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=1.146e^-19)
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
In_2L_t	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	37.1648	8.5066e-09
In_2R_NS	8.6694	0.0131

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

5329 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
X	12722153	X_12722153_SNP [dm3] X_12828120_SNP [dm6]	A	C	7.868e^-9	0.015	INTRON Pde9
X	12722117	X_12722117_SNP [dm3] X_12828084_SNP [dm6]	A	G	2.505e^-8	0.019	INTRON Pde9
3R	27081378	3R_27081378_SNP [dm3] 3R_31255656_SNP [dm6]	C	A	3.976e^-8	0.019	SYNONYMOUS_CODING spn-F UPSTREAM CG1750	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	10420231	2L_10420231_SNP [dm3] 2L_10420231_SNP [dm6]	A	C	4.108e^-8	0.019	DOWNSTREAM pie INTRON RfC3	TF binding site mE1_TFBS_ttk
2L	8895468	2L_8895468_SNP [dm3] 2L_8895468_SNP [dm6]	A	T	5.190e^-8	0.019	INTERGENIC
2L	13020068	2L_13020068_DEL [dm3] 2L_13020068_DEL [dm6]	AAA	A	8.805e^-8	0.02	UPSTREAM CG9934 INTRON A16	TF binding site mE1_TFBS_cad
2L	10693487	2L_10693487_SNP [dm3] 2L_10693487_SNP [dm6]	T	C	8.969e^-8	0.02	NON_SYNONYMOUS_CODING CG17108	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	5188939	2L_5188939_SNP [dm3] 2L_5188939_SNP [dm6]	G	A	1.056e^-7	0.02	NON_SYNONYMOUS_CODING Msp300	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5158162	2L_5158162_SNP [dm3] 2L_5158162_SNP [dm6]	T	A	1.105e^-7	0.02	UTR_3_PRIME Msp300 INTRON Msp300
2R	16489867	2R_16489867_SNP [dm3] 2R_20602362_SNP [dm6]	A	C	1.138e^-7	0.02	UPSTREAM bl INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	4657401	2L_4657401_SNP [dm3] 2L_4657401_SNP [dm6]	A	G	1.155e^-7	0.02	INTERGENIC
2L	8892181	2L_8892181_SNP [dm3] 2L_8892181_SNP [dm6]	C	T	1.370e^-7	0.021	DOWNSTREAM CG42713 INTERGENIC
2L	5076791	2L_5076791_DEL [dm3] 2L_5076791_DEL [dm6]	GGTG	G	1.591e^-7	0.022	INTRON pgant5
2L	5074881	2L_5074881_SNP [dm3] 2L_5074881_SNP [dm6]	A	G	1.846e^-7	0.022	INTRON pgant5
3L	18460323	3L_18460323_SNP [dm3] 3L_18467223_SNP [dm6]	T	C	1.982e^-7	0.022	INTERGENIC
2L	18669276	2L_18669276_SNP [dm3] 2L_18669276_SNP [dm6]	T	A	2.069e^-7	0.022	SYNONYMOUS_CODING CG43338	TF binding site mE1_TFBS_cad
3L	18460309	3L_18460309_SNP [dm3] 3L_18467209_SNP [dm6]	A	G	2.080e^-7	0.022	INTERGENIC
3R	5749736	3R_5749736_SNP [dm3] 3R_9924014_SNP [dm6]	G	T	2.081e^-7	0.022	INTRON Glut4EF
X	9083143	X_9083143_SNP [dm3] X_9189110_SNP [dm6]	G	A	2.340e^-7	0.023	UTR_3_PRIME mei-P26 DOWNSTREAM CG12115
3R	14591678	3R_14591678_SNP [dm3] 3R_18765956_SNP [dm6]	G	C	2.546e^-7	0.024	INTRON CG7720
X	12722141	X_12722141_SNP [dm3] X_12828108_SNP [dm6]	C	T	2.786e^-7	0.024	INTRON Pde9
3L	18453521	3L_18453521_SNP [dm3] 3L_18460421_SNP [dm6]	A	T	2.805e^-7	0.024	INTRON CG32196	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	16707826	X_16707826_SNP [dm3] X_16813793_SNP [dm6]	T	C	2.910e^-7	0.024	INTRON CG4829
3L	10091812	3L_10091812_SNP [dm3] 3L_10098712_SNP [dm6]	G	C	3.217e^-7	0.024	UPSTREAM CG42825 DOWNSTREAM CG42826 INTRON dpr6
3R	5749737	3R_5749737_SNP [dm3] 3R_9924015_SNP [dm6]	T	A	3.227e^-7	0.024	INTRON Glut4EF
X	15579895	X_15579895_SNP [dm3] X_15685862_SNP [dm6]	A	T	3.592e^-7	0.026	NON_SYNONYMOUS_CODING CG15599	TF binding site BDTNP1_TFBS_prd mE1_TFBS_sens
2L	8891353	2L_8891353_SNP [dm3] 2L_8891353_SNP [dm6]	T	G	3.970e^-7	0.027	UPSTREAM CG42713 INTERGENIC
2L	17868806	2L_17868806_SNP [dm3] 2L_17868806_SNP [dm6]	T	A	4.346e^-7	0.027	INTRON CadN2
3L	18460729	3L_18460729_SNP [dm3] 3L_18467629_SNP [dm6]	C	A	4.430e^-7	0.027	INTERGENIC
3L	13072190	3L_13072190_SNP [dm3] 3L_13079090_SNP [dm6]	A	T	4.527e^-7	0.027	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3R	14591888	3R_14591888_SNP [dm3] 3R_18766166_SNP [dm6]	C	T	4.785e^-7	0.027	INTRON CG7720
3L	3848033	3L_3848033_SNP [dm3] 3L_3848033_SNP [dm6]	C	T	4.843e^-7	0.027	INTRON Awh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
2L	5071171	2L_5071171_SNP [dm3] 2L_5071171_SNP [dm6]	A	G	5.036e^-7	0.027	UPSTREAM CR45305 DOWNSTREAM qtc & 1 other INTRON RpL37A	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
2L	17868789	2L_17868789_SNP [dm3] 2L_17868789_SNP [dm6]	C	T	5.296e^-7	0.027	INTRON CadN2
2L	5193348	2L_5193348_SNP [dm3] 2L_5193348_SNP [dm6]	A	T	5.346e^-7	0.027	SYNONYMOUS_CODING Msp300 UPSTREAM snmRNA:765	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	18730258	3L_18730258_SNP [dm3] 3L_18737158_SNP [dm6]	G	A	5.547e^-7	0.027	INTERGENIC
2L	17878801	2L_17878801_SNP [dm3] 2L_17878801_SNP [dm6]	A	G	5.603e^-7	0.027	INTERGENIC
3L	2570088	3L_2570088_SNP [dm3] 3L_2570088_SNP [dm6]	C	T	5.746e^-7	0.027	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	8893211	2L_8893211_SNP [dm3] 2L_8893211_SNP [dm6]	G	A	5.770e^-7	0.027	INTERGENIC
2L	2640597	2L_2640597_SNP [dm3] 2L_2640597_SNP [dm6]	T	G	5.819e^-7	0.027	INTERGENIC
2L	5079419	2L_5079419_SNP [dm3] 2L_5079419_SNP [dm6]	C	T	6.135e^-7	0.028	UTR_5_PRIME pgant5	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	18444671	3L_18444671_SNP [dm3] 3L_18451571_SNP [dm6]	T	C	6.616e^-7	0.03	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	18459325	3L_18459325_SNP [dm3] 3L_18466225_SNP [dm6]	G	A	6.884e^-7	0.03	INTERGENIC
2L	5069554	2L_5069554_SNP [dm3] 2L_5069554_SNP [dm6]	C	T	7.544e^-7	0.032	DOWNSTREAM mir-2495 & 1 other INTRON qtc
2L	5071179	2L_5071179_SNP [dm3] 2L_5071179_SNP [dm6]	T	C	7.912e^-7	0.033	UPSTREAM CR45305 DOWNSTREAM qtc & 1 other INTRON RpL37A	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
2L	12827807	2L_12827807_SNP [dm3] 2L_12827807_SNP [dm6]	C	G	8.276e^-7	0.034	INTERGENIC
2L	14326965	2L_14326965_SNP [dm3] 2L_14326965_SNP [dm6]	C	T	8.639e^-7	0.034	SYNONYMOUS_CODING wb DOWNSTREAM wb
2L	5076084	2L_5076084_SNP [dm3] 2L_5076084_SNP [dm6]	G	T	8.704e^-7	0.034	INTRON pgant5
3R	5424509	3R_5424509_SNP [dm3] 3R_9598787_SNP [dm6]	T	A	8.783e^-7	0.034	INTRON CG8312	TF binding site BDTNP1_TFBS_hb
3R	5919522	3R_5919522_SNP [dm3] 3R_10093800_SNP [dm6]	T	C	9.273e^-7	0.034	EXON CR43459	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	15319467	2L_15319467_SNP [dm3] 2L_15319467_SNP [dm6]	A	G	9.311e^-7	0.034	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
X	9410112	X_9410112_INS [dm3] X_9516079_INS [dm6]	A	AC	9.476e^-7	0.034	INTRON CG32700
X	12239910	X_12239910_SNP [dm3] X_12345877_SNP [dm6]	C	T	9.681e^-7	0.034	INTERGENIC
2L	18676857	2L_18676857_SNP [dm3] 2L_18676857_SNP [dm6]	A	G	1.095e^-6	0.036	NON_SYNONYMOUS_CODING Mst36Fa UPSTREAM CG31751	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	5118987	2L_5118987_SNP [dm3] 2L_5118987_SNP [dm6]	A	T	1.097e^-6	0.036	INTRON Msp300
3L	18444670	3L_18444670_SNP [dm3] 3L_18451570_SNP [dm6]	G	A	1.130e^-6	0.036	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	5144810	2L_5144810_DEL [dm3] 2L_5144810_DEL [dm6]	GTGTATCTGGGAT...	G	1.182e^-6	0.036	INTRON Msp300	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	15304111	2L_15304111_SNP [dm3] 2L_15304111_SNP [dm6]	A	T	1.183e^-6	0.036	INTERGENIC
2L	14542303	2L_14542303_SNP [dm3] 2L_14542303_SNP [dm6]	A	G	1.187e^-6	0.036	INTERGENIC
X	11237150	X_11237150_INS [dm3] X_11343117_INS [dm6]	T	TT	1.192e^-6	0.036	INTRON CG34348
2L	15319276	2L_15319276_SNP [dm3] 2L_15319276_SNP [dm6]	G	A	1.216e^-6	0.036	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5144828	2L_5144828_SNP [dm3] 2L_5144828_SNP [dm6]	A	G	1.227e^-6	0.036	INTRON Msp300	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	12722144	X_12722144_SNP [dm3] X_12828111_SNP [dm6]	C	G	1.246e^-6	0.036	INTRON Pde9
X	7037223	X_7037223_SNP [dm3] X_7143190_SNP [dm6]	G	C	1.253e^-6	0.036	INTRON CG9650
2L	17867777	2L_17867777_SNP [dm3] 2L_17867777_SNP [dm6]	C	A	1.257e^-6	0.036	INTRON CadN2
2L	14544975	2L_14544975_SNP [dm3] 2L_14544975_SNP [dm6]	C	G	1.265e^-6	0.036	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	15479915	X_15479915_SNP [dm3] X_15585882_SNP [dm6]	C	T	1.277e^-6	0.036	UTR_3_PRIME CG9220 DOWNSTREAM CG8097	TF binding site mE1_TFBS_cad
X	5502595	X_5502595_SNP [dm3] X_5608562_SNP [dm6]	C	A	1.356e^-6	0.037	INTRON Vsx1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	5076070	2L_5076070_SNP [dm3] 2L_5076070_SNP [dm6]	A	T	1.366e^-6	0.037	INTRON pgant5
3R	3498858	3R_3498858_SNP [dm3] 3R_7673136_SNP [dm6]	C	G	1.418e^-6	0.038	INTRON Nlg1
2L	5139666	2L_5139666_SNP [dm3] 2L_5139666_SNP [dm6]	C	T	1.464e^-6	0.039	NON_SYNONYMOUS_CODING Msp300
3L	18730260	3L_18730260_SNP [dm3] 3L_18737160_SNP [dm6]	G	A	1.512e^-6	0.039	INTERGENIC
3L	18730262	3L_18730262_SNP [dm3] 3L_18737162_SNP [dm6]	C	T	1.646e^-6	0.041	INTERGENIC
2L	17879005	2L_17879005_SNP [dm3] 2L_17879005_SNP [dm6]	C	T	1.696e^-6	0.041	INTERGENIC
3R	5427721	3R_5427721_SNP [dm3] 3R_9601999_SNP [dm6]	C	G	1.708e^-6	0.041	INTRON CG8312
3R	5427722	3R_5427722_SNP [dm3] 3R_9602000_SNP [dm6]	C	A	1.708e^-6	0.041	INTRON CG8312
2L	8890520	2L_8890520_SNP [dm3] 2L_8890520_SNP [dm6]	T	A	1.712e^-6	0.041	UPSTREAM CG42713 INTERGENIC
2R	19138692	2R_19138692_SNP [dm3] 2R_23251169_SNP [dm6]	C	A	1.733e^-6	0.041	INTERGENIC
3L	18473922	3L_18473922_SNP [dm3] 3L_18480822_SNP [dm6]	A	T	1.762e^-6	0.041	INTERGENIC
2L	12177261	2L_12177261_DEL [dm3] 2L_12177261_DEL [dm6]	TAT	T	1.774e^-6	0.041	INTRON aret & 1 other	TF binding site BDTNP1_TFBS_z
2L	17868621	2L_17868621_SNP [dm3] 2L_17868621_SNP [dm6]	C	A	1.778e^-6	0.041	INTRON CadN2
2L	12177229	2L_12177229_SNP [dm3] 2L_12177229_SNP [dm6]	G	T	1.826e^-6	0.041	INTRON aret & 1 other	TF binding site BDTNP1_TFBS_z
3R	15515037	3R_15515037_SNP [dm3] 3R_19689315_SNP [dm6]	G	A	1.826e^-6	0.041	INTRON Naam
2L	8889085	2L_8889085_SNP [dm3] 2L_8889085_SNP [dm6]	C	T	1.829e^-6	0.041	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk
X	12722960	X_12722960_SNP [dm3] X_12828927_SNP [dm6]	G	T	1.922e^-6	0.042	INTRON Pde9
3L	8463332	3L_8463332_SNP [dm3] 3L_8470232_SNP [dm6]	C	T	2.125e^-6	0.046	INTRON Gug
3L	3492624	3L_3492624_SNP [dm3] 3L_3492624_SNP [dm6]	C	A	2.185e^-6	0.046	INTRON CG42324
2L	4657379	2L_4657379_SNP [dm3] 2L_4657379_SNP [dm6]	A	G	2.195e^-6	0.046	INTERGENIC
2L	18676884	2L_18676884_SNP [dm3] 2L_18676884_SNP [dm6]	C	T	2.213e^-6	0.046	NON_SYNONYMOUS_CODING Mst36Fa UPSTREAM CG31751	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	5193516	2L_5193516_SNP [dm3] 2L_5193516_SNP [dm6]	T	A	2.233e^-6	0.046	NON_SYNONYMOUS_CODING Msp300 EXON snmRNA:765	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	18672643	2L_18672643_SNP [dm3] 2L_18672643_SNP [dm6]	T	A	2.312e^-6	0.046	NON_SYNONYMOUS_CODING CG43339 DOWNSTREAM Mst36Fb
2L	17868295	2L_17868295_SNP [dm3] 2L_17868295_SNP [dm6]	G	T	2.315e^-6	0.046	INTRON CadN2
2L	5059841	2L_5059841_SNP [dm3] 2L_5059841_SNP [dm6]	T	C	2.328e^-6	0.046	UPSTREAM Rpn11 & 1 other DOWNSTREAM CR45291 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA
X	10148017	X_10148017_SNP [dm3] X_10253984_SNP [dm6]	G	C	2.331e^-6	0.046	INTRON Hk
2L	672959	2L_672959_SNP [dm3] 2L_672959_SNP [dm6]	A	G	2.428e^-6	0.048	INTRON ds
3L	3871831	3L_3871831_SNP [dm3] 3L_3871831_SNP [dm6]	C	A	2.447e^-6	0.048	INTERGENIC
3L	18453726	3L_18453726_SNP [dm3] 3L_18460626_SNP [dm6]	T	A	2.500e^-6	0.048	INTRON CG32196	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	10016616	3L_10016616_SNP [dm3] 3L_10023516_SNP [dm6]	A	G	2.508e^-6	0.048	INTRON dpr6
3L	18450365	3L_18450365_SNP [dm3] 3L_18457265_SNP [dm6]	C	T	2.571e^-6	0.049	UPSTREAM CR44670 EXON CR44671
2L	17868790	2L_17868790_SNP [dm3] 2L_17868790_SNP [dm6]	G	T	2.644e^-6	0.049	INTRON CadN2

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_2L phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results