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=1.989e^-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_2L_t	0.004011

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.4427	0.0147

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2180 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	21691827	2L_21691827_SNP [dm3] 2L_21691827_SNP [dm6]	G	A	4.307e^-7	0.656	INTRON CG31619
X	19368536	X_19368536_SNP [dm3] X_19474503_SNP [dm6]	G	A	6.996e^-7	0.656	SYNONYMOUS_CODING CG32533 UPSTREAM CG12200	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18411378	3L_18411378_SNP [dm3] 3L_18418278_SNP [dm6]	A	C	3.788e^-6	0.754	INTERGENIC
2L	21702529	2L_21702529_INS [dm3] 2L_21702529_INS [dm6]	A	AAACAGCCACCAAA...	3.862e^-6	0.754	INTRON CG31619
3R	24364663	3R_24364663_SNP [dm3] 3R_28538941_SNP [dm6]	C	T	4.548e^-6	0.754	INTRON Ppn
X	14638071	X_14638071_SNP [dm3] X_14744038_SNP [dm6]	A	T	4.625e^-6	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19368582	X_19368582_SNP [dm3] X_19474549_SNP [dm6]	G	A	4.976e^-6	0.754	NON_SYNONYMOUS_CODING CG32533 UPSTREAM CG12200	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	7609639	3L_7609639_SNP [dm3] 3L_7616539_SNP [dm6]	A	G	5.625e^-6	0.754	INTRON CG33275
3R	25465246	3R_25465246_SNP [dm3] 3R_29639524_SNP [dm6]	T	C	7.117e^-6	0.754	INTRON Dop1R2
2L	15388352	2L_15388352_SNP [dm3] 2L_15388352_SNP [dm6]	C	A	8.432e^-6	0.754	INTERGENIC
3L	3872751	3L_3872751_SNP [dm3] 3L_3872751_SNP [dm6]	A	T	9.089e^-6	0.754	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Ubx
3R	10966801	3R_10966801_SNP [dm3] 3R_15141079_SNP [dm6]	C	T	9.119e^-6	0.754	NON_SYNONYMOUS_CODING CG3987 UPSTREAM CR45600 DOWNSTREAM GlyS	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	22149820	X_22149820_INS [dm3] X_22747984_INS [dm6]	C	CGCC	9.121e^-6	0.754	INTRON CR44997
X	9794055	X_9794055_DEL [dm3] X_9900022_DEL [dm6]	AAACAATATTTTAA...	A	9.400e^-6	0.754	UPSTREAM CG15249 INTERGENIC
2R	16033833	2R_16033833_SNP [dm3] 2R_20146328_SNP [dm6]	T	C	9.790e^-6	0.754	NON_SYNONYMOUS_CODING CG11041
2L	21708060	2L_21708060_SNP [dm3] 2L_21708060_SNP [dm6]	T	A	1.020e^-5	0.754	INTRON CG31619	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA transposable element FlyBase
X	4666281	X_4666281_SNP [dm3] X_4772248_SNP [dm6]	G	A	1.039e^-5	0.754	UPSTREAM Bteb2 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14638048	X_14638048_SNP [dm3] X_14744015_SNP [dm6]	G	A	1.053e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8060936	3R_8060936_SNP [dm3] 3R_12235214_SNP [dm6]	C	T	1.063e^-5	0.754	NON_SYNONYMOUS_CODING Cyp313a2 UPSTREAM Cyp313a5
3R	6702388	3R_6702388_SNP [dm3] 3R_10876666_SNP [dm6]	T	A	1.071e^-5	0.754	DOWNSTREAM CR45195 INTRON Sodh-2
2L	512473	2L_512473_SNP [dm3] 2L_512473_SNP [dm6]	A	C	1.105e^-5	0.754	INTRON ush	regulatory region REDfly_CRMs TF binding site mE1_TFBS_inv
3L	7609670	3L_7609670_SNP [dm3] 3L_7616570_SNP [dm6]	G	A	1.122e^-5	0.754	INTRON CG33275
X	14638047	X_14638047_SNP [dm3] X_14744014_SNP [dm6]	T	G	1.124e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	16763437	3R_16763437_SNP [dm3] 3R_20937715_SNP [dm6]	T	C	1.138e^-5	0.754	INTRON CG31191
3R	26926104	3R_26926104_SNP [dm3] 3R_31100382_SNP [dm6]	T	C	1.183e^-5	0.754	NON_SYNONYMOUS_CODING CG15553
3R	16763618	3R_16763618_SNP [dm3] 3R_20937896_SNP [dm6]	T	A	1.190e^-5	0.754	INTRON CG31191
3R	16763609	3R_16763609_SNP [dm3] 3R_20937887_SNP [dm6]	G	A	1.239e^-5	0.754	INTRON CG31191
X	14638058	X_14638058_SNP [dm3] X_14744025_SNP [dm6]	A	G	1.300e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	512404	2L_512404_SNP [dm3] 2L_512404_SNP [dm6]	T	C	1.332e^-5	0.754	INTRON ush	regulatory region REDfly_CRMs TF binding site mE1_TFBS_inv
2L	2589439	2L_2589439_SNP [dm3] 2L_2589439_SNP [dm6]	A	T	1.436e^-5	0.754	INTERGENIC
3R	24605408	3R_24605408_DEL [dm3] 3R_28779686_DEL [dm6]	CT	A	1.437e^-5	0.754	INTERGENIC
X	9765024	X_9765024_SNP [dm3] X_9870991_SNP [dm6]	C	T	1.440e^-5	0.754	DOWNSTREAM CG45061 INTERGENIC
3L	3872673	3L_3872673_SNP [dm3] 3L_3872673_SNP [dm6]	T	C	1.454e^-5	0.754	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_Ubx
X	14638053	X_14638053_SNP [dm3] X_14744020_SNP [dm6]	T	A	1.471e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20574803	3R_20574803_SNP [dm3] 3R_24749081_SNP [dm6]	T	A	1.502e^-5	0.754	UTR_3_PRIME tok UPSTREAM tld	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10317242	2R_10317242_SNP [dm3] 2R_14429737_SNP [dm6]	G	C	1.508e^-5	0.754	INTRON phyl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	13821096	2L_13821096_SNP [dm3] 2L_13821096_SNP [dm6]	T	C	1.569e^-5	0.754	UPSTREAM b INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	14638005	X_14638005_SNP [dm3] X_14743972_SNP [dm6]	C	T	1.584e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	9764833	X_9764833_SNP [dm3] X_9870800_SNP [dm6]	A	T	1.645e^-5	0.754	DOWNSTREAM CG45061 INTERGENIC
3R	26529461	3R_26529461_SNP [dm3] 3R_30703739_SNP [dm6]	T	G	1.652e^-5	0.754	INTERGENIC
3L	464730	3L_464730_SNP [dm3] 3L_464730_SNP [dm6]	C	T	1.660e^-5	0.754	INTRON klar
2L	21933627	2L_21933627_SNP [dm3] 2L_21933627_SNP [dm6]	T	A	1.712e^-5	0.754	INTERGENIC
2L	512435	2L_512435_DEL [dm3] 2L_512435_DEL [dm6]	TT	T	1.743e^-5	0.754	INTRON ush	regulatory region REDfly_CRMs TF binding site mE1_TFBS_inv
X	14637985	X_14637985_DEL [dm3] X_14743952_DEL [dm6]	TAGAATATTT	T	1.813e^-5	0.754	INTRON NetB	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11999442	3L_11999442_SNP [dm3] 3L_12006342_SNP [dm6]	T	A	1.823e^-5	0.754	INTRON CG6928
2L	11702623	2L_11702623_SNP [dm3] 2L_11702623_SNP [dm6]	C	T	1.891e^-5	0.754	INTERGENIC
3L	18371963	3L_18371963_SNP [dm3] 3L_18378863_SNP [dm6]	T	A	1.914e^-5	0.754	INTERGENIC	TF binding site mE1_TFBS_Kr
3R	26465959	3R_26465959_DEL [dm3] 3R_30640237_DEL [dm6]	CG	C	1.986e^-5	0.754	INTERGENIC
3L	1071260	3L_1071260_DEL [dm3] 3L_1071260_DEL [dm6]	CTTCGCTCTGC...	C	2.022e^-5	0.754	INTRON bab1	TF binding site BDTNP1_TFBS_twi
3L	4057796	3L_4057796_SNP [dm3] 3L_4057796_SNP [dm6]	A	T	2.113e^-5	0.754	SYNONYMOUS_CODING CG1136	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	22008099	2L_22008099_INS [dm3] 2L_22008099_INS [dm6]	T	TT	2.118e^-5	0.754	INTERGENIC
3R	16670978	3R_16670978_DEL [dm3] 3R_20845256_DEL [dm6]	AAAACCTATTC...	A	2.121e^-5	0.754	DOWNSTREAM CG15695 INTERGENIC
3L	18062419	3L_18062419_SNP [dm3] 3L_18069319_SNP [dm6]	G	A	2.132e^-5	0.754	NON_SYNONYMOUS_CODING CG44006 DOWNSTREAM CG44005
2L	16500686	2L_16500686_SNP [dm3] 2L_16500686_SNP [dm6]	T	C	2.170e^-5	0.754	INTRON Tpr2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	24605406	3R_24605406_SNP [dm3] 3R_28779684_SNP [dm6]	A	G	2.341e^-5	0.774	INTERGENIC
2L	13807573	2L_13807573_SNP [dm3] 2L_13807573_SNP [dm6]	G	C	2.533e^-5	0.774	DOWNSTREAM adat INTRON CAH1
3R	22129899	3R_22129899_SNP [dm3] 3R_26304177_SNP [dm6]	C	A	2.554e^-5	0.774	INTERGENIC
2R	16170840	2R_16170840_SNP [dm3] 2R_20283335_SNP [dm6]	T	A	2.583e^-5	0.774	SYNONYMOUS_CODING CG16868	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	22574074	3R_22574074_DEL [dm3] 3R_26748352_DEL [dm6]	ACGGACGCA	A	2.631e^-5	0.774	INTERGENIC
3R	21622577	3R_21622577_SNP [dm3] 3R_25796855_SNP [dm6]	T	C	2.693e^-5	0.774	EXON CR43847	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	9794050	X_9794050_SNP [dm3] X_9900017_SNP [dm6]	T	A	2.709e^-5	0.774	UPSTREAM CG15249 INTERGENIC
2R	6825299	2R_6825299_SNP [dm3] 2R_10937794_SNP [dm6]	G	A	2.737e^-5	0.774	DOWNSTREAM Spn47C INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	12641673	3R_12641673_SNP [dm3] 3R_16815951_SNP [dm6]	A	G	2.803e^-5	0.774	INTRON abd-A	enhancer mE1_CBP_Enhancers regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	21816185	3R_21816185_SNP [dm3] 3R_25990463_SNP [dm6]	T	C	2.836e^-5	0.774	SYNONYMOUS_CODING Nf1	TF binding site mE1_TFBS_sens
2R	5046276	2R_5046276_SNP [dm3] 2R_9158771_SNP [dm6]	T	C	2.984e^-5	0.774	SPLICE_SITE_REGION CG8008 INTRON CG8008
2L	17996916	2L_17996916_SNP [dm3] 2L_17996916_SNP [dm6]	G	C	3.019e^-5	0.774	INTERGENIC
2L	4503091	2L_4503091_SNP [dm3] 2L_4503091_SNP [dm6]	T	G	3.040e^-5	0.774	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	15389284	2L_15389284_SNP [dm3] 2L_15389284_SNP [dm6]	T	C	3.114e^-5	0.774	INTERGENIC
2L	11702562	2L_11702562_SNP [dm3] 2L_11702562_SNP [dm6]	G	C	3.137e^-5	0.774	INTERGENIC
2L	5153746	2L_5153746_SNP [dm3] 2L_5153746_SNP [dm6]	T	A	3.155e^-5	0.774	INTRON Msp300
2L	21688676	2L_21688676_SNP [dm3] 2L_21688676_SNP [dm6]	C	A	3.183e^-5	0.774	INTRON CG31619
X	11218057	X_11218057_SNP [dm3] X_11324024_SNP [dm6]	G	A	3.210e^-5	0.774	DOWNSTREAM l_1_10Bb INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	21365002	2L_21365002_SNP [dm3] 2L_21365002_SNP [dm6]	G	A	3.211e^-5	0.774	NON_SYNONYMOUS_CODING dtr
2L	13891112	2L_13891112_SNP [dm3] 2L_13891112_SNP [dm6]	G	A	3.217e^-5	0.774	INTRON CenG1A
3R	22936285	3R_22936285_SNP [dm3] 3R_27110563_SNP [dm6]	T	C	3.333e^-5	0.774	SYNONYMOUS_CODING gb EXON CR45209	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	26956994	3R_26956994_SNP [dm3] 3R_31131272_SNP [dm6]	A	T	3.336e^-5	0.774	UPSTREAM CG15556 INTERGENIC
2R	9101659	2R_9101659_SNP [dm3] 2R_13214154_SNP [dm6]	C	T	3.412e^-5	0.774	UPSTREAM CG4627 & 1 other INTRON AQP	TF binding site mE1_TFBS_run
2L	17328205	2L_17328205_SNP [dm3] 2L_17328205_SNP [dm6]	T	C	3.564e^-5	0.774	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	18846008	2R_18846008_SNP [dm3] 2R_22958485_SNP [dm6]	T	C	3.699e^-5	0.774	INTERGENIC
3R	18801151	3R_18801151_SNP [dm3] 3R_22975429_SNP [dm6]	G	A	3.699e^-5	0.774	INTERGENIC
2L	4416374	2L_4416374_SNP [dm3] 2L_4416374_SNP [dm6]	T	A	3.713e^-5	0.774	INTRON CG15431
2L	17302634	2L_17302634_SNP [dm3] 2L_17302634_SNP [dm6]	A	G	3.859e^-5	0.774	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	20414753	3R_20414753_SNP [dm3] 3R_24589031_SNP [dm6]	A	G	4.153e^-5	0.774	UPSTREAM mld INTRON mld	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl
3L	10998992	3L_10998992_SNP [dm3] 3L_11005892_SNP [dm6]	G	A	4.185e^-5	0.774	INTRON klu
3R	16923840	3R_16923840_SNP [dm3] 3R_21098118_SNP [dm6]	A	G	4.210e^-5	0.774	UPSTREAM RhoGAP93B DOWNSTREAM CG7044 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	13749041	2L_13749041_SNP [dm3] 2L_13749041_SNP [dm6]	G	A	4.231e^-5	0.774	INTRON CR44846 & 1 other	TF binding site BDTNP1_TFBS_twi
3R	16763675	3R_16763675_SNP [dm3] 3R_20937953_SNP [dm6]	C	G	4.261e^-5	0.774	INTRON CG31191
X	8756926	X_8756926_SNP [dm3] X_8862893_SNP [dm6]	T	G	4.299e^-5	0.774	INTRON CG12075
2R	12457114	2R_12457114_SNP [dm3] 2R_16569609_SNP [dm6]	G	A	4.307e^-5	0.774	NON_SYNONYMOUS_CODING CG4945 DOWNSTREAM RpS15 INTRON CG4945	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	5681952	3L_5681952_SNP [dm3] 3L_5688852_SNP [dm6]	G	T	4.336e^-5	0.774	INTRON sif
3R	18654837	3R_18654837_SNP [dm3] 3R_22829115_SNP [dm6]	C	A	4.401e^-5	0.774	INTERGENIC
2L	17328407	2L_17328407_SNP [dm3] 2L_17328407_SNP [dm6]	T	A	4.442e^-5	0.774	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	10313935	2R_10313935_SNP [dm3] 2R_14426430_SNP [dm6]	G	A	4.477e^-5	0.774	DOWNSTREAM phyl INTERGENIC
3R	16763559	3R_16763559_SNP [dm3] 3R_20937837_SNP [dm6]	A	C	4.563e^-5	0.774	INTRON CG31191
X	20579493	X_20579493_SNP [dm3] X_20708466_SNP [dm6]	C	A	4.607e^-5	0.774	INTERGENIC	regulatory region REDfly_CRMs
3R	10955487	3R_10955487_SNP [dm3] 3R_15129765_SNP [dm6]	T	G	4.627e^-5	0.774	DOWNSTREAM mir-2493 INTRON CG42788
2L	17302472	2L_17302472_SNP [dm3] 2L_17302472_SNP [dm6]	G	T	4.637e^-5	0.774	INTERGENIC	TF binding site mE1_TFBS_sbb
3R	17786640	3R_17786640_SNP [dm3] 3R_21960918_SNP [dm6]	C	T	4.652e^-5	0.774	INTRON Eip93F
3R	22936312	3R_22936312_SNP [dm3] 3R_27110590_SNP [dm6]	G	A	4.662e^-5	0.774	SYNONYMOUS_CODING gb EXON CR45209	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	18062598	3L_18062598_SNP [dm3] 3L_18069498_SNP [dm6]	G	A	4.676e^-5	0.774	DOWNSTREAM CG44005 INTRON CG44006

Showing 1 to 100 of 1,000 entries

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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=5.555e^-10)
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_2R_NS	0.007119
In_3R_K	0.071494

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.159	0.0758
In_3R_K	7.262	0.0265

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2075 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	15879364	3R_15879364_DEL [dm3] 3R_20053642_DEL [dm6]	TT	T	2.011e^-6	0.893	INTRON CG17193	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	1976242	3R_1976242_SNP [dm3] 3R_6150520_SNP [dm6]	A	G	2.097e^-6	0.893	UTR_3_PRIME CG31559
3L	7705321	3L_7705321_DEL [dm3] 3L_7712221_DEL [dm6]	AA	A	2.523e^-6	0.893	INTRON CG32373 & 1 other
2R	7038076	2R_7038076_SNP [dm3] 2R_11150571_SNP [dm6]	T	C	2.542e^-6	0.893	UPSTREAM CG12391 INTRON CG13229	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13677883	3L_13677883_DEL [dm3] 3L_13684783_DEL [dm6]	TT	T	2.565e^-6	0.893	INTRON bru-3
X	7088979	X_7088979_DEL [dm3] X_7194946_DEL [dm6]	GG	G	2.942e^-6	0.893	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	7088963	X_7088963_SNP [dm3] X_7194930_SNP [dm6]	G	A	3.879e^-6	0.893	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	24499219	3R_24499219_SNP [dm3] 3R_28673497_SNP [dm6]	A	G	4.416e^-6	0.893	INTERGENIC
2R	10800918	2R_10800918_SNP [dm3] 2R_14913413_SNP [dm6]	G	A	5.432e^-6	0.893	INTRON CG10249
2R	8831715	2R_8831715_SNP [dm3] 2R_12944210_SNP [dm6]	T	G	7.611e^-6	0.893	INTRON Mdr49
3R	25600926	3R_25600926_SNP [dm3] 3R_29775204_SNP [dm6]	T	C	7.664e^-6	0.893	INTRON kay	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	15098578	3R_15098578_SNP [dm3] 3R_19272856_SNP [dm6]	T	C	8.559e^-6	0.893	INTERGENIC
3R	15143976	3R_15143976_INS [dm3] 3R_19318254_INS [dm6]	C	CT	1.143e^-5	0.893	INTRON Dl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	13880214	2L_13880214_INS [dm3] 2L_13880214_INS [dm6]	A	AA	1.304e^-5	0.893	INTRON CenG1A
3L	1675225	3L_1675225_SNP [dm3] 3L_1675225_SNP [dm6]	G	A	1.364e^-5	0.893	INTRON CG7991	TF binding site mE1_TFBS_HSA
3R	14725001	3R_14725001_SNP [dm3] 3R_18899279_SNP [dm6]	T	A	1.454e^-5	0.893	UTR_3_PRIME CG14297 UPSTREAM Rh2	regulatory region REDfly_CRMs
3L	3890973	3L_3890973_SNP [dm3] 3L_3890973_SNP [dm6]	A	G	1.470e^-5	0.893	DOWNSTREAM CR45422 INTERGENIC
3L	680550	3L_680550_DEL [dm3] 3L_680550_DEL [dm6]	TAT	T	1.488e^-5	0.893	UTR_3_PRIME CG3386 UPSTREAM CG17129 DOWNSTREAM CG3386	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
2L	12179395	2L_12179395_SNP [dm3] 2L_12179395_SNP [dm6]	A	T	1.501e^-5	0.893	INTRON aret
3R	15143982	3R_15143982_SNP [dm3] 3R_19318260_SNP [dm6]	C	T	1.696e^-5	0.893	INTRON Dl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
X	4587468	X_4587468_SNP [dm3] X_4693435_SNP [dm6]	G	A	1.697e^-5	0.893	INTRON ctp	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	5449531	2R_5449531_SNP [dm3] 2R_9562026_SNP [dm6]	G	A	1.698e^-5	0.893	DOWNSTREAM Or45b INTRON CG1809 EXON CR45281
3L	13677839	3L_13677839_SNP [dm3] 3L_13684739_SNP [dm6]	C	T	1.706e^-5	0.893	INTRON bru-3
2L	12179430	2L_12179430_SNP [dm3] 2L_12179430_SNP [dm6]	A	T	1.710e^-5	0.893	INTRON aret
2L	12179419	2L_12179419_SNP [dm3] 2L_12179419_SNP [dm6]	C	T	1.733e^-5	0.893	INTRON aret
3R	20010947	3R_20010947_SNP [dm3] 3R_24185225_SNP [dm6]	A	T	1.793e^-5	0.893	INTERGENIC
2L	12179422	2L_12179422_SNP [dm3] 2L_12179422_SNP [dm6]	G	A	1.801e^-5	0.893	INTRON aret
3R	15144168	3R_15144168_INS [dm3] 3R_19318446_INS [dm6]	C	TGT	1.871e^-5	0.893	INTRON Dl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	11410638	2L_11410638_INS [dm3] 2L_11410638_INS [dm6]	A	AA	1.968e^-5	0.893	INTERGENIC	regulatory region REDfly_CRMs
3R	18116537	3R_18116537_SNP [dm3] 3R_22290815_SNP [dm6]	C	G	2.122e^-5	0.893	INTRON SKIP
2L	12179484	2L_12179484_SNP [dm3] 2L_12179484_SNP [dm6]	G	A	2.156e^-5	0.893	INTRON aret
3L	5343037	3L_5343037_SNP [dm3] 3L_5349937_SNP [dm6]	T	C	2.345e^-5	0.893	INTRON lama
2R	14268526	2R_14268526_SNP [dm3] 2R_18381021_SNP [dm6]	C	G	2.512e^-5	0.893	DOWNSTREAM CG43202 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	4501478	2R_4501478_SNP [dm3] 2R_8613973_SNP [dm6]	G	C	2.601e^-5	0.893	NON_SYNONYMOUS_CODING CG8642 UPSTREAM Cirl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	13677847	3L_13677847_SNP [dm3] 3L_13684747_SNP [dm6]	C	T	2.714e^-5	0.893	INTRON bru-3
2L	19441096	2L_19441096_SNP [dm3] 2L_19441096_SNP [dm6]	A	T	2.761e^-5	0.893	UPSTREAM CG10237 & 1 other INTRON CG10237	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	14133741	3R_14133741_SNP [dm3] 3R_18308019_SNP [dm6]	T	C	2.768e^-5	0.893	INTRON PKD
X	12518903	X_12518903_SNP [dm3] X_12624870_SNP [dm6]	G	C	2.863e^-5	0.893	INTRON CG15728
2L	8837253	2L_8837253_SNP [dm3] 2L_8837253_SNP [dm6]	G	A	2.938e^-5	0.893	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	7200507	3L_7200507_SNP [dm3] 3L_7207407_SNP [dm6]	G	A	2.986e^-5	0.893	INTERGENIC
2L	10264865	2L_10264865_SNP [dm3] 2L_10264865_SNP [dm6]	T	C	3.063e^-5	0.893	SYNONYMOUS_CODING CG18619 UPSTREAM Mob3	TF binding site BDTNP1_TFBS_dl
2R	10521380	2R_10521380_SNP [dm3] 2R_14633875_SNP [dm6]	G	C	3.113e^-5	0.893	INTERGENIC
2L	11133084	2L_11133084_SNP [dm3] 2L_11133084_SNP [dm6]	G	A	3.166e^-5	0.893	SYNONYMOUS_CODING CG4751	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	505010	X_505010_SNP [dm3] X_610977_SNP [dm6]	T	A	3.284e^-5	0.893	UTR_3_PRIME CG13366 INTRON CG13366
2L	3060270	2L_3060270_SNP [dm3] 2L_3060270_SNP [dm6]	T	G	3.417e^-5	0.893	NON_SYNONYMOUS_CODING CG3523	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	12340909	3L_12340909_SNP [dm3] 3L_12347809_SNP [dm6]	G	C	3.445e^-5	0.893	SYNONYMOUS_CODING CrzR
X	14814936	X_14814936_SNP [dm3] X_14920903_SNP [dm6]	T	G	3.447e^-5	0.893	SYNONYMOUS_CODING CG9503 INTRON Flo2
3L	676864	3L_676864_SNP [dm3] 3L_676864_SNP [dm6]	C	T	3.473e^-5	0.893	INTERGENIC
2R	8444769	2R_8444769_SNP [dm3] 2R_12557264_SNP [dm6]	G	A	3.496e^-5	0.893	SYNONYMOUS_CODING fra	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	10483100	2L_10483100_SNP [dm3] 2L_10483100_SNP [dm6]	G	A	3.512e^-5	0.893	UPSTREAM Grip75 DOWNSTREAM RluA-2 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA
X	4576081	X_4576081_SNP [dm3] X_4682048_SNP [dm6]	G	A	3.523e^-5	0.893	SYNONYMOUS_CODING Pp2C1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	18983329	X_18983329_SNP [dm3] X_19089296_SNP [dm6]	G	A	3.564e^-5	0.893	INTERGENIC
2R	9308858	2R_9308858_SNP [dm3] 2R_13421353_SNP [dm6]	T	C	3.622e^-5	0.893	SYNONYMOUS_CODING CG42321
3R	25600917	3R_25600917_SNP [dm3] 3R_29775195_SNP [dm6]	A	T	3.668e^-5	0.893	INTRON kay	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	14818860	X_14818860_SNP [dm3] X_14924827_SNP [dm6]	T	C	3.720e^-5	0.893	INTRON Flo2
3R	25486259	3R_25486259_SNP [dm3] 3R_29660537_SNP [dm6]	A	T	3.781e^-5	0.893	UPSTREAM Dop1R2 INTERGENIC
2R	14245023	2R_14245023_SNP [dm3] 2R_18357518_SNP [dm6]	G	T	3.870e^-5	0.893	UPSTREAM sbb INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	5113619	2L_5113619_SNP [dm3] 2L_5113619_SNP [dm6]	C	T	3.912e^-5	0.893	INTRON Msp300	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21581956	3R_21581956_SNP [dm3] 3R_25756234_SNP [dm6]	A	T	3.938e^-5	0.893	INTRON LpR1
3R	4009619	3R_4009619_SNP [dm3] 3R_8183897_SNP [dm6]	C	A	3.944e^-5	0.893	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	6825155	2R_6825155_SNP [dm3] 2R_10937650_SNP [dm6]	A	C	3.970e^-5	0.893	DOWNSTREAM Spn47C INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	7705418	3L_7705418_SNP [dm3] 3L_7712318_SNP [dm6]	T	A	3.990e^-5	0.893	INTRON CG32373 & 1 other
2R	14245486	2R_14245486_SNP [dm3] 2R_18357981_SNP [dm6]	C	T	4.009e^-5	0.893	UPSTREAM sbb INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	12340849	3L_12340849_SNP [dm3] 3L_12347749_SNP [dm6]	G	A	4.028e^-5	0.893	SYNONYMOUS_CODING CrzR
3R	16252598	3R_16252598_SNP [dm3] 3R_20426876_SNP [dm6]	G	C	4.040e^-5	0.893	INTRON Gfrl
X	505221	X_505221_DEL [dm3] X_611188_DEL [dm6]	CCCCACGAATACTGCACAAA...	C	4.048e^-5	0.893	UTR_3_PRIME CG13366 INTRON CG13366	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	14428237	3R_14428237_SNP [dm3] 3R_18602515_SNP [dm6]	G	A	4.069e^-5	0.893	INTRON qin & 1 other
3R	25673500	3R_25673500_DEL [dm3] 3R_29847778_DEL [dm6]	TAATGT	T	4.096e^-5	0.893	INTRON Cad99C
3R	25673509	3R_25673509_SNP [dm3] 3R_29847787_SNP [dm6]	C	T	4.096e^-5	0.893	INTRON Cad99C
3L	20667234	3L_20667234_SNP [dm3] 3L_20674134_SNP [dm6]	G	A	4.112e^-5	0.893	INTERGENIC
3R	4514610	3R_4514610_SNP [dm3] 3R_8688888_SNP [dm6]	C	T	4.151e^-5	0.893	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_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10076757	2L_10076757_SNP [dm3] 2L_10076757_SNP [dm6]	T	C	4.183e^-5	0.893	INTRON CG44153	TF binding site mE1_TFBS_cad
X	561120	X_561120_SNP [dm3] X_667087_SNP [dm6]	A	G	4.192e^-5	0.893	INTERGENIC
X	20580471	X_20580471_SNP [dm3] X_20709444_SNP [dm6]	A	T	4.218e^-5	0.893	INTERGENIC	regulatory region REDfly_CRMs
3R	21581946	3R_21581946_SNP [dm3] 3R_25756224_SNP [dm6]	C	T	4.222e^-5	0.893	INTRON LpR1
3R	23998234	3R_23998234_SNP [dm3] 3R_28172512_SNP [dm6]	A	T	4.272e^-5	0.893	INTRON CG34354
X	21892943	X_21892943_SNP [dm3] X_22491107_SNP [dm6]	T	A	4.400e^-5	0.893	UPSTREAM l_1_G0196 & 1 other INTRON l_1_G0196
X	8813199	X_8813199_INS [dm3] X_8919166_INS [dm6]	G	GAG	4.629e^-5	0.893	DOWNSTREAM CR44111 INTRON rdgA
2R	15088579	2R_15088579_SNP [dm3] 2R_19201074_SNP [dm6]	A	G	4.632e^-5	0.893	INTRON hppy
2L	5113550	2L_5113550_SNP [dm3] 2L_5113550_SNP [dm6]	G	T	4.645e^-5	0.893	INTRON Msp300	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	4505288	2R_4505288_SNP [dm3] 2R_8617783_SNP [dm6]	G	T	4.651e^-5	0.893	SYNONYMOUS_CODING Cirl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	11418546	2L_11418546_SNP [dm3] 2L_11418546_SNP [dm6]	A	G	4.657e^-5	0.893	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14981531	3R_14981531_SNP [dm3] 3R_19155809_SNP [dm6]	C	G	4.659e^-5	0.893	INTRON CG11779	TF binding site mE1_TFBS_sens
X	18229558	X_18229558_SNP [dm3] X_18335525_SNP [dm6]	A	T	4.676e^-5	0.893	INTRON CG6123
3L	9440661	3L_9440661_SNP [dm3] 3L_9447561_SNP [dm6]	C	A	4.714e^-5	0.893	INTRON CG3529	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_zfh1
3R	15143970	3R_15143970_SNP [dm3] 3R_19318248_SNP [dm6]	T	A	4.719e^-5	0.893	INTRON Dl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	20010887	3R_20010887_SNP [dm3] 3R_24185165_SNP [dm6]	C	G	4.763e^-5	0.893	INTERGENIC
3L	677215	3L_677215_SNP [dm3] 3L_677215_SNP [dm6]	C	T	4.812e^-5	0.893	DOWNSTREAM CG17129 INTERGENIC
2R	11700156	2R_11700156_SNP [dm3] 2R_15812651_SNP [dm6]	A	G	4.870e^-5	0.893	INTRON tun & 1 other
3R	5688359	3R_5688359_SNP [dm3] 3R_9862637_SNP [dm6]	T	A	4.920e^-5	0.893	INTRON Teh1
2L	10484777	2L_10484777_SNP [dm3] 2L_10484777_SNP [dm6]	A	T	5.022e^-5	0.893	DOWNSTREAM CG7456 INTRON Grip75	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	7088954	X_7088954_SNP [dm3] X_7194921_SNP [dm6]	G	A	5.057e^-5	0.893	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	24492880	3R_24492880_SNP [dm3] 3R_28667158_SNP [dm6]	A	G	5.144e^-5	0.893	INTERGENIC
2R	6596633	2R_6596633_SNP [dm3] 2R_10709128_SNP [dm6]	C	T	5.152e^-5	0.893	SYNONYMOUS_CODING stan	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	14133624	3R_14133624_DEL [dm3] 3R_18307902_DEL [dm6]	TG	T	5.207e^-5	0.893	INTRON PKD	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	14981738	3R_14981738_SNP [dm3] 3R_19156016_SNP [dm6]	A	G	5.231e^-5	0.893	SYNONYMOUS_CODING CG11779	TF binding site mE1_TFBS_sens
3L	22888702	3L_22888702_SNP [dm3] 3L_22895602_SNP [dm6]	A	G	5.255e^-5	0.893	UPSTREAM CR44688 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	10891132	X_10891132_SNP [dm3] X_10997099_SNP [dm6]	A	G	5.280e^-5	0.893	INTRON CG42339
3R	5902226	3R_5902226_DEL [dm3] 3R_10076504_DEL [dm6]	ACATGAA	A	5.288e^-5	0.893	INTERGENIC
3R	19029915	3R_19029915_SNP [dm3] 3R_23204193_SNP [dm6]	T	C	5.453e^-5	0.893	UPSTREAM fzo INTRON cnc

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By genomic position
Variant impact
Gene name

se_PhototaxisScor_4w phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results