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=2.208e^-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

1901 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	10204066	X_10204066_SNP [dm3] X_10310033_SNP [dm6]	G	T	1.566e^-7	0.294	UPSTREAM alpha-Man-I INTRON alpha-Man-I
X	10204071	X_10204071_SNP [dm3] X_10310038_SNP [dm6]	A	C	1.195e^-6	0.89	UPSTREAM alpha-Man-I INTRON alpha-Man-I
2L	905217	2L_905217_SNP [dm3] 2L_905217_SNP [dm6]	C	T	2.249e^-6	0.89	DOWNSTREAM CR45261 INTERGENIC
X	10203656	X_10203656_SNP [dm3] X_10309623_SNP [dm6]	A	G	2.840e^-6	0.89	UPSTREAM alpha-Man-I INTRON alpha-Man-I	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5613631	3L_5613631_SNP [dm3] 3L_5620531_SNP [dm6]	C	T	4.405e^-6	0.89	INTERGENIC	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
X	10203229	X_10203229_SNP [dm3] X_10309196_SNP [dm6]	T	A	5.216e^-6	0.89	UPSTREAM alpha-Man-I INTRON alpha-Man-I	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	2486804	3L_2486804_SNP [dm3] 3L_2486804_SNP [dm6]	T	C	5.519e^-6	0.89	INTRON CG45186	TF binding site BDTNP1_TFBS_dl
X	10202727	X_10202727_SNP [dm3] X_10308694_SNP [dm6]	A	G	5.605e^-6	0.89	UTR_5_PRIME alpha-Man-I INTRON alpha-Man-I	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	12245826	X_12245826_SNP [dm3] X_12351793_SNP [dm6]	A	G	5.636e^-6	0.89	INTERGENIC
3R	26693181	3R_26693181_SNP [dm3] 3R_30867459_SNP [dm6]	G	A	6.270e^-6	0.89	UPSTREAM Cpr100A INTERGENIC
3L	10820424	3L_10820424_DEL [dm3] 3L_10827324_DEL [dm6]	GTGTGTG	G	6.567e^-6	0.89	INTERGENIC
X	18215848	X_18215848_SNP [dm3] X_18321815_SNP [dm6]	C	A	6.731e^-6	0.89	UPSTREAM CG6023 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	15308095	2R_15308095_SNP [dm3] 2R_19420590_SNP [dm6]	C	A	7.404e^-6	0.89	INTRON hts	TF binding site BDTNP1_TFBS_dl
3R	15429801	3R_15429801_SNP [dm3] 3R_19604079_SNP [dm6]	G	A	8.392e^-6	0.89	UTR_5_PRIME CG7342
X	15467790	X_15467790_SNP [dm3] X_15573757_SNP [dm6]	G	A	9.044e^-6	0.89	NON_SYNONYMOUS_CODING CG9213	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	13664001	3R_13664001_SNP [dm3] 3R_17838279_SNP [dm6]	G	A	9.473e^-6	0.89	INTRON tinc	TF binding site mE1_TFBS_inv
X	3124079	X_3124079_INS [dm3] X_3230046_INS [dm6]	C	CC	1.178e^-5	0.89	INTRON dnc
3L	7861973	3L_7861973_DEL [dm3] 3L_7868873_DEL [dm6]	CT	C	1.250e^-5	0.89	UPSTREAM CG32365 INTERGENIC	insulator Insulator_Class_II.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	17972810	3R_17972810_SNP [dm3] 3R_22147088_SNP [dm6]	A	C	1.361e^-5	0.89	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad
X	10512188	X_10512188_SNP [dm3] X_10618155_SNP [dm6]	A	G	1.374e^-5	0.89	SYNONYMOUS_CODING CG43347	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11127832	3L_11127832_SNP [dm3] 3L_11134732_SNP [dm6]	G	T	1.380e^-5	0.89	UPSTREAM CG14143 DOWNSTREAM CG42575 INTERGENIC
3R	26659834	3R_26659834_SNP [dm3] 3R_30834112_SNP [dm6]	G	A	1.385e^-5	0.89	INTRON CG15544
3R	26659883	3R_26659883_SNP [dm3] 3R_30834161_SNP [dm6]	C	T	1.385e^-5	0.89	INTRON CG15544
3R	2350925	3R_2350925_DEL [dm3] 3R_6525203_DEL [dm6]	GTG	AA	1.396e^-5	0.89	INTERGENIC
3R	17972821	3R_17972821_SNP [dm3] 3R_22147099_SNP [dm6]	T	C	1.486e^-5	0.89	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
3L	7877829	3L_7877829_SNP [dm3] 3L_7884729_SNP [dm6]	G	A	1.505e^-5	0.89	INTRON CG32365
3R	5725761	3R_5725761_SNP [dm3] 3R_9900039_SNP [dm6]	T	G	1.566e^-5	0.89	INTRON Glut4EF
2R	14795174	2R_14795174_SNP [dm3] 2R_18907669_SNP [dm6]	C	G	1.588e^-5	0.89	INTRON sano	TF binding site mE1_TFBS_cad
2R	18573438	2R_18573438_DEL [dm3] 2R_22685933_DEL [dm6]	TATT	T	1.613e^-5	0.89	UTR_3_PRIME ppa	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	17972809	3R_17972809_SNP [dm3] 3R_22147087_SNP [dm6]	A	T	1.640e^-5	0.89	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad
3L	5613313	3L_5613313_SNP [dm3] 3L_5620213_SNP [dm6]	A	C	1.658e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	5522530	2L_5522530_SNP [dm3] 2L_5522530_SNP [dm6]	T	C	1.767e^-5	0.89	SYNONYMOUS_CODING CG7371
3L	7877628	3L_7877628_SNP [dm3] 3L_7884528_SNP [dm6]	T	C	1.778e^-5	0.89	INTRON CG32365
X	16052034	X_16052034_SNP [dm3] X_16158001_SNP [dm6]	G	A	1.807e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	14609240	2R_14609240_SNP [dm3] 2R_18721735_SNP [dm6]	C	A	1.810e^-5	0.89	INTRON Hs3st-A
3R	18711937	3R_18711937_SNP [dm3] 3R_22886215_SNP [dm6]	G	A	2.024e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	23492557	3R_23492557_SNP [dm3] 3R_27666835_SNP [dm6]	T	C	2.161e^-5	0.89	INTRON unc80
3L	10737194	3L_10737194_SNP [dm3] 3L_10744094_SNP [dm6]	T	A	2.334e^-5	0.89	INTERGENIC
3L	10736424	3L_10736424_SNP [dm3] 3L_10743324_SNP [dm6]	A	T	2.408e^-5	0.89	INTERGENIC	TF binding site mE1_TFBS_Trl
X	18215510	X_18215510_SNP [dm3] X_18321477_SNP [dm6]	T	C	2.412e^-5	0.89	UPSTREAM CG6023 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	18506106	3L_18506106_SNP [dm3] 3L_18513006_SNP [dm6]	C	A	2.475e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3L	12262583	3L_12262583_SNP [dm3] 3L_12269483_SNP [dm6]	A	G	2.480e^-5	0.89	UTR_3_PRIME CG32100 & 1 other DOWNSTREAM Pbgs
2R	14010302	2R_14010302_SNP [dm3] 2R_18122797_SNP [dm6]	C	G	2.534e^-5	0.89	NON_SYNONYMOUS_CODING stau UTR_5_PRIME stau	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	11159918	3R_11159918_SNP [dm3] 3R_15334196_SNP [dm6]	G	A	2.627e^-5	0.89	SYNONYMOUS_CODING Sra-1	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3R	26704997	3R_26704997_SNP [dm3] 3R_30879275_SNP [dm6]	C	T	2.642e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	2683796	2R_2683796_SNP [dm3] 2R_6796291_SNP [dm6]	T	C	2.672e^-5	0.89	INTRON Epac
2L	9251347	2L_9251347_SNP [dm3] 2L_9251347_SNP [dm6]	G	A	2.765e^-5	0.89	UPSTREAM aust DOWNSTREAM borr EXON CR43734
2R	2683863	2R_2683863_SNP [dm3] 2R_6796358_SNP [dm6]	C	T	2.774e^-5	0.89	INTRON Epac
3L	7039334	3L_7039334_SNP [dm3] 3L_7046234_SNP [dm6]	A	G	2.789e^-5	0.89	INTRON Mp
3R	26692750	3R_26692750_SNP [dm3] 3R_30867028_SNP [dm6]	C	T	2.877e^-5	0.89	UPSTREAM Cpr100A INTERGENIC
2R	2683849	2R_2683849_SNP [dm3] 2R_6796344_SNP [dm6]	T	A	2.913e^-5	0.89	INTRON Epac
3R	26692742	3R_26692742_DEL [dm3] 3R_30867020_DEL [dm6]	CTCTT	C	3.062e^-5	0.89	UPSTREAM Cpr100A INTERGENIC
3R	26696911	3R_26696911_SNP [dm3] 3R_30871189_SNP [dm6]	G	T	3.062e^-5	0.89	NON_SYNONYMOUS_CODING CG15545	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3R	26704326	3R_26704326_SNP [dm3] 3R_30878604_SNP [dm6]	A	G	3.062e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	26704340	3R_26704340_SNP [dm3] 3R_30878618_SNP [dm6]	A	G	3.062e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	26704353	3R_26704353_SNP [dm3] 3R_30878631_SNP [dm6]	C	A	3.062e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	26704811	3R_26704811_SNP [dm3] 3R_30879089_SNP [dm6]	A	C	3.062e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12016575	2L_12016575_SNP [dm3] 2L_12016575_SNP [dm6]	G	A	3.079e^-5	0.89	INTRON CG6734	TF binding site mE1_TFBS_cad
3R	14869719	3R_14869719_SNP [dm3] 3R_19043997_SNP [dm6]	G	A	3.092e^-5	0.89	SYNONYMOUS_CODING CG6026 DOWNSTREAM cdi	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	2485006	3L_2485006_SNP [dm3] 3L_2485006_SNP [dm6]	G	A	3.093e^-5	0.89	INTRON CG45186	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	19728013	X_19728013_SNP [dm3] X_19833980_SNP [dm6]	G	A	3.151e^-5	0.89	SYNONYMOUS_CODING pico	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_Mad BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	21057156	3L_21057156_SNP [dm3] 3L_21064056_SNP [dm6]	G	C	3.188e^-5	0.89	UTR_5_PRIME siz INTRON siz
3L	8074949	3L_8074949_SNP [dm3] 3L_8081849_SNP [dm6]	A	G	3.399e^-5	0.89	DOWNSTREAM CR43974 INTRON Ect4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	10382345	3L_10382345_INS [dm3] 3L_10389245_INS [dm6]	A	AA	3.458e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	10210601	X_10210601_SNP [dm3] X_10316568_SNP [dm6]	T	C	3.495e^-5	0.89	INTRON alpha-Man-I
3R	14113387	3R_14113387_SNP [dm3] 3R_18287665_SNP [dm6]	G	A	3.731e^-5	0.89	SYNONYMOUS_CODING CG7131	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	20469393	X_20469393_SNP [dm3] X_20598366_SNP [dm6]	T	C	3.756e^-5	0.89	INTRON RunxA
3L	12252840	3L_12252840_DEL [dm3] 3L_12259740_DEL [dm6]	CGTAT	C	3.783e^-5	0.89	INTRON app
2R	14609238	2R_14609238_SNP [dm3] 2R_18721733_SNP [dm6]	T	A	3.923e^-5	0.89	INTRON Hs3st-A
X	6436052	X_6436052_SNP [dm3] X_6542019_SNP [dm6]	C	T	3.984e^-5	0.89	INTRON CG34417
2R	3593672	2R_3593672_SNP [dm3] 2R_7706167_SNP [dm6]	G	T	4.007e^-5	0.89	INTRON tor	TF binding site mE1_TFBS_sens
3R	26705711	3R_26705711_SNP [dm3] 3R_30879989_SNP [dm6]	T	A	4.041e^-5	0.89	INTRON CG12071	TF binding site mE1_TFBS_HSA
3L	1646255	3L_1646255_SNP [dm3] 3L_1646255_SNP [dm6]	C	T	4.086e^-5	0.89	SYNONYMOUS_CODING CG17249 DOWNSTREAM CG13919	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	15429803	3R_15429803_SNP [dm3] 3R_19604081_SNP [dm6]	A	G	4.097e^-5	0.89	UTR_5_PRIME CG7342
2L	5227843	2L_5227843_SNP [dm3] 2L_5227843_SNP [dm6]	G	A	4.124e^-5	0.89	INTRON tkv
3L	9490827	3L_9490827_SNP [dm3] 3L_9497727_SNP [dm6]	C	G	4.182e^-5	0.89	UPSTREAM path INTRON path
X	10202226	X_10202226_SNP [dm3] X_10308193_SNP [dm6]	C	T	4.206e^-5	0.89	SYNONYMOUS_CODING alpha-Man-I INTRON alpha-Man-I	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
2R	3531469	2R_3531469_SNP [dm3] 2R_7643964_SNP [dm6]	C	G	4.221e^-5	0.89	NON_SYNONYMOUS_CODING CG43340 INTRON CG43340
3L	4947709	3L_4947709_SNP [dm3] 3L_4947709_SNP [dm6]	C	T	4.268e^-5	0.89	INTRON Con
2L	2483881	2L_2483881_DEL [dm3] 2L_2483881_DEL [dm6]	ACACACA	A	4.347e^-5	0.89	INTERGENIC	enhancer FlyBase regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3R	26705029	3R_26705029_SNP [dm3] 3R_30879307_SNP [dm6]	A	T	4.374e^-5	0.89	INTRON CG12071	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2484953	3L_2484953_SNP [dm3] 3L_2484953_SNP [dm6]	C	A	4.498e^-5	0.89	INTRON CG45186	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	19077000	X_19077000_SNP [dm3] X_19182967_SNP [dm6]	T	A	4.543e^-5	0.89	UPSTREAM CG33253 DOWNSTREAM CG7453 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8521070	3R_8521070_SNP [dm3] 3R_12695348_SNP [dm6]	G	A	4.694e^-5	0.89	UTR_5_PRIME NijC UPSTREAM CG14391 & 1 other
2L	2738720	2L_2738720_SNP [dm3] 2L_2738720_SNP [dm6]	C	T	4.791e^-5	0.89	SYNONYMOUS_CODING CG31689
3L	9710304	3L_9710304_SNP [dm3] 3L_9717204_SNP [dm6]	G	A	4.850e^-5	0.89	UTR_3_PRIME vsg DOWNSTREAM CG18178 & 1 other
3L	18506110	3L_18506110_DEL [dm3] 3L_18513010_DEL [dm6]	TTTGGTGTGCCCCTAAGT...	T	4.851e^-5	0.89	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3R	15429856	3R_15429856_SNP [dm3] 3R_19604134_SNP [dm6]	A	G	4.869e^-5	0.89	SYNONYMOUS_CODING CG7342	TF binding site mE1_TFBS_sens
3R	26692739	3R_26692739_SNP [dm3] 3R_30867017_SNP [dm6]	C	A	4.881e^-5	0.89	UPSTREAM Cpr100A INTERGENIC
3R	26692754	3R_26692754_SNP [dm3] 3R_30867032_SNP [dm6]	A	G	4.881e^-5	0.89	UPSTREAM Cpr100A INTERGENIC
3R	26697927	3R_26697927_SNP [dm3] 3R_30872205_SNP [dm6]	G	C	4.881e^-5	0.89	SPLICE_SITE_REGION CG15545 INTRON CG15545	TF binding site mE1_TFBS_cad
3R	2350909	3R_2350909_SNP [dm3] 3R_6525187_SNP [dm6]	A	T	4.888e^-5	0.89	INTERGENIC
3L	832259	3L_832259_SNP [dm3] 3L_832259_SNP [dm6]	A	G	4.926e^-5	0.89	SYNONYMOUS_CODING CG13900 UPSTREAM snoRNA:Psi18S-110 DOWNSTREAM snoRNA:Psi28S-3308 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	1021517	3L_1021517_SNP [dm3] 3L_1021517_SNP [dm6]	A	T	4.960e^-5	0.89	INTRON trio
3L	8076321	3L_8076321_SNP [dm3] 3L_8083221_SNP [dm6]	A	G	4.974e^-5	0.89	UPSTREAM CR43974 INTRON Ect4	TF binding site mE1_TFBS_cad
X	10210609	X_10210609_SNP [dm3] X_10316576_SNP [dm6]	C	T	4.994e^-5	0.89	INTRON alpha-Man-I
X	10212146	X_10212146_SNP [dm3] X_10318113_SNP [dm6]	T	A	4.994e^-5	0.89	INTRON alpha-Man-I
X	20880955	X_20880955_SNP [dm3] X_21009928_SNP [dm6]	A	T	5.049e^-5	0.89	INTERGENIC
3L	11110566	3L_11110566_SNP [dm3] 3L_11117466_SNP [dm6]	G	A	5.061e^-5	0.89	SYNONYMOUS_CODING fd68A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	2398346	3L_2398346_SNP [dm3] 3L_2398346_SNP [dm6]	T	A	5.083e^-5	0.89	INTRON CG45186	TF binding site mE1_TFBS_inv

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By genomic position
Variant impact
Gene name

W2 Vial 4 ascension (cm) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results