6672439_INS [dm3] 2R_10784934_INS [dm6]	A	AACATTCG	4.470e^-5	0.864	DOWNSTREAM CR44300 INTRON CG33144 EXON CR44299
3R	6562159	3R_6562159_SNP [dm3] 3R_10736437_SNP [dm6]	G	T	4.667e^-5	0.889	UPSTREAM tomboy20 INTERGENIC
X	6807221	X_6807221_INS [dm3] X_6913188_INS [dm6]	C	CTACCATACACACAC...	4.751e^-5	0.889	INTRON CG14431
2L	1523356	2L_1523356_SNP [dm3] 2L_1523356_SNP [dm6]	C	A	4.767e^-5	0.889	SYNONYMOUS_CODING Or22b

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By genomic position
Variant impact
Gene name

mn_Glycerol_Pooled phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results