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=1.353e^-4)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.7519	0.0564
In_3R_Mo	5.8931	0.0525

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1696 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
3L	13014946	3L_13014946_INS [dm3] 3L_13021846_INS [dm6]	T	AAAGG	1.311e^-7	0.19	UPSTREAM AdenoK INTRON AdenoK	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	9551413	2L_9551413_SNP [dm3] 2L_9551413_SNP [dm6]	G	A	2.030e^-7	0.19	UPSTREAM jp INTRON jp
2R	16670126	2R_16670126_SNP [dm3] 2R_20782621_SNP [dm6]	G	A	1.219e^-6	0.72	INTERGENIC	TF binding site mE1_TFBS_sens
3R	26547598	3R_26547598_SNP [dm3] 3R_30721876_SNP [dm6]	T	C	1.957e^-6	0.72	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19573545	2R_19573545_SNP [dm3] 2R_23686022_SNP [dm6]	G	T	2.204e^-6	0.72	UPSTREAM l_2_efl INTRON St3
3L	13024133	3L_13024133_SNP [dm3] 3L_13031033_SNP [dm6]	T	G	3.031e^-6	0.72	INTRON CG17672	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
2L	17399803	2L_17399803_DEL [dm3] 2L_17399803_DEL [dm6]	TT	T	4.036e^-6	0.72	INTRON CLIP-190
2R	14817766	2R_14817766_SNP [dm3] 2R_18930261_SNP [dm6]	G	C	4.365e^-6	0.72	INTRON sano
3R	25377380	3R_25377380_SNP [dm3] 3R_29551658_SNP [dm6]	G	A	4.708e^-6	0.72	INTERGENIC
2L	5770556	2L_5770556_SNP [dm3] 2L_5770556_SNP [dm6]	C	G	5.226e^-6	0.72	SYNONYMOUS_CODING CG9171 EXON CR31912	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13010086	3L_13010086_SNP [dm3] 3L_13016986_SNP [dm6]	C	T	5.599e^-6	0.72	DOWNSTREAM mRpL20 & 1 other INTERGENIC	TF binding site mE1_TFBS_Ubx
2R	15185605	2R_15185605_SNP [dm3] 2R_19298100_SNP [dm6]	T	G	6.124e^-6	0.72	UPSTREAM Tab2 INTRON Tab2	TF binding site mE1_TFBS_Trl
2L	22307960	2L_22307960_SNP [dm3] 2L_22307960_SNP [dm6]	T	G	6.412e^-6	0.72	UPSTREAM CG17018 INTERGENIC	transposable element FlyBase
X	14760530	X_14760530_SNP [dm3] X_14866497_SNP [dm6]	T	C	6.666e^-6	0.72	INTRON Flo2 & 1 other
3R	13037534	3R_13037534_INS [dm3] 3R_17211812_INS [dm6]	GA	CTTTGGCTACTC...	7.197e^-6	0.72	INTERGENIC
2R	10435524	2R_10435524_SNP [dm3] 2R_14548019_SNP [dm6]	G	T	7.498e^-6	0.72	INTRON ttv
2L	22307965	2L_22307965_SNP [dm3] 2L_22307965_SNP [dm6]	C	A	7.666e^-6	0.72	UPSTREAM CG17018 INTERGENIC	transposable element FlyBase
2L	22307935	2L_22307935_SNP [dm3] 2L_22307935_SNP [dm6]	A	G	8.101e^-6	0.72	UPSTREAM CG17018 INTERGENIC	transposable element FlyBase
2R	15185604	2R_15185604_SNP [dm3] 2R_19298099_SNP [dm6]	G	A	8.527e^-6	0.72	UPSTREAM Tab2 INTRON Tab2	TF binding site mE1_TFBS_Trl
3R	12687652	3R_12687652_SNP [dm3] 3R_16861930_SNP [dm6]	A	C	8.534e^-6	0.72	INTRON iab-8	TF binding site mE1_TFBS_cad
2R	16452141	2R_16452141_SNP [dm3] 2R_20564636_SNP [dm6]	C	T	9.120e^-6	0.72	INTRON qsm
X	13775573	X_13775573_SNP [dm3] X_13881540_SNP [dm6]	G	T	9.159e^-6	0.72	INTRON mamo
3L	13024195	3L_13024195_SNP [dm3] 3L_13031095_SNP [dm6]	C	T	9.169e^-6	0.72	INTRON CG17672	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
3R	13044704	3R_13044704_SNP [dm3] 3R_17218982_SNP [dm6]	G	A	9.362e^-6	0.72	SYNONYMOUS_CODING CG31262 UTR_3_PRIME CG31262
2R	10434832	2R_10434832_SNP [dm3] 2R_14547327_SNP [dm6]	C	T	1.013e^-5	0.72	UPSTREAM CG30076 INTRON ttv
2R	2142085	2R_2142085_SNP [dm3] 2R_6254580_SNP [dm6]	C	A	1.017e^-5	0.72	INTRON Pld	transposable element FlyBase
2L	634354	2L_634354_SNP [dm3] 2L_634354_SNP [dm6]	A	G	1.036e^-5	0.72	INTERGENIC
2R	16485578	2R_16485578_SNP [dm3] 2R_20598073_SNP [dm6]	A	C	1.075e^-5	0.72	INTRON bl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	21808406	2L_21808406_SNP [dm3] 2L_21808406_SNP [dm6]	T	A	1.156e^-5	0.727	INTERGENIC
2R	16670323	2R_16670323_SNP [dm3] 2R_20782818_SNP [dm6]	A	T	1.186e^-5	0.727	INTERGENIC
3L	5242209	3L_5242209_DEL [dm3] 3L_5249109_DEL [dm6]	GAG	G	1.201e^-5	0.727	UPSTREAM shep INTRON shep
3L	13018112	3L_13018112_SNP [dm3] 3L_13025012_SNP [dm6]	G	A	1.251e^-5	0.733	SYNONYMOUS_CODING Zmynd10 DOWNSTREAM snoRNA:Me28S-A774a & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	13407748	2R_13407748_SNP [dm3] 2R_17520243_SNP [dm6]	A	T	1.360e^-5	0.746	UTR_3_PRIME Patronin DOWNSTREAM Patronin
3R	9569924	3R_9569924_SNP [dm3] 3R_13744202_SNP [dm6]	T	G	1.389e^-5	0.746	INTRON CG34383
3L	14373650	3L_14373650_SNP [dm3] 3L_14380550_SNP [dm6]	T	C	1.397e^-5	0.746	INTERGENIC
3L	13014981	3L_13014981_SNP [dm3] 3L_13021881_SNP [dm6]	C	T	1.437e^-5	0.746	UPSTREAM AdenoK INTRON AdenoK	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	843701	X_843701_SNP [dm3] X_949668_SNP [dm6]	C	A	1.510e^-5	0.746	SYNONYMOUS_CODING CG3690
3L	11158202	3L_11158202_SNP [dm3] 3L_11165102_SNP [dm6]	G	T	1.512e^-5	0.746	SYNONYMOUS_CODING Alg10 UPSTREAM CR43989
2L	19393382	2L_19393382_SNP [dm3] 2L_19393382_SNP [dm6]	A	G	1.556e^-5	0.748	UPSTREAM CG31798 INTRON CG17544	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	2214610	2R_2214610_SNP [dm3] 2R_6327105_SNP [dm6]	C	G	1.626e^-5	0.762	INTERGENIC	TF binding site mE1_TFBS_cad transposable element FlyBase
3L	5242137	3L_5242137_SNP [dm3] 3L_5249037_SNP [dm6]	T	C	1.667e^-5	0.762	UPSTREAM shep INTRON shep
3L	2593483	3L_2593483_SNP [dm3] 3L_2593483_SNP [dm6]	A	C	1.786e^-5	0.768	SYNONYMOUS_CODING dos	TF binding site mE1_TFBS_cad
3L	2593376	3L_2593376_SNP [dm3] 3L_2593376_SNP [dm6]	T	A	1.792e^-5	0.768	INTRON dos	TF binding site mE1_TFBS_cad
3R	12907399	3R_12907399_SNP [dm3] 3R_17081677_SNP [dm6]	T	G	1.801e^-5	0.768	UPSTREAM kuk INTRON kuk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	9436691	2L_9436691_SNP [dm3] 2L_9436691_SNP [dm6]	C	G	1.852e^-5	0.772	SYNONYMOUS_CODING CG3769 UPSTREAM RpS28-like & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	12687105	3R_12687105_SNP [dm3] 3R_16861383_SNP [dm6]	C	T	2.019e^-5	0.823	INTRON iab-8	TF binding site mE1_TFBS_cad
2R	16670308	2R_16670308_SNP [dm3] 2R_20782803_SNP [dm6]	A	G	2.121e^-5	0.847	INTERGENIC
X	843474	X_843474_SNP [dm3] X_949441_SNP [dm6]	C	G	2.215e^-5	0.859	NON_SYNONYMOUS_CODING CG3690
3R	4200704	3R_4200704_SNP [dm3] 3R_8374982_SNP [dm6]	G	A	2.280e^-5	0.859	INTRON CG45263
3R	12679975	3R_12679975_SNP [dm3] 3R_16854253_SNP [dm6]	G	T	2.289e^-5	0.859	DOWNSTREAM iab-8 INTRON iab-8 & 1 other EXON iab-4	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	634305	2L_634305_SNP [dm3] 2L_634305_SNP [dm6]	T	A	2.434e^-5	0.891	INTERGENIC
2L	12723512	2L_12723512_SNP [dm3] 2L_12723512_SNP [dm6]	C	T	2.639e^-5	0.891	SYNONYMOUS_CODING MRP	TF binding site BDTNP1_TFBS_bcd mE1_TFBS_sens
3R	12687065	3R_12687065_SNP [dm3] 3R_16861343_SNP [dm6]	C	T	2.706e^-5	0.891	INTRON iab-8	TF binding site mE1_TFBS_cad
3L	12710967	3L_12710967_DEL [dm3] 3L_12717867_DEL [dm6]	ATTA	A	2.746e^-5	0.891	INTERGENIC
X	12901514	X_12901514_SNP [dm3] X_13007481_SNP [dm6]	G	A	2.753e^-5	0.891	INTRON rad
2L	12723518	2L_12723518_SNP [dm3] 2L_12723518_SNP [dm6]	A	G	2.841e^-5	0.891	SYNONYMOUS_CODING MRP	TF binding site BDTNP1_TFBS_bcd mE1_TFBS_sens
2R	6089357	2R_6089357_SNP [dm3] 2R_10201852_SNP [dm6]	C	T	2.851e^-5	0.891	INTERGENIC
2R	16670422	2R_16670422_SNP [dm3] 2R_20782917_SNP [dm6]	T	G	2.869e^-5	0.891	INTERGENIC
3L	5241981	3L_5241981_SNP [dm3] 3L_5248881_SNP [dm6]	G	A	2.896e^-5	0.891	UPSTREAM shep INTRON shep
X	19430691	X_19430691_INS [dm3] X_19536658_INS [dm6]	C	CGCC	2.993e^-5	0.891	INTRON CG32532
3L	12225620	3L_12225620_SNP [dm3] 3L_12232520_SNP [dm6]	G	A	3.039e^-5	0.891	INTRON app
2L	17399522	2L_17399522_SNP [dm3] 2L_17399522_SNP [dm6]	A	G	3.091e^-5	0.891	INTRON CLIP-190
2L	634331	2L_634331_SNP [dm3] 2L_634331_SNP [dm6]	G	T	3.167e^-5	0.891	INTERGENIC
3L	4389296	3L_4389296_SNP [dm3] 3L_4389296_SNP [dm6]	C	A	3.208e^-5	0.891	INTRON slow	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	634314	2L_634314_DEL [dm3] 2L_634314_DEL [dm6]	AT	A	3.241e^-5	0.891	INTERGENIC
X	13205542	X_13205542_SNP [dm3] X_13311509_SNP [dm6]	C	T	3.254e^-5	0.891	INTRON IP3K2
2R	5792037	2R_5792037_SNP [dm3] 2R_9904532_SNP [dm6]	G	C	3.273e^-5	0.891	INTERGENIC
2L	12725317	2L_12725317_SNP [dm3] 2L_12725317_SNP [dm6]	C	T	3.365e^-5	0.891	INTRON MRP
2L	6523453	2L_6523453_SNP [dm3] 2L_6523453_SNP [dm6]	T	A	3.407e^-5	0.891	INTRON CG31637
2L	22307897	2L_22307897_SNP [dm3] 2L_22307897_SNP [dm6]	A	T	3.418e^-5	0.891	UPSTREAM CG17018 INTERGENIC	transposable element FlyBase
2L	634321	2L_634321_SNP [dm3] 2L_634321_SNP [dm6]	C	T	3.463e^-5	0.891	INTERGENIC
3R	12686527	3R_12686527_SNP [dm3] 3R_16860805_SNP [dm6]	T	G	3.485e^-5	0.891	INTRON iab-8	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
2L	12811934	2L_12811934_DEL [dm3] 2L_12811934_DEL [dm6]	GCACT	C	3.511e^-5	0.891	INTERGENIC
3L	8759370	3L_8759370_SNP [dm3] 3L_8766270_SNP [dm6]	T	C	3.515e^-5	0.891	UPSTREAM Fhos INTRON Fhos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	21034401	3R_21034401_DEL [dm3] 3R_25208679_DEL [dm6]	CT	C	3.647e^-5	0.901	UPSTREAM CG13654 & 1 other INTRON CG13654	TF binding site mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	4376840	3L_4376840_SNP [dm3] 3L_4376840_SNP [dm6]	A	G	3.653e^-5	0.901	DOWNSTREAM CR44360 INTRON DopEcR
3R	20552967	3R_20552967_SNP [dm3] 3R_24727245_SNP [dm6]	C	T	3.766e^-5	0.917	INTRON tok	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	6089360	2R_6089360_SNP [dm3] 2R_10201855_SNP [dm6]	A	C	3.929e^-5	0.921	INTERGENIC
X	19010001	X_19010001_DEL [dm3] X_19115968_DEL [dm6]	AG	T	4.083e^-5	0.921	INTERGENIC
3L	10766877	3L_10766877_SNP [dm3] 3L_10773777_SNP [dm6]	C	T	4.139e^-5	0.921	DOWNSTREAM CG43245 INTERGENIC
2L	22310214	2L_22310214_SNP [dm3] 2L_22310214_SNP [dm6]	T	G	4.214e^-5	0.921	INTRON CG17018	transposable element FlyBase
3L	12994053	3L_12994053_SNP [dm3] 3L_13000953_SNP [dm6]	A	G	4.237e^-5	0.921	INTERGENIC
3R	21034404	3R_21034404_SNP [dm3] 3R_25208682_SNP [dm6]	A	C	4.255e^-5	0.921	UPSTREAM CG13654 & 1 other INTRON CG13654	TF binding site mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	12907394	3R_12907394_SNP [dm3] 3R_17081672_SNP [dm6]	C	A	4.298e^-5	0.921	UPSTREAM kuk INTRON kuk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
3L	5242237	3L_5242237_SNP [dm3] 3L_5249137_SNP [dm6]	C	G	4.362e^-5	0.921	UPSTREAM shep INTRON shep
2L	9589572	2L_9589572_SNP [dm3] 2L_9589572_SNP [dm6]	A	G	4.445e^-5	0.921	UTR_5_PRIME CG3841 UPSTREAM CG3841	regulatory region REDfly_CRMs
3L	6351640	3L_6351640_SNP [dm3] 3L_6358540_SNP [dm6]	C	A	4.463e^-5	0.921	INTERGENIC
3L	23078553	3L_23078553_DEL [dm3] 3L_23085453_DEL [dm6]	TT	T	4.495e^-5	0.921	INTERGENIC	transposable element FlyBase
3R	19012467	3R_19012467_SNP [dm3] 3R_23186745_SNP [dm6]	C	T	4.511e^-5	0.921	UTR_3_PRIME cnc
3L	14373494	3L_14373494_SNP [dm3] 3L_14380394_SNP [dm6]	G	T	4.523e^-5	0.921	INTERGENIC
3L	8354552	3L_8354552_SNP [dm3] 3L_8361452_SNP [dm6]	T	A	4.566e^-5	0.921	UPSTREAM Idh INTERGENIC
3R	12906971	3R_12906971_SNP [dm3] 3R_17081249_SNP [dm6]	C	T	4.575e^-5	0.921	UPSTREAM kuk INTRON kuk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	12683709	3R_12683709_SNP [dm3] 3R_16857987_SNP [dm6]	G	T	4.630e^-5	0.921	INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	3283462	2L_3283462_SNP [dm3] 2L_3283462_SNP [dm6]	G	A	4.653e^-5	0.921	INTERGENIC	TF binding site mE1_TFBS_inv
X	3162562	X_3162562_SNP [dm3] X_3268529_SNP [dm6]	C	A	4.837e^-5	0.921	INTRON dnc
2L	646500	2L_646500_SNP [dm3] 2L_646500_SNP [dm6]	C	A	4.889e^-5	0.921	INTRON ds
3R	26061019	3R_26061019_SNP [dm3] 3R_30235297_SNP [dm6]	A	T	4.939e^-5	0.921	INTERGENIC
3R	24902209	3R_24902209_SNP [dm3] 3R_29076487_SNP [dm6]	G	A	4.997e^-5	0.921	INTRON CG11873
2R	16670295	2R_16670295_SNP [dm3] 2R_20782790_SNP [dm6]	G	T	5.027e^-5	0.921	INTERGENIC
2L	9587665	2L_9587665_SNP [dm3] 2L_9587665_SNP [dm6]	T	A	5.031e^-5	0.921	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Sample.size Experience 1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results