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=8.126e^-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_2L_t	0.0986

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

986 significant hits at p-value < 0.001.

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
2R	13270958	2R_13270958_SNP [dm3] 2R_17383453_SNP [dm6]	A	G	3.628e^-7	0.242	INTERGENIC
2R	13270898	2R_13270898_SNP [dm3] 2R_17383393_SNP [dm6]	A	G	4.000e^-7	0.242	INTERGENIC
2R	13270943	2R_13270943_SNP [dm3] 2R_17383438_SNP [dm6]	T	C	4.000e^-7	0.242	INTERGENIC
2R	13270922	2R_13270922_SNP [dm3] 2R_17383417_SNP [dm6]	G	A	1.093e^-6	0.496	INTERGENIC
X	19733556	X_19733556_SNP [dm3] X_19839523_SNP [dm6]	A	C	5.942e^-6	0.981	INTRON pico
X	19733579	X_19733579_DEL [dm3] X_19839546_DEL [dm6]	ATTGTG	TCC	5.942e^-6	0.981	INTRON pico
X	19733587	X_19733587_DEL [dm3] X_19839554_DEL [dm6]	TTGGA	T	5.942e^-6	0.981	INTRON pico
X	19733667	X_19733667_SNP [dm3] X_19839634_SNP [dm6]	T	A	5.942e^-6	0.981	INTRON pico
X	19733682	X_19733682_INS [dm3] X_19839649_INS [dm6]	AA	TCATT	5.942e^-6	0.981	INTRON pico
X	19733687	X_19733687_SNP [dm3] X_19839654_SNP [dm6]	A	T	5.942e^-6	0.981	INTRON pico
X	19733690	X_19733690_INS [dm3] X_19839657_INS [dm6]	A	ATTA	5.942e^-6	0.981	INTRON pico
3L	4160835	3L_4160835_SNP [dm3] 3L_4160835_SNP [dm6]	A	T	8.483e^-6	1	UTR_5_PRIME nab DOWNSTREAM mas	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
2R	14089065	2R_14089065_SNP [dm3] 2R_18201560_SNP [dm6]	G	A	8.632e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14089075	2R_14089075_SNP [dm3] 2R_18201570_SNP [dm6]	T	A	8.632e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9312830	2L_9312830_SNP [dm3] 2L_9312830_SNP [dm6]	G	A	1.187e^-5	1	INTERGENIC
3L	4160837	3L_4160837_SNP [dm3] 3L_4160837_SNP [dm6]	A	T	1.575e^-5	1	UTR_5_PRIME nab DOWNSTREAM mas	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
X	19733666	X_19733666_SNP [dm3] X_19839633_SNP [dm6]	A	T	1.650e^-5	1	INTRON pico
2R	14089068	2R_14089068_SNP [dm3] 2R_18201563_SNP [dm6]	A	G	1.708e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19733502	X_19733502_INS [dm3] X_19839469_INS [dm6]	G	GAT	1.841e^-5	1	INTRON pico
X	19733517	X_19733517_SNP [dm3] X_19839484_SNP [dm6]	T	C	1.841e^-5	1	INTRON pico
X	19733516	X_19733516_SNP [dm3] X_19839483_SNP [dm6]	G	A	2.403e^-5	1	INTRON pico
X	19311636	X_19311636_DEL [dm3] X_19417603_DEL [dm6]	TT	T	2.794e^-5	1	INTRON kek5
2L	13294440	2L_13294440_SNP [dm3] 2L_13294440_SNP [dm6]	A	G	2.877e^-5	1	INTRON CG31729	TF binding site BDTNP1_TFBS_twi
3L	3911987	3L_3911987_SNP [dm3] 3L_3911987_SNP [dm6]	A	T	3.362e^-5	1	INTRON Eip63F-1
3L	3911986	3L_3911986_SNP [dm3] 3L_3911986_SNP [dm6]	A	T	3.469e^-5	1	INTRON Eip63F-1
3L	13705299	3L_13705299_SNP [dm3] 3L_13712199_SNP [dm6]	C	T	3.592e^-5	1	INTRON bru-3
2R	12356352	2R_12356352_SNP [dm3] 2R_16468847_SNP [dm6]	C	T	3.716e^-5	1	SYNONYMOUS_CODING CheB53b
3R	22458144	3R_22458144_SNP [dm3] 3R_26632422_SNP [dm6]	A	T	3.865e^-5	1	SYNONYMOUS_CODING TwdlN	TF binding site mE1_TFBS_HSA
3R	17238771	3R_17238771_SNP [dm3] 3R_21413049_SNP [dm6]	G	T	3.979e^-5	1	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7631661	2L_7631661_SNP [dm3] 2L_7631661_SNP [dm6]	T	C	4.064e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_hb
3R	20464852	3R_20464852_SNP [dm3] 3R_24639130_SNP [dm6]	A	C	4.348e^-5	1	INTRON puf
2L	1433301	2L_1433301_SNP [dm3] 2L_1433301_SNP [dm6]	A	T	4.669e^-5	1	DOWNSTREAM snRNA:U3:22A INTERGENIC
2R	11972589	2R_11972589_SNP [dm3] 2R_16085084_SNP [dm6]	G	A	4.965e^-5	1	SYNONYMOUS_CODING Dg	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3L	12488494	3L_12488494_SNP [dm3] 3L_12495394_SNP [dm6]	A	T	5.349e^-5	1	INTRON CG10657	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	15872435	2R_15872435_SNP [dm3] 2R_19984930_SNP [dm6]	G	T	5.756e^-5	1	DOWNSTREAM CG8654 INTERGENIC
3L	12896929	3L_12896929_SNP [dm3] 3L_12903829_SNP [dm6]	A	T	6.137e^-5	1	UPSTREAM CG32117 INTERGENIC
2R	6362378	2R_6362378_SNP [dm3] 2R_10474873_SNP [dm6]	T	G	6.453e^-5	1	INTRON whd
2R	18294779	2R_18294779_SNP [dm3] 2R_22407274_SNP [dm6]	C	G	6.455e^-5	1	NON_SYNONYMOUS_CODING CG6044	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	10964271	3L_10964271_SNP [dm3] 3L_10971171_SNP [dm6]	G	A	7.042e^-5	1	INTERGENIC
2R	9740764	2R_9740764_SNP [dm3] 2R_13853259_SNP [dm6]	C	G	7.199e^-5	1	SYNONYMOUS_CODING CG6543 DOWNSTREAM CG30485	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_sna mE1_TFBS_inv
2L	14496315	2L_14496315_SNP [dm3] 2L_14496315_SNP [dm6]	A	G	7.520e^-5	1	DOWNSTREAM tRNA:P:35Bd & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
X	2893998	X_2893998_SNP [dm3] X_2999965_SNP [dm6]	T	A	7.626e^-5	1	INTRON kirre
3L	1287791	3L_1287791_SNP [dm3] 3L_1287791_SNP [dm6]	C	G	7.672e^-5	1	INTRON CG32333
3R	25139782	3R_25139782_SNP [dm3] 3R_29314060_SNP [dm6]	C	T	7.993e^-5	1	INTERGENIC
2L	9464953	2L_9464953_MNP [dm3] 2L_9464953_MNP [dm6]	TTGT	GACA	8.220e^-5	1	DOWNSTREAM numb INTERGENIC	TF binding site mE1_TFBS_bab1
3R	15319882	3R_15319882_SNP [dm3] 3R_19494160_SNP [dm6]	T	G	8.275e^-5	1	INTRON Dys
3R	17238120	3R_17238120_SNP [dm3] 3R_21412398_SNP [dm6]	G	A	8.634e^-5	1	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
2R	11042873	2R_11042873_SNP [dm3] 2R_15155368_SNP [dm6]	C	A	8.879e^-5	1	UPSTREAM igl INTERGENIC
3L	3911964	3L_3911964_SNP [dm3] 3L_3911964_SNP [dm6]	A	T	8.930e^-5	1	INTRON Eip63F-1
2R	8381782	2R_8381782_SNP [dm3] 2R_12494277_SNP [dm6]	T	C	9.007e^-5	1	INTRON fdl
2R	6675954	2R_6675954_SNP [dm3] 2R_10788449_SNP [dm6]	C	T	9.138e^-5	1	INTRON CG33144
2L	2837302	2L_2837302_SNP [dm3] 2L_2837302_SNP [dm6]	A	T	9.185e^-5	1	INTRON CG3119	TF binding site mE1_TFBS_cad
2L	17036882	2L_17036882_SNP [dm3] 2L_17036882_SNP [dm6]	G	C	9.188e^-5	1	INTERGENIC
3R	15675157	3R_15675157_INS [dm3] 3R_19849435_INS [dm6]	G	GTCCCCAG	9.278e^-5	1	INTRON CG4662
2L	6008506	2L_6008506_SNP [dm3] 2L_6008506_SNP [dm6]	A	G	9.289e^-5	1	SPLICE_SITE_REGION CG9098 INTRON CG9098
2R	6582321	2R_6582321_SNP [dm3] 2R_10694816_SNP [dm6]	A	T	9.524e^-5	1	INTRON stan	TF binding site mE1_TFBS_HSA
2R	3236828	2R_3236828_SNP [dm3] 2R_7349323_SNP [dm6]	C	T	9.603e^-5	1	INTRON Dscam1
3L	13368524	3L_13368524_SNP [dm3] 3L_13375424_SNP [dm6]	T	C	9.630e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	13225531	3L_13225531_SNP [dm3] 3L_13232431_SNP [dm6]	C	T	9.916e^-5	1	INTRON caps
3L	1384957	3L_1384957_SNP [dm3] 3L_1384957_SNP [dm6]	C	T	1.018e^-4	1	INTRON Ptp61F & 1 other
3L	3023485	3L_3023485_SNP [dm3] 3L_3023485_SNP [dm6]	G	A	1.082e^-4	1	DOWNSTREAM aly INTERGENIC
2R	13373129	2R_13373129_SNP [dm3] 2R_17485624_SNP [dm6]	T	C	1.166e^-4	1	UTR_5_PRIME CG43110 INTRON NT5E-2
2R	13383336	2R_13383336_SNP [dm3] 2R_17495831_SNP [dm6]	C	T	1.167e^-4	1	UTR_3_PRIME CG30103	TF binding site mE1_TFBS_cad
2L	20474889	2L_20474889_SNP [dm3] 2L_20474889_SNP [dm6]	C	T	1.175e^-4	1	INTRON CR44980
2L	20474914	2L_20474914_SNP [dm3] 2L_20474914_SNP [dm6]	G	T	1.175e^-4	1	INTRON CR44980
3R	26601969	3R_26601969_SNP [dm3] 3R_30776247_SNP [dm6]	C	T	1.186e^-4	1	INTRON zfh1	TF binding site BDTNP1_TFBS_dl
3R	21948838	3R_21948838_SNP [dm3] 3R_26123116_SNP [dm6]	T	A	1.190e^-4	1	INTRON CG31324
2R	19645557	2R_19645557_SNP [dm3] 2R_23758034_SNP [dm6]	A	G	1.202e^-4	1	SYNONYMOUS_CODING CG9850
2L	13710150	2L_13710150_SNP [dm3] 2L_13710150_SNP [dm6]	G	C	1.205e^-4	1	NON_SYNONYMOUS_CODING CG7311 UTR_3_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	2916599	2R_2916599_SNP [dm3] 2R_7029094_SNP [dm6]	G	A	1.245e^-4	1	UTR_5_PRIME Tsp42Eg
3R	19211856	3R_19211856_SNP [dm3] 3R_23386134_SNP [dm6]	A	G	1.303e^-4	1	INTERGENIC	TF binding site mE1_TFBS_Trl
2L	9339118	2L_9339118_SNP [dm3] 2L_9339118_SNP [dm6]	C	T	1.322e^-4	1	INTRON Eaat1
X	7875913	X_7875913_SNP [dm3] X_7981880_SNP [dm6]	T	C	1.339e^-4	1	INTRON sn
3L	3596801	3L_3596801_SNP [dm3] 3L_3596801_SNP [dm6]	T	A	1.341e^-4	1	INTRON Eip63E
3R	2285727	3R_2285727_SNP [dm3] 3R_6460005_SNP [dm6]	T	C	1.355e^-4	1	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	5692185	3L_5692185_SNP [dm3] 3L_5699085_SNP [dm6]	A	G	1.376e^-4	1	INTRON sif	TF binding site mE1_TFBS_chinmo
2L	6957910	2L_6957910_SNP [dm3] 2L_6957910_SNP [dm6]	C	T	1.386e^-4	1	SYNONYMOUS_CODING CG3430 UPSTREAM CG13775	TF binding site mE1_TFBS_sens
3R	13572008	3R_13572008_SNP [dm3] 3R_17746286_SNP [dm6]	C	T	1.395e^-4	1	UTR_3_PRIME TyrRII DOWNSTREAM TyrRII
3R	13572015	3R_13572015_INS [dm3] 3R_17746293_INS [dm6]	A	AA	1.395e^-4	1	UTR_3_PRIME TyrRII DOWNSTREAM TyrRII
2L	9464925	2L_9464925_SNP [dm3] 2L_9464925_SNP [dm6]	C	G	1.459e^-4	1	DOWNSTREAM numb INTERGENIC	TF binding site mE1_TFBS_bab1
X	10717022	X_10717022_INS [dm3] X_10822989_INS [dm6]	T	TGTA	1.498e^-4	1	UPSTREAM Imp INTRON Imp	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 BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	8661008	2L_8661008_SNP [dm3] 2L_8661008_SNP [dm6]	C	T	1.499e^-4	1	INTRON Sema-1a
2R	18260070	2R_18260070_SNP [dm3] 2R_22372565_SNP [dm6]	T	C	1.515e^-4	1	INTRON Liprin-gamma	TF binding site BDTNP1_TFBS_dl
2R	18260071	2R_18260071_SNP [dm3] 2R_22372566_SNP [dm6]	T	A	1.515e^-4	1	INTRON Liprin-gamma	TF binding site BDTNP1_TFBS_dl
2R	18260089	2R_18260089_SNP [dm3] 2R_22372584_SNP [dm6]	A	C	1.515e^-4	1	INTRON Liprin-gamma	TF binding site BDTNP1_TFBS_dl
2R	18260101	2R_18260101_SNP [dm3] 2R_22372596_SNP [dm6]	T	C	1.515e^-4	1	INTRON Liprin-gamma	TF binding site BDTNP1_TFBS_dl
2L	381570	2L_381570_INS [dm3] 2L_381570_INS [dm6]	T	TT	1.518e^-4	1	INTRON al	TF binding site mE1_TFBS_HSA
2R	12356183	2R_12356183_SNP [dm3] 2R_16468678_SNP [dm6]	C	T	1.543e^-4	1	SYNONYMOUS_CODING CheB53b
2R	13496591	2R_13496591_SNP [dm3] 2R_17609086_SNP [dm6]	C	T	1.565e^-4	1	SYNONYMOUS_CODING CG10936
3L	13702833	3L_13702833_SNP [dm3] 3L_13709733_SNP [dm6]	C	T	1.617e^-4	1	INTRON bru-3
3R	13572036	3R_13572036_SNP [dm3] 3R_17746314_SNP [dm6]	G	T	1.618e^-4	1	UTR_3_PRIME TyrRII DOWNSTREAM TyrRII
2R	9895520	2R_9895520_SNP [dm3] 2R_14008015_SNP [dm6]	C	T	1.643e^-4	1	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	13821783	2R_13821783_SNP [dm3] 2R_17934278_SNP [dm6]	C	G	1.651e^-4	1	INTERGENIC
2R	9334303	2R_9334303_SNP [dm3] 2R_13446798_SNP [dm6]	G	A	1.667e^-4	1	UPSTREAM CG30062 INTRON cnn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2R	3460236	2R_3460236_SNP [dm3] 2R_7572731_SNP [dm6]	T	G	1.716e^-4	1	INTRON Vps13
3L	13368981	3L_13368981_SNP [dm3] 3L_13375881_SNP [dm6]	T	G	1.719e^-4	1	INTERGENIC
3L	14075057	3L_14075057_SNP [dm3] 3L_14081957_SNP [dm6]	A	C	1.727e^-4	1	SYNONYMOUS_CODING btl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	3492110	2R_3492110_SNP [dm3] 2R_7604605_SNP [dm6]	G	A	1.768e^-4	1	INTRON CG1358	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14089030	2R_14089030_SNP [dm3] 2R_18201525_SNP [dm6]	C	G	1.775e^-4	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	6951584	2L_6951584_SNP [dm3] 2L_6951584_SNP [dm6]	C	G	1.786e^-4	1	INTRON SA

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Missing results

By genomic position
Variant impact
Gene name

pc_Deletion_PElem_GC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results