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=1.168e^-2)
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
wolba	0.02309

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.9953	0.0835

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1655 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	13328028	2L_13328028_DEL [dm3] 2L_13328028_DEL [dm6]	GCTATG	A	1.978e^-6	0.964	INTRON CG43778
3R	14449216	3R_14449216_SNP [dm3] 3R_18623494_SNP [dm6]	G	A	3.452e^-6	0.964	INTRON qin	TF binding site mE1_TFBS_inv
2R	18022014	2R_18022014_SNP [dm3] 2R_22134509_SNP [dm6]	G	A	4.791e^-6	0.964	INTERGENIC
2R	18022102	2R_18022102_SNP [dm3] 2R_22134597_SNP [dm6]	G	A	5.474e^-6	0.964	INTERGENIC
2L	1902004	2L_1902004_SNP [dm3] 2L_1902004_SNP [dm6]	A	G	5.971e^-6	0.964	INTRON CG7337
2L	2965147	2L_2965147_SNP [dm3] 2L_2965147_SNP [dm6]	A	G	6.237e^-6	0.964	UTR_3_PRIME Rbp9 DOWNSTREAM Rbp9
2R	15420871	2R_15420871_SNP [dm3] 2R_19533366_SNP [dm6]	T	A	7.057e^-6	0.964	INTRON sm
3R	5121457	3R_5121457_SNP [dm3] 3R_9295735_SNP [dm6]	A	G	7.171e^-6	0.964	SYNONYMOUS_CODING CG8861
3R	22563163	3R_22563163_SNP [dm3] 3R_26737441_SNP [dm6]	T	C	8.185e^-6	0.964	UPSTREAM CG14247 INTERGENIC
3L	13112945	3L_13112945_SNP [dm3] 3L_13119845_SNP [dm6]	A	T	8.334e^-6	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
2R	20107921	2R_20107921_SNP [dm3] 2R_24220398_SNP [dm6]	C	T	8.959e^-6	0.964	INTRON CG30419
2L	13286109	2L_13286109_SNP [dm3] 2L_13286109_SNP [dm6]	C	T	1.182e^-5	0.964	UPSTREAM Uvrag INTRON Drep-4 EXON CR44083	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	13215115	3L_13215115_SNP [dm3] 3L_13222015_SNP [dm6]	G	A	1.235e^-5	0.964	INTERGENIC
2L	13711478	2L_13711478_SNP [dm3] 2L_13711478_SNP [dm6]	T	A	1.334e^-5	0.964	DOWNSTREAM CG7311 INTRON CG31814
2L	7684261	2L_7684261_SNP [dm3] 2L_7684261_SNP [dm6]	A	G	1.582e^-5	0.964	UTR_3_PRIME Myo28B1 DOWNSTREAM CR44148 INTRON Myo28B1
2R	13801109	2R_13801109_SNP [dm3] 2R_17913604_SNP [dm6]	T	C	1.652e^-5	0.964	INTRON Elk
3L	13215116	3L_13215116_SNP [dm3] 3L_13222016_SNP [dm6]	C	T	1.863e^-5	0.964	INTERGENIC
3L	13210612	3L_13210612_SNP [dm3] 3L_13217512_SNP [dm6]	C	G	1.898e^-5	0.964	DOWNSTREAM CR45098 EXON CR43914
2R	18962403	2R_18962403_SNP [dm3] 2R_23074880_SNP [dm6]	T	C	1.966e^-5	0.964	UTR_5_PRIME CG3085 UPSTREAM snoRNA:229 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	15105633	X_15105633_SNP [dm3] X_15211600_SNP [dm6]	A	G	1.998e^-5	0.964	DOWNSTREAM CG5662 INTERGENIC
2L	11577871	2L_11577871_SNP [dm3] 2L_11577871_SNP [dm6]	T	A	2.056e^-5	0.964	INTERGENIC
2R	15673400	2R_15673400_SNP [dm3] 2R_19785895_SNP [dm6]	G	T	2.107e^-5	0.964	EXON CR45231	regulatory region REDfly_CRMs
3L	1848737	3L_1848737_SNP [dm3] 3L_1848737_SNP [dm6]	T	C	2.477e^-5	0.964	INTERGENIC
3L	13215111	3L_13215111_SNP [dm3] 3L_13222011_SNP [dm6]	C	T	2.490e^-5	0.964	INTERGENIC
X	15614937	X_15614937_SNP [dm3] X_15720904_SNP [dm6]	G	A	2.541e^-5	0.964	SYNONYMOUS_CODING CG8184	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2R	18021778	2R_18021778_SNP [dm3] 2R_22134273_SNP [dm6]	A	G	2.599e^-5	0.964	INTERGENIC
2R	18021821	2R_18021821_SNP [dm3] 2R_22134316_SNP [dm6]	C	T	2.599e^-5	0.964	INTERGENIC
2R	18021822	2R_18021822_SNP [dm3] 2R_22134317_SNP [dm6]	A	G	2.599e^-5	0.964	INTERGENIC
3L	1848757	3L_1848757_SNP [dm3] 3L_1848757_SNP [dm6]	G	A	2.659e^-5	0.964	INTERGENIC
3L	12094551	3L_12094551_SNP [dm3] 3L_12101451_SNP [dm6]	A	T	2.773e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2R	18022040	2R_18022040_SNP [dm3] 2R_22134535_SNP [dm6]	G	C	2.846e^-5	0.964	INTERGENIC
2L	13963497	2L_13963497_SNP [dm3] 2L_13963497_SNP [dm6]	A	G	2.860e^-5	0.964	UPSTREAM NimB1 DOWNSTREAM NimA INTERGENIC
2L	14005649	2L_14005649_SNP [dm3] 2L_14005649_SNP [dm6]	T	C	2.877e^-5	0.964	INTERGENIC
2L	13976987	2L_13976987_SNP [dm3] 2L_13976987_SNP [dm6]	G	A	2.984e^-5	0.964	UPSTREAM NimC1 & 1 other INTERGENIC
2R	11676477	2R_11676477_SNP [dm3] 2R_15788972_SNP [dm6]	T	G	3.080e^-5	0.964	INTRON Zasp52
3R	25367062	3R_25367062_DEL [dm3] 3R_29541340_DEL [dm6]	CTCGAGTGC	C	3.176e^-5	0.964	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
3R	21288219	3R_21288219_SNP [dm3] 3R_25462497_SNP [dm6]	C	A	3.199e^-5	0.964	INTRON Fur1
X	2709528	X_2709528_SNP [dm3] X_2815495_SNP [dm6]	A	C	3.435e^-5	0.964	INTRON kirre
2R	18021840	2R_18021840_DEL [dm3] 2R_22134335_DEL [dm6]	TC	T	3.672e^-5	0.964	INTERGENIC
2R	20446945	2R_20446945_SNP [dm3] 2R_24559422_SNP [dm6]	G	A	3.720e^-5	0.964	UTR_3_PRIME Nurf-38 DOWNSTREAM ITP INTRON Nurf-38
3R	22750306	3R_22750306_SNP [dm3] 3R_26924584_SNP [dm6]	A	G	3.932e^-5	0.964	INTRON sda
X	15105613	X_15105613_SNP [dm3] X_15211580_SNP [dm6]	A	C	4.038e^-5	0.964	DOWNSTREAM CG5662 INTERGENIC
X	15105638	X_15105638_SNP [dm3] X_15211605_SNP [dm6]	G	A	4.038e^-5	0.964	DOWNSTREAM CG5662 INTERGENIC
2R	119721	2R_119721_SNP [dm3] 2R_4232216_SNP [dm6]	G	C	4.098e^-5	0.964	INTERGENIC
2R	18962374	2R_18962374_SNP [dm3] 2R_23074851_SNP [dm6]	T	C	4.112e^-5	0.964	UTR_5_PRIME CG3085 UPSTREAM snoRNA:229 & 2 others	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6954714	3L_6954714_SNP [dm3] 3L_6961614_SNP [dm6]	T	A	4.159e^-5	0.964	INTRON sgl
2L	2966823	2L_2966823_SNP [dm3] 2L_2966823_SNP [dm6]	T	A	4.269e^-5	0.964	UTR_3_PRIME Rbp9
2L	13284730	2L_13284730_SNP [dm3] 2L_13284730_SNP [dm6]	G	T	4.423e^-5	0.964	SYNONYMOUS_CODING Drep-4 UPSTREAM CR44083 DOWNSTREAM CG44085	TF binding site mE1_TFBS_cad
3R	13902722	3R_13902722_SNP [dm3] 3R_18077000_SNP [dm6]	G	A	4.503e^-5	0.964	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	20113973	2R_20113973_SNP [dm3] 2R_24226450_SNP [dm6]	T	C	4.508e^-5	0.964	INTRON CG30419
X	19037553	X_19037553_SNP [dm3] X_19143520_SNP [dm6]	A	C	4.705e^-5	0.964	UTR_3_PRIME RhoGAP18B
2L	14003529	2L_14003529_SNP [dm3] 2L_14003529_SNP [dm6]	A	G	4.783e^-5	0.964	INTERGENIC
3R	13902749	3R_13902749_SNP [dm3] 3R_18077027_SNP [dm6]	G	A	4.804e^-5	0.964	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	10241780	3L_10241780_SNP [dm3] 3L_10248680_SNP [dm6]	A	T	4.848e^-5	0.964	UPSTREAM CR44540 DOWNSTREAM CR44539 INTERGENIC
2R	18021838	2R_18021838_SNP [dm3] 2R_22134333_SNP [dm6]	C	T	4.865e^-5	0.964	INTERGENIC
3L	12094572	3L_12094572_SNP [dm3] 3L_12101472_SNP [dm6]	C	T	4.893e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3L	6752674	3L_6752674_SNP [dm3] 3L_6759574_SNP [dm6]	T	A	4.975e^-5	0.964	INTRON CG32392
2L	15635067	2L_15635067_SNP [dm3] 2L_15635067_SNP [dm6]	A	G	5.023e^-5	0.964	DOWNSTREAM CG18480 INTERGENIC
3L	15613828	3L_15613828_SNP [dm3] 3L_15620728_SNP [dm6]	T	C	5.039e^-5	0.964	SYNONYMOUS_CODING CG7372 INTRON comm3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_sens mE1_TFBS_Trl
3L	1853270	3L_1853270_SNP [dm3] 3L_1853270_SNP [dm6]	C	T	5.084e^-5	0.964	INTRON CG13936
3L	9791400	3L_9791400_SNP [dm3] 3L_9798300_SNP [dm6]	T	G	5.089e^-5	0.964	UPSTREAM Ilp1 & 2 others INTERGENIC
3L	1867336	3L_1867336_SNP [dm3] 3L_1867336_SNP [dm6]	T	C	5.092e^-5	0.964	SYNONYMOUS_CODING CG12025	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13711370	2L_13711370_SNP [dm3] 2L_13711370_SNP [dm6]	T	A	5.103e^-5	0.964	DOWNSTREAM CG7311 INTRON CG31814
X	15105628	X_15105628_SNP [dm3] X_15211595_SNP [dm6]	C	T	5.122e^-5	0.964	DOWNSTREAM CG5662 INTERGENIC
3L	7131490	3L_7131490_SNP [dm3] 3L_7138390_SNP [dm6]	C	A	5.218e^-5	0.964	UTR_5_PRIME melt INTRON melt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	7684286	2L_7684286_SNP [dm3] 2L_7684286_SNP [dm6]	G	A	5.242e^-5	0.964	UTR_3_PRIME Myo28B1 DOWNSTREAM CR44148 INTRON Myo28B1
2R	3080452	2R_3080452_SNP [dm3] 2R_7192947_SNP [dm6]	G	A	5.498e^-5	0.964	UTR_5_PRIME pk INTRON pk	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	12343326	3R_12343326_SNP [dm3] 3R_16517604_SNP [dm6]	G	A	5.629e^-5	0.964	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13999527	2L_13999527_SNP [dm3] 2L_13999527_SNP [dm6]	G	A	5.963e^-5	0.964	INTRON rk
2R	16240342	2R_16240342_SNP [dm3] 2R_20352837_SNP [dm6]	A	G	6.147e^-5	0.964	INTERGENIC
X	18401883	X_18401883_SNP [dm3] X_18507850_SNP [dm6]	G	T	6.448e^-5	0.964	SYNONYMOUS_CODING Ggt-1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	5358964	X_5358964_SNP [dm3] X_5464931_SNP [dm6]	A	C	6.460e^-5	0.964	UTR_5_PRIME SPR INTRON SPR
3L	1865490	3L_1865490_DEL [dm3] 3L_1865490_DEL [dm6]	TT	T	6.519e^-5	0.964	UTR_5_PRIME CG12025 UPSTREAM HBS1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2R	18962442	2R_18962442_DEL [dm3] 2R_23074919_DEL [dm6]	TTTT	T	6.562e^-5	0.964	UPSTREAM snoRNA:229 & 2 others INTRON CG3085	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19698647	3L_19698647_SNP [dm3] 3L_19705547_SNP [dm6]	T	G	6.608e^-5	0.964	INTRON serp
2L	10575763	2L_10575763_SNP [dm3] 2L_10575763_SNP [dm6]	T	C	6.830e^-5	0.964	DOWNSTREAM w-cup INTRON Trim9
3L	1391434	3L_1391434_SNP [dm3] 3L_1391434_SNP [dm6]	T	G	6.890e^-5	0.964	INTRON Ptp61F	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15705258	3L_15705258_SNP [dm3] 3L_15712158_SNP [dm6]	A	G	7.053e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Stat92E
2R	20443466	2R_20443466_SNP [dm3] 2R_24555943_SNP [dm6]	C	T	7.070e^-5	0.964	SPLICE_SITE_REGION CG4622 UTR_5_PRIME CG4622 INTRON ITP
2L	9150191	2L_9150191_SNP [dm3] 2L_9150191_SNP [dm6]	G	C	7.106e^-5	0.964	INTRON CG32982	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_eve mE1_TFBS_HSA
X	15105650	X_15105650_DEL [dm3] X_15211617_DEL [dm6]	AA	T	7.195e^-5	0.964	DOWNSTREAM CG5662 INTERGENIC
3L	16166122	3L_16166122_SNP [dm3] 3L_16173022_SNP [dm6]	G	T	7.212e^-5	0.964	INTERGENIC
3R	13961636	3R_13961636_SNP [dm3] 3R_18135914_SNP [dm6]	A	G	7.272e^-5	0.964	DOWNSTREAM sr INTERGENIC
3R	21626974	3R_21626974_SNP [dm3] 3R_25801252_SNP [dm6]	A	G	7.300e^-5	0.964	INTERGENIC
3L	13312273	3L_13312273_SNP [dm3] 3L_13319173_SNP [dm6]	A	G	7.356e^-5	0.964	INTERGENIC
3L	13312295	3L_13312295_SNP [dm3] 3L_13319195_SNP [dm6]	T	A	7.356e^-5	0.964	INTERGENIC
2R	13801541	2R_13801541_SNP [dm3] 2R_17914036_SNP [dm6]	G	A	7.378e^-5	0.964	INTRON Elk
2L	13999491	2L_13999491_SNP [dm3] 2L_13999491_SNP [dm6]	C	A	7.445e^-5	0.964	INTRON rk
X	16018845	X_16018845_SNP [dm3] X_16124812_SNP [dm6]	T	G	7.504e^-5	0.964	UPSTREAM disco-r INTRON disco-r
2R	19575351	2R_19575351_SNP [dm3] 2R_23687828_SNP [dm6]	T	G	7.671e^-5	0.964	UTR_3_PRIME St3 UPSTREAM Pal2	TF binding site mE1_TFBS_cad
3L	2187166	3L_2187166_SNP [dm3] 3L_2187166_SNP [dm6]	A	G	7.858e^-5	0.964	SYNONYMOUS_CODING CG13810	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8183480	3L_8183480_INS [dm3] 3L_8190380_INS [dm6]	G	GACGGCG	7.982e^-5	0.964	UTR_3_PRIME Atg18a UPSTREAM MED24	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	1568423	X_1568423_SNP [dm3] X_1674390_SNP [dm6]	G	A	8.021e^-5	0.964	UTR_3_PRIME CG32809 DOWNSTREAM hfw & 1 other
3R	12343306	3R_12343306_SNP [dm3] 3R_16517584_SNP [dm6]	T	C	8.121e^-5	0.964	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14327915	3L_14327915_SNP [dm3] 3L_14334815_SNP [dm6]	A	G	8.158e^-5	0.964	INTRON fz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	3140959	2R_3140959_SNP [dm3] 2R_7253454_SNP [dm6]	G	C	8.196e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	3140972	2R_3140972_SNP [dm3] 2R_7253467_SNP [dm6]	A	T	8.196e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	3140994	2R_3140994_SNP [dm3] 2R_7253489_SNP [dm6]	G	A	8.196e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	3141009	2R_3141009_SNP [dm3] 2R_7253504_SNP [dm6]	A	T	8.196e^-5	0.964	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	16954241	X_16954241_SNP [dm3] X_17060208_SNP [dm6]	T	C	8.251e^-5	0.964	INTRON CG45002

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Missing results

By genomic position
Variant impact
Gene name

pc_FPKP_PElem_HS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results