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=5.056e^-20)
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	54.3202	1.6015e-12

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4580 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
2L	5074858	2L_5074858_DEL [dm3] 2L_5074858_DEL [dm6]	AA	A	1.758e^-8	0.033	INTRON pgant5
2L	2687538	2L_2687538_SNP [dm3] 2L_2687538_SNP [dm6]	C	T	8.225e^-8	0.06	INTRON CG31690
3R	1206780	3R_1206780_DEL [dm3] 3R_5381058_DEL [dm6]	AA	A	1.133e^-7	0.06	INTRON kkv
3R	20661039	3R_20661039_SNP [dm3] 3R_24835317_SNP [dm6]	T	C	1.554e^-7	0.06	UPSTREAM CR45216 & 1 other INTRON sosie	TF binding site BDTNP1_TFBS_dl
2L	4819399	2L_4819399_DEL [dm3] 2L_4819399_DEL [dm6]	AA	A	1.597e^-7	0.06	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	3217742	2L_3217742_DEL [dm3] 2L_3217742_DEL [dm6]	TA	T	4.707e^-7	0.147	INTERGENIC
2L	4820028	2L_4820028_DEL [dm3] 2L_4820028_DEL [dm6]	CATTGTC	C	6.349e^-7	0.148	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	19496052	X_19496052_INS [dm3] X_19602019_INS [dm6]	T	TTT	6.369e^-7	0.148	UPSTREAM CG14220 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	19895004	3R_19895004_SNP [dm3] 3R_24069282_SNP [dm6]	T	C	7.528e^-7	0.148	INTRON 4EHP
3R	20652144	3R_20652144_DEL [dm3] 3R_24826422_DEL [dm6]	ATATTTA	A	8.347e^-7	0.148	CODON_DELETION CG43166 UPSTREAM niki DOWNSTREAM RabX4
2L	2827074	2L_2827074_SNP [dm3] 2L_2827074_SNP [dm6]	A	G	9.721e^-7	0.148	INTRON Duox
3R	13166803	3R_13166803_SNP [dm3] 3R_17341081_SNP [dm6]	T	C	1.101e^-6	0.148	INTRON beat-IIa
2L	12279048	2L_12279048_SNP [dm3] 2L_12279048_SNP [dm6]	G	A	1.349e^-6	0.148	INTRON aret
2L	12283056	2L_12283056_SNP [dm3] 2L_12283056_SNP [dm6]	G	T	1.478e^-6	0.148	INTRON aret
2R	16762358	2R_16762358_SNP [dm3] 2R_20874853_SNP [dm6]	C	T	1.510e^-6	0.148	NON_SYNONYMOUS_CODING Ipk1 INTRON Ipk1
2L	2804588	2L_2804588_SNP [dm3] 2L_2804588_SNP [dm6]	C	G	1.683e^-6	0.148	UPSTREAM daw INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	13355483	3L_13355483_DEL [dm3] 3L_13362383_DEL [dm6]	AT	A	1.695e^-6	0.148	INTERGENIC
2R	6828776	2R_6828776_SNP [dm3] 2R_10941271_SNP [dm6]	T	C	1.752e^-6	0.148	SYNONYMOUS_CODING Spn47C
2L	2827081	2L_2827081_DEL [dm3] 2L_2827081_DEL [dm6]	GTTAG	G	2.117e^-6	0.148	INTRON Duox
3R	20476089	3R_20476089_DEL [dm3] 3R_24650367_DEL [dm6]	TT	T	2.197e^-6	0.148	UPSTREAM puf & 1 other INTRON ash2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
2L	2625695	2L_2625695_SNP [dm3] 2L_2625695_SNP [dm6]	C	A	2.206e^-6	0.148	EXON CR45705
2L	4861953	2L_4861953_DEL [dm3] 2L_4861953_DEL [dm6]	GG	G	2.227e^-6	0.148	INTRON pog
3R	20653625	3R_20653625_SNP [dm3] 3R_24827903_SNP [dm6]	C	T	2.336e^-6	0.148	SYNONYMOUS_CODING RabX4 DOWNSTREAM CG31357
3R	15489993	3R_15489993_SNP [dm3] 3R_19664271_SNP [dm6]	C	A	2.344e^-6	0.148	UPSTREAM CG7432 DOWNSTREAM ort INTERGENIC
2L	14846877	2L_14846877_SNP [dm3] 2L_14846877_SNP [dm6]	T	C	2.374e^-6	0.148	NON_SYNONYMOUS_CODING CG15279 INTRON CG15279
2L	10072028	2L_10072028_SNP [dm3] 2L_10072028_SNP [dm6]	G	C	2.510e^-6	0.148	INTRON CG44153
2L	2628645	2L_2628645_SNP [dm3] 2L_2628645_SNP [dm6]	C	G	2.697e^-6	0.148	UPSTREAM CR45705 INTERGENIC
2L	12289242	2L_12289242_SNP [dm3] 2L_12289242_SNP [dm6]	T	C	2.733e^-6	0.148	UTR_5_PRIME aret INTRON aret	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	4621187	2L_4621187_SNP [dm3] 2L_4621187_SNP [dm6]	A	G	2.776e^-6	0.148	DOWNSTREAM CR44609 INTERGENIC
2L	4830920	2L_4830920_SNP [dm3] 2L_4830920_SNP [dm6]	G	C	2.812e^-6	0.148	UTR_3_PRIME Ir25a UPSTREAM mir-4912 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
2R	18066920	2R_18066920_DEL [dm3] 2R_22179415_DEL [dm6]	TT	T	2.831e^-6	0.148	UPSTREAM CG11170 & 1 other INTRON CG11170	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	4679336	2L_4679336_SNP [dm3] 2L_4679336_SNP [dm6]	A	G	2.996e^-6	0.148	INTERGENIC
2L	6707116	2L_6707116_DEL [dm3] 2L_6707116_DEL [dm6]	TCCC	T	3.126e^-6	0.148	INTRON Tsp
2L	3725084	2L_3725084_SNP [dm3] 2L_3725084_SNP [dm6]	G	A	3.165e^-6	0.148	UTR_3_PRIME Shaw INTRON Shaw
3R	13270270	3R_13270270_DEL [dm3] 3R_17444548_DEL [dm6]	TGT	T	3.397e^-6	0.148	INTRON CG5873
2L	19806150	2L_19806150_SNP [dm3] 2L_19806150_SNP [dm6]	A	G	3.434e^-6	0.148	INTRON sick
2L	2275192	2L_2275192_SNP [dm3] 2L_2275192_SNP [dm6]	G	A	3.546e^-6	0.148	DOWNSTREAM CR43753 INTRON CR43753
2L	3217451	2L_3217451_SNP [dm3] 2L_3217451_SNP [dm6]	G	C	3.614e^-6	0.148	INTERGENIC
2L	2626814	2L_2626814_SNP [dm3] 2L_2626814_SNP [dm6]	T	A	3.624e^-6	0.148	EXON CR45705
2L	4654535	2L_4654535_SNP [dm3] 2L_4654535_SNP [dm6]	G	A	3.666e^-6	0.148	INTERGENIC
2L	6779679	2L_6779679_INS [dm3] 2L_6779679_INS [dm6]	C	TCG	3.813e^-6	0.148	INTRON nrv1
3R	4134760	3R_4134760_SNP [dm3] 3R_8309038_SNP [dm6]	A	G	3.837e^-6	0.148	SYNONYMOUS_CODING CG11693 UPSTREAM mir-4918 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3R	15723694	3R_15723694_SNP [dm3] 3R_19897972_SNP [dm6]	G	A	3.852e^-6	0.148	SYNONYMOUS_CODING CG4733 DOWNSTREAM CG4538 INTRON CG4538
2L	2633508	2L_2633508_SNP [dm3] 2L_2633508_SNP [dm6]	A	T	3.945e^-6	0.148	INTERGENIC
3R	20652456	3R_20652456_SNP [dm3] 3R_24826734_SNP [dm6]	T	A	4.018e^-6	0.148	UTR_3_PRIME RabX4 UPSTREAM CG43166
3R	20652658	3R_20652658_SNP [dm3] 3R_24826936_SNP [dm6]	C	T	4.095e^-6	0.148	UTR_3_PRIME RabX4 UPSTREAM CG43166
X	3656985	X_3656985_INS [dm3] X_3762952_INS [dm6]	A	AAA	4.147e^-6	0.148	INTRON tlk
2L	4679586	2L_4679586_SNP [dm3] 2L_4679586_SNP [dm6]	G	C	4.178e^-6	0.148	INTERGENIC
2L	5196705	2L_5196705_SNP [dm3] 2L_5196705_SNP [dm6]	A	C	4.251e^-6	0.148	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	20652127	3R_20652127_SNP [dm3] 3R_24826405_SNP [dm6]	G	C	4.306e^-6	0.148	NON_SYNONYMOUS_CODING CG43166 UPSTREAM niki DOWNSTREAM RabX4
2L	2638381	2L_2638381_SNP [dm3] 2L_2638381_SNP [dm6]	C	T	4.345e^-6	0.148	INTERGENIC
2L	2998993	2L_2998993_SNP [dm3] 2L_2998993_SNP [dm6]	C	T	4.351e^-6	0.148	UPSTREAM CG17265 DOWNSTREAM CG3558 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_h
2L	12552342	2L_12552342_SNP [dm3] 2L_12552342_SNP [dm6]	T	A	4.380e^-6	0.148	INTERGENIC
2L	2628627	2L_2628627_SNP [dm3] 2L_2628627_SNP [dm6]	A	G	4.381e^-6	0.148	UPSTREAM CR45705 INTERGENIC
2L	12283030	2L_12283030_SNP [dm3] 2L_12283030_SNP [dm6]	C	T	4.518e^-6	0.148	INTRON aret
2L	19549387	2L_19549387_INS [dm3] 2L_19549387_INS [dm6]	T	TGAAT	4.546e^-6	0.148	UPSTREAM Tep4 INTRON Tep4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sbb
3R	20647928	3R_20647928_SNP [dm3] 3R_24822206_SNP [dm6]	C	G	4.845e^-6	0.148	UTR_3_PRIME Saf-B DOWNSTREAM niki	TF binding site mE1_TFBS_cad
2L	5026634	2L_5026634_SNP [dm3] 2L_5026634_SNP [dm6]	C	T	4.905e^-6	0.148	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	4679653	2L_4679653_SNP [dm3] 2L_4679653_SNP [dm6]	G	A	5.097e^-6	0.148	INTERGENIC
3R	22741710	3R_22741710_SNP [dm3] 3R_26915988_SNP [dm6]	C	T	5.244e^-6	0.148	INTRON sda	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2L	2635320	2L_2635320_SNP [dm3] 2L_2635320_SNP [dm6]	A	C	5.257e^-6	0.148	INTERGENIC
3R	20652465	3R_20652465_SNP [dm3] 3R_24826743_SNP [dm6]	T	A	5.271e^-6	0.148	UTR_3_PRIME RabX4 UPSTREAM CG43166
3R	20652561	3R_20652561_SNP [dm3] 3R_24826839_SNP [dm6]	C	A	5.271e^-6	0.148	UTR_3_PRIME RabX4 UPSTREAM CG43166
2L	2827068	2L_2827068_SNP [dm3] 2L_2827068_SNP [dm6]	A	T	5.292e^-6	0.148	INTRON Duox
3R	20652517	3R_20652517_INS [dm3] 3R_24826795_INS [dm6]	A	AGTGTACCTTA...	5.333e^-6	0.148	UTR_3_PRIME RabX4 UPSTREAM CG43166
2R	4171853	2R_4171853_SNP [dm3] 2R_8284348_SNP [dm6]	T	A	5.339e^-6	0.148	INTERGENIC
2L	19004441	2L_19004441_SNP [dm3] 2L_19004441_SNP [dm6]	T	A	5.377e^-6	0.148	INTRON CG31793	TF binding site mE1_TFBS_chinmo
3R	24253120	3R_24253120_SNP [dm3] 3R_28427398_SNP [dm6]	T	G	5.391e^-6	0.148	INTRON beat-VI
3L	6293706	3L_6293706_INS [dm3] 3L_6300606_INS [dm6]	T	TAG	5.499e^-6	0.148	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	20652128	3R_20652128_SNP [dm3] 3R_24826406_SNP [dm6]	G	A	5.510e^-6	0.148	SYNONYMOUS_CODING CG43166 UPSTREAM niki DOWNSTREAM RabX4
3R	20647912	3R_20647912_DEL [dm3] 3R_24822190_DEL [dm6]	AGG	A	5.721e^-6	0.151	UTR_3_PRIME Saf-B DOWNSTREAM niki	TF binding site mE1_TFBS_cad
2L	2921664	2L_2921664_SNP [dm3] 2L_2921664_SNP [dm6]	G	C	5.788e^-6	0.151	INTRON lilli
2L	2637971	2L_2637971_SNP [dm3] 2L_2637971_SNP [dm6]	A	G	6.157e^-6	0.155	INTERGENIC
2L	4833550	2L_4833550_SNP [dm3] 2L_4833550_SNP [dm6]	A	G	6.249e^-6	0.155	SYNONYMOUS_CODING Ir25a
3R	22520225	3R_22520225_INS [dm3] 3R_26694503_INS [dm6]	G	GTTGG	6.388e^-6	0.155	UPSTREAM TwdlQ INTERGENIC
3R	25222382	3R_25222382_DEL [dm3] 3R_29396660_DEL [dm6]	AG	A	6.468e^-6	0.155	INTRON Ptp99A
2L	2632286	2L_2632286_SNP [dm3] 2L_2632286_SNP [dm6]	G	A	6.601e^-6	0.155	INTERGENIC
2R	19616121	2R_19616121_DEL [dm3] 2R_23728598_DEL [dm6]	GG	A	6.681e^-6	0.155	INTRON Sesn
2L	12552359	2L_12552359_SNP [dm3] 2L_12552359_SNP [dm6]	G	A	6.780e^-6	0.155	INTERGENIC
2L	12552355	2L_12552355_SNP [dm3] 2L_12552355_SNP [dm6]	T	C	6.845e^-6	0.155	INTERGENIC
3R	20652418	3R_20652418_SNP [dm3] 3R_24826696_SNP [dm6]	C	G	6.860e^-6	0.155	UTR_3_PRIME RabX4 UPSTREAM CG43166
3R	20656469	3R_20656469_SNP [dm3] 3R_24830747_SNP [dm6]	G	A	6.930e^-6	0.155	START_LOST CG43273 NON_SYNONYMOUS_CODING CG43273 UPSTREAM CG31357	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	20651809	3R_20651809_SNP [dm3] 3R_24826087_SNP [dm6]	A	G	6.986e^-6	0.155	UPSTREAM niki DOWNSTREAM RabX4 INTRON CG43166	transposable element FlyBase
3R	20647911	3R_20647911_SNP [dm3] 3R_24822189_SNP [dm6]	G	T	7.008e^-6	0.155	UTR_3_PRIME Saf-B DOWNSTREAM niki	TF binding site mE1_TFBS_cad
2L	4830032	2L_4830032_SNP [dm3] 2L_4830032_SNP [dm6]	C	T	7.055e^-6	0.155	SPLICE_SITE_REGION CG2976 DOWNSTREAM Ir25a INTRON CG2976 EXON mir-4912	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	4861942	2L_4861942_SNP [dm3] 2L_4861942_SNP [dm6]	A	G	7.089e^-6	0.155	INTRON pog
2L	12043031	2L_12043031_DEL [dm3] 2L_12043031_DEL [dm6]	GG	G	7.191e^-6	0.155	UTR_5_PRIME CG6785	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	20660703	3R_20660703_SNP [dm3] 3R_24834981_SNP [dm6]	T	C	7.358e^-6	0.155	UPSTREAM CR45216 & 1 other INTRON sosie
3R	13166776	3R_13166776_SNP [dm3] 3R_17341054_SNP [dm6]	G	C	7.422e^-6	0.155	INTRON beat-IIa
2L	12280905	2L_12280905_SNP [dm3] 2L_12280905_SNP [dm6]	A	C	7.482e^-6	0.155	INTRON aret	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	5664884	2R_5664884_DEL [dm3] 2R_9777379_DEL [dm6]	GCCCAGAACTCAG...	G	7.636e^-6	0.155	INTRON CG1688
2L	12289447	2L_12289447_SNP [dm3] 2L_12289447_SNP [dm6]	T	G	7.661e^-6	0.155	INTRON aret
2L	2276015	2L_2276015_SNP [dm3] 2L_2276015_SNP [dm6]	G	C	7.729e^-6	0.155	INTRON CR43753 EXON CR43753
3R	20655889	3R_20655889_SNP [dm3] 3R_24830167_SNP [dm6]	T	C	7.968e^-6	0.155	UPSTREAM CG43273 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	2617684	2L_2617684_SNP [dm3] 2L_2617684_SNP [dm6]	C	T	8.051e^-6	0.155	INTERGENIC
3L	17023818	3L_17023818_SNP [dm3] 3L_17030718_SNP [dm6]	G	T	8.081e^-6	0.155	SYNONYMOUS_CODING Ilp8 DOWNSTREAM CG7730
X	19011897	X_19011897_INS [dm3] X_19117864_INS [dm6]	G	GG	8.111e^-6	0.155	INTERGENIC
2L	12552322	2L_12552322_SNP [dm3] 2L_12552322_SNP [dm6]	C	T	8.153e^-6	0.155	INTERGENIC
2L	4833523	2L_4833523_SNP [dm3] 2L_4833523_SNP [dm6]	T	C	8.166e^-6	0.155	SYNONYMOUS_CODING Ir25a
2L	4862010	2L_4862010_SNP [dm3] 2L_4862010_SNP [dm6]	T	C	8.368e^-6	0.157	INTRON pog

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Missing results

By genomic position
Variant impact
Gene name

SegregVariants_2L phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results