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=4.930e^-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
In_3R_P	0.0009318

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	13.598	0.0011

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2966 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
2R	11580064	2R_11580064_SNP [dm3] 2R_15692559_SNP [dm6]	A	C	1.190e^-6	0.449	NON_SYNONYMOUS_CODING CG30087 DOWNSTREAM CG30088 EXON CR44372
2L	12272691	2L_12272691_INS [dm3] 2L_12272691_INS [dm6]	A	ATA	1.713e^-6	0.449	INTRON aret
3L	12875986	3L_12875986_SNP [dm3] 3L_12882886_SNP [dm6]	T	C	1.729e^-6	0.449	INTERGENIC
2R	12282447	2R_12282447_SNP [dm3] 2R_16394942_SNP [dm6]	G	A	2.577e^-6	0.449	INTRON Sema-2b
2R	13906501	2R_13906501_SNP [dm3] 2R_18018996_SNP [dm6]	A	C	2.713e^-6	0.449	INTRON CG5084
3L	13789012	3L_13789012_SNP [dm3] 3L_13795912_SNP [dm6]	C	T	2.870e^-6	0.449	INTRON bru-3
3L	13789013	3L_13789013_SNP [dm3] 3L_13795913_SNP [dm6]	C	T	2.870e^-6	0.449	INTRON bru-3
2R	10917425	2R_10917425_SNP [dm3] 2R_15029920_SNP [dm6]	A	G	3.016e^-6	0.449	INTRON hbs	TF binding site BDTNP1_TFBS_hb mE1_TFBS_cad
3L	12839968	3L_12839968_SNP [dm3] 3L_12846868_SNP [dm6]	A	C	3.176e^-6	0.449	INTRON CG10948	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	17107284	2R_17107284_SNP [dm3] 2R_21219779_SNP [dm6]	G	A	3.645e^-6	0.449	SYNONYMOUS_CODING ASPP	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	2105839	X_2105839_SNP [dm3] X_2211806_SNP [dm6]	G	T	3.829e^-6	0.449	INTRON msta
3L	5880498	3L_5880498_SNP [dm3] 3L_5887398_SNP [dm6]	C	G	4.123e^-6	0.449	INTERGENIC
X	15505151	X_15505151_SNP [dm3] X_15611118_SNP [dm6]	A	G	4.277e^-6	0.449	INTRON sog	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	12875890	3L_12875890_SNP [dm3] 3L_12882790_SNP [dm6]	T	C	4.296e^-6	0.449	INTERGENIC
2R	19719975	2R_19719975_SNP [dm3] 2R_23832452_SNP [dm6]	C	G	4.303e^-6	0.449	INTRON CG5549
2R	13906509	2R_13906509_INS [dm3] 2R_18019004_INS [dm6]	A	AGCTATGCCAGAA...	4.750e^-6	0.449	INTRON CG5084
2R	19312397	2R_19312397_SNP [dm3] 2R_23424874_SNP [dm6]	G	A	4.768e^-6	0.449	INTRON CG9815
3R	14169264	3R_14169264_SNP [dm3] 3R_18343542_SNP [dm6]	A	G	4.988e^-6	0.449	INTRON CG15803
3R	13854142	3R_13854142_SNP [dm3] 3R_18028420_SNP [dm6]	C	T	5.311e^-6	0.449	INTERGENIC
2L	7665675	2L_7665675_SNP [dm3] 2L_7665675_SNP [dm6]	A	G	5.343e^-6	0.449	UPSTREAM Myo28B1 INTRON Slob
2L	8390856	2L_8390856_SNP [dm3] 2L_8390856_SNP [dm6]	T	G	5.665e^-6	0.449	SYNONYMOUS_CODING CG42820	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3840696	2R_3840696_SNP [dm3] 2R_7953191_SNP [dm6]	G	T	5.811e^-6	0.449	INTRON CG14764
3L	12875918	3L_12875918_SNP [dm3] 3L_12882818_SNP [dm6]	A	C	5.875e^-6	0.449	INTERGENIC
X	14681272	X_14681272_SNP [dm3] X_14787239_SNP [dm6]	G	T	6.038e^-6	0.449	UPSTREAM Ag5r DOWNSTREAM rut EXON CR45522
2R	12627802	2R_12627802_SNP [dm3] 2R_16740297_SNP [dm6]	T	C	6.684e^-6	0.449	INTERGENIC
X	15505086	X_15505086_SNP [dm3] X_15611053_SNP [dm6]	T	G	6.935e^-6	0.449	INTRON sog	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11568376	3L_11568376_SNP [dm3] 3L_11575276_SNP [dm6]	C	G	7.016e^-6	0.449	SYNONYMOUS_CODING CG33489 UPSTREAM CG33490	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	1851422	3L_1851422_SNP [dm3] 3L_1851422_SNP [dm6]	G	C	8.120e^-6	0.449	INTRON CG13936
3L	5717704	3L_5717704_SNP [dm3] 3L_5724604_SNP [dm6]	G	T	8.123e^-6	0.449	INTRON sif
3L	5880499	3L_5880499_SNP [dm3] 3L_5887399_SNP [dm6]	T	A	8.272e^-6	0.449	INTERGENIC
2L	12272668	2L_12272668_SNP [dm3] 2L_12272668_SNP [dm6]	G	T	8.373e^-6	0.449	INTRON aret
3R	25141654	3R_25141654_SNP [dm3] 3R_29315932_SNP [dm6]	T	C	8.606e^-6	0.449	INTRON Cnx99A
2R	12282492	2R_12282492_SNP [dm3] 2R_16394987_SNP [dm6]	A	G	8.755e^-6	0.449	INTRON Sema-2b
3L	12876117	3L_12876117_SNP [dm3] 3L_12883017_SNP [dm6]	C	A	8.766e^-6	0.449	INTERGENIC
3R	25141651	3R_25141651_SNP [dm3] 3R_29315929_SNP [dm6]	T	C	9.250e^-6	0.449	INTRON Cnx99A
2L	10273936	2L_10273936_SNP [dm3] 2L_10273936_SNP [dm6]	C	T	9.291e^-6	0.449	INTRON Utx
2R	10281424	2R_10281424_DEL [dm3] 2R_14393919_DEL [dm6]	CGGCTTTAAGGGATAAAAAT...	C	9.617e^-6	0.449	INTERGENIC
2L	10054421	2L_10054421_SNP [dm3] 2L_10054421_SNP [dm6]	G	A	9.865e^-6	0.449	DOWNSTREAM CR44875 INTRON Cpr31A
X	15125193	X_15125193_SNP [dm3] X_15231160_SNP [dm6]	C	A	1.028e^-5	0.449	INTERGENIC
X	8433755	X_8433755_SNP [dm3] X_8539722_SNP [dm6]	A	G	1.058e^-5	0.449	INTRON Nrg
X	6678498	X_6678498_SNP [dm3] X_6784465_SNP [dm6]	C	T	1.063e^-5	0.449	NON_SYNONYMOUS_CODING C3G	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12839957	3L_12839957_SNP [dm3] 3L_12846857_SNP [dm6]	A	T	1.091e^-5	0.449	INTRON CG10948	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2L	11777322	2L_11777322_SNP [dm3] 2L_11777322_SNP [dm6]	G	A	1.092e^-5	0.449	INTERGENIC
3L	12875919	3L_12875919_SNP [dm3] 3L_12882819_SNP [dm6]	T	A	1.121e^-5	0.449	INTERGENIC
3R	14974114	3R_14974114_SNP [dm3] 3R_19148392_SNP [dm6]	A	G	1.122e^-5	0.449	UPSTREAM Ppcs & 1 other DOWNSTREAM CG5835 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Ubx
2R	8990694	2R_8990694_SNP [dm3] 2R_13103189_SNP [dm6]	G	C	1.125e^-5	0.449	UPSTREAM CG44341 INTERGENIC
2R	3840694	2R_3840694_SNP [dm3] 2R_7953189_SNP [dm6]	T	A	1.161e^-5	0.449	INTRON CG14764
2R	13906362	2R_13906362_SNP [dm3] 2R_18018857_SNP [dm6]	A	G	1.167e^-5	0.449	INTRON CG5084
2R	12282481	2R_12282481_SNP [dm3] 2R_16394976_SNP [dm6]	T	C	1.173e^-5	0.449	INTRON Sema-2b
2R	11580013	2R_11580013_SNP [dm3] 2R_15692508_SNP [dm6]	G	A	1.201e^-5	0.451	NON_SYNONYMOUS_CODING CG30087 DOWNSTREAM CG30088 EXON CR44372
3R	8204019	3R_8204019_SNP [dm3] 3R_12378297_SNP [dm6]	A	C	1.234e^-5	0.454	UPSTREAM GstD7 DOWNSTREAM GstD6 INTERGENIC
2L	2389583	2L_2389583_SNP [dm3] 2L_2389583_SNP [dm6]	A	G	1.387e^-5	0.5	UTR_3_PRIME CG43750 DOWNSTREAM CG43750
2R	6653166	2R_6653166_SNP [dm3] 2R_10765661_SNP [dm6]	C	T	1.479e^-5	0.518	INTRON CG33144
2R	16737013	2R_16737013_SNP [dm3] 2R_20849508_SNP [dm6]	C	T	1.513e^-5	0.518	DOWNSTREAM CG9993 INTRON CG17999	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12098534	3L_12098534_SNP [dm3] 3L_12105434_SNP [dm6]	C	G	1.519e^-5	0.518	INTERGENIC
3L	16231793	3L_16231793_SNP [dm3] 3L_16238693_SNP [dm6]	T	C	1.550e^-5	0.518	SYNONYMOUS_CODING l_3_72Dr	TF binding site mE1_TFBS_cad
2R	18874046	2R_18874046_SNP [dm3] 2R_22986523_SNP [dm6]	G	C	1.573e^-5	0.518	UPSTREAM CG9897 INTRON twi EXON CR42742
2R	16935701	2R_16935701_SNP [dm3] 2R_21048196_SNP [dm6]	T	C	1.609e^-5	0.52	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_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
X	8634422	X_8634422_SNP [dm3] X_8740389_SNP [dm6]	T	A	1.786e^-5	0.555	INTERGENIC
3R	7095408	3R_7095408_SNP [dm3] 3R_11269686_SNP [dm6]	A	T	1.820e^-5	0.555	EXON CR31386	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9744284	2R_9744284_SNP [dm3] 2R_13856779_SNP [dm6]	A	G	1.861e^-5	0.555	SYNONYMOUS_CODING tum DOWNSTREAM CR44367	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	10901572	3L_10901572_SNP [dm3] 3L_10908472_SNP [dm6]	C	T	1.872e^-5	0.555	INTERGENIC
3L	5713040	3L_5713040_SNP [dm3] 3L_5719940_SNP [dm6]	G	A	1.920e^-5	0.555	UPSTREAM snoRNA:Me18S-A1494 INTRON sif
3R	25142637	3R_25142637_SNP [dm3] 3R_29316915_SNP [dm6]	G	A	1.939e^-5	0.555	SPLICE_SITE_REGION Cnx99A INTRON Cnx99A	TF binding site BDTNP1_TFBS_da mE1_TFBS_sens
2R	18841412	2R_18841412_SNP [dm3] 2R_22953889_SNP [dm6]	T	C	1.964e^-5	0.555	UPSTREAM CR32835 INTERGENIC
3R	19499155	3R_19499155_SNP [dm3] 3R_23673433_SNP [dm6]	T	A	2.011e^-5	0.555	INTERGENIC
3L	13351847	3L_13351847_SNP [dm3] 3L_13358747_SNP [dm6]	C	T	2.053e^-5	0.555	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	4790653	3L_4790653_SNP [dm3] 3L_4790653_SNP [dm6]	G	A	2.058e^-5	0.555	SYNONYMOUS_CODING RhoGEF64C	TF binding site mE1_TFBS_chinmo
2L	10079342	2L_10079342_SNP [dm3] 2L_10079342_SNP [dm6]	A	G	2.070e^-5	0.555	INTRON CG44153
3L	13927463	3L_13927463_SNP [dm3] 3L_13934363_SNP [dm6]	A	T	2.071e^-5	0.555	UTR_3_PRIME Gl	TF binding site mE1_TFBS_cad
3R	13980325	3R_13980325_SNP [dm3] 3R_18154603_SNP [dm6]	A	G	2.145e^-5	0.56	DOWNSTREAM CG14316 INTERGENIC
3L	12774926	3L_12774926_SNP [dm3] 3L_12781826_SNP [dm6]	A	T	2.149e^-5	0.56	NON_SYNONYMOUS_CODING CG17666 UPSTREAM CG10969
3L	7317463	3L_7317463_SNP [dm3] 3L_7324363_SNP [dm6]	C	A	2.306e^-5	0.571	NON_SYNONYMOUS_CODING Rint1 UPSTREAM RhoGEF4
2L	12994612	2L_12994612_SNP [dm3] 2L_12994612_SNP [dm6]	G	T	2.312e^-5	0.571	INTRON CG12404
2R	16282465	2R_16282465_SNP [dm3] 2R_20394960_SNP [dm6]	T	C	2.378e^-5	0.571	INTERGENIC
3L	13355584	3L_13355584_SNP [dm3] 3L_13362484_SNP [dm6]	A	C	2.390e^-5	0.571	INTERGENIC
3R	14169204	3R_14169204_SNP [dm3] 3R_18343482_SNP [dm6]	T	C	2.410e^-5	0.571	INTRON CG15803
3L	5590806	3L_5590806_SNP [dm3] 3L_5597706_SNP [dm6]	T	C	2.416e^-5	0.571	DOWNSTREAM CG5150 & 1 other INTERGENIC
3L	16767741	3L_16767741_SNP [dm3] 3L_16774641_SNP [dm6]	C	G	2.418e^-5	0.571	SYNONYMOUS_CODING Nrt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	10281175	2R_10281175_SNP [dm3] 2R_14393670_SNP [dm6]	C	G	2.437e^-5	0.571	INTERGENIC
2R	10917298	2R_10917298_SNP [dm3] 2R_15029793_SNP [dm6]	A	G	2.500e^-5	0.573	INTRON hbs	TF binding site mE1_TFBS_cad
2R	3836695	2R_3836695_SNP [dm3] 2R_7949190_SNP [dm6]	A	C	2.524e^-5	0.573	UPSTREAM CG11165 INTRON CG14764	TF binding site BDTNP1_TFBS_da
2L	12994576	2L_12994576_SNP [dm3] 2L_12994576_SNP [dm6]	C	A	2.596e^-5	0.573	INTRON CG12404
3R	14169212	3R_14169212_SNP [dm3] 3R_18343490_SNP [dm6]	T	A	2.621e^-5	0.573	INTRON CG15803
2L	5855604	2L_5855604_SNP [dm3] 2L_5855604_SNP [dm6]	T	C	2.653e^-5	0.573	INTRON TrissinR
3L	5344684	3L_5344684_SNP [dm3] 3L_5351584_SNP [dm6]	C	G	2.664e^-5	0.573	UPSTREAM lama INTRON lama
3L	12098550	3L_12098550_SNP [dm3] 3L_12105450_SNP [dm6]	C	A	2.726e^-5	0.573	INTERGENIC
2L	8217978	2L_8217978_SNP [dm3] 2L_8217978_SNP [dm6]	A	G	2.733e^-5	0.573	UTR_5_PRIME CG8292 DOWNSTREAM Snx6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	18386849	X_18386849_SNP [dm3] X_18492816_SNP [dm6]	G	A	2.759e^-5	0.573	UPSTREAM CG15044 DOWNSTREAM CG15043 INTERGENIC
2R	8984401	2R_8984401_SNP [dm3] 2R_13096896_SNP [dm6]	T	A	2.931e^-5	0.573	INTERGENIC
2R	15430753	2R_15430753_SNP [dm3] 2R_19543248_SNP [dm6]	A	G	2.956e^-5	0.573	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb
2R	15430459	2R_15430459_SNP [dm3] 2R_19542954_SNP [dm6]	C	T	2.963e^-5	0.573	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	2337351	2L_2337351_SNP [dm3] 2L_2337351_SNP [dm6]	A	G	3.145e^-5	0.573	INTRON CG9967 & 1 other
3L	5273681	3L_5273681_SNP [dm3] 3L_5280581_SNP [dm6]	G	C	3.184e^-5	0.573	INTERGENIC
3R	19499582	3R_19499582_SNP [dm3] 3R_23673860_SNP [dm6]	G	C	3.228e^-5	0.573	INTERGENIC	TF binding site mE1_TFBS_inv
2L	16042145	2L_16042145_SNP [dm3] 2L_16042145_SNP [dm6]	T	C	3.241e^-5	0.573	UTR_5_PRIME BicC & 1 other UPSTREAM BicC & 1 other DOWNSTREAM beat-Ic	TF binding site BDTNP1_TFBS_twi
X	8433696	X_8433696_SNP [dm3] X_8539663_SNP [dm6]	C	T	3.254e^-5	0.573	INTRON Nrg
2R	8990693	2R_8990693_SNP [dm3] 2R_13103188_SNP [dm6]	C	G	3.263e^-5	0.573	UPSTREAM CG44341 INTERGENIC
2R	10281171	2R_10281171_SNP [dm3] 2R_14393666_SNP [dm6]	A	G	3.308e^-5	0.573	INTERGENIC
3L	7065826	3L_7065826_SNP [dm3] 3L_7072726_SNP [dm6]	A	C	3.342e^-5	0.573	DOWNSTREAM CG34030 INTRON CG8641	TF binding site mE1_TFBS_inv

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By genomic position
Variant impact
Gene name

Locomot_Activity_SUC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results