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=2.899e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1990 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	5025290	2L_5025290_SNP [dm3] 2L_5025290_SNP [dm6]	G	T	1.232e^-7	0.231	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_Trl
2R	17220640	2R_17220640_SNP [dm3] 2R_21333135_SNP [dm6]	C	T	3.330e^-7	0.299	SYNONYMOUS_CODING dom UPSTREAM snoRNA:Psi18S-1389a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	17221075	2R_17221075_SNP [dm3] 2R_21333570_SNP [dm6]	C	T	4.788e^-7	0.299	SYNONYMOUS_CODING dom UPSTREAM snoRNA:Psi18S-1389a & 1 other	TF binding site mE1_TFBS_cad
2L	5025252	2L_5025252_SNP [dm3] 2L_5025252_SNP [dm6]	C	A	6.600e^-7	0.309	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_Trl
2R	17220646	2R_17220646_SNP [dm3] 2R_21333141_SNP [dm6]	T	C	8.706e^-7	0.326	SYNONYMOUS_CODING dom UPSTREAM snoRNA:Psi18S-1389a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	12955420	X_12955420_SNP [dm3] X_13061387_SNP [dm6]	G	C	1.221e^-6	0.357	UPSTREAM mir-971 INTRON rad
2R	7213844	2R_7213844_SNP [dm3] 2R_11326339_SNP [dm6]	G	A	1.333e^-6	0.357	INTRON sha	TF binding site mE1_TFBS_Trl
2L	5025248	2L_5025248_SNP [dm3] 2L_5025248_SNP [dm6]	A	G	4.208e^-6	0.827	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_Trl
X	19647084	X_19647084_SNP [dm3] X_19753051_SNP [dm6]	C	G	4.542e^-6	0.827	INTRON Pmp70	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt mE1_TFBS_sens
3L	21612306	3L_21612306_SNP [dm3] 3L_21619206_SNP [dm6]	C	A	4.570e^-6	0.827	DOWNSTREAM CG7166 INTRON CG11307	TF binding site mE1_TFBS_HSA
3R	3543896	3R_3543896_SNP [dm3] 3R_7718174_SNP [dm6]	A	C	4.978e^-6	0.827	INTERGENIC
3L	21612307	3L_21612307_SNP [dm3] 3L_21619207_SNP [dm6]	A	C	5.295e^-6	0.827	DOWNSTREAM CG7166 INTRON CG11307	TF binding site mE1_TFBS_HSA
X	12955430	X_12955430_SNP [dm3] X_13061397_SNP [dm6]	A	G	6.237e^-6	0.893	UPSTREAM mir-971 INTRON rad
2R	17220550	2R_17220550_SNP [dm3] 2R_21333045_SNP [dm6]	A	G	6.992e^-6	0.893	SYNONYMOUS_CODING dom UPSTREAM snoRNA:Psi18S-1389a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5025236	2L_5025236_SNP [dm3] 2L_5025236_SNP [dm6]	A	C	7.270e^-6	0.893	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_Trl
2L	5025247	2L_5025247_SNP [dm3] 2L_5025247_SNP [dm6]	T	A	9.113e^-6	0.893	INTRON vkg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_Trl
2R	14077242	2R_14077242_SNP [dm3] 2R_18189737_SNP [dm6]	A	C	9.652e^-6	0.893	DOWNSTREAM CG14500 INTRON CG33958
3R	18968168	3R_18968168_SNP [dm3] 3R_23142446_SNP [dm6]	T	G	9.786e^-6	0.893	UPSTREAM hh INTERGENIC	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_zfh1
2R	5295020	2R_5295020_SNP [dm3] 2R_9407515_SNP [dm6]	G	C	9.938e^-6	0.893	INTRON wun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3L	461631	3L_461631_SNP [dm3] 3L_461631_SNP [dm6]	C	G	9.999e^-6	0.893	INTRON klar
2L	1094471	2L_1094471_SNP [dm3] 2L_1094471_SNP [dm6]	T	G	1.019e^-5	0.893	INTRON CG4629
3L	10109219	3L_10109219_DEL [dm3] 3L_10116119_DEL [dm6]	TT	T	1.051e^-5	0.893	INTRON dpr6
3L	2147069	3L_2147069_SNP [dm3] 3L_2147069_SNP [dm6]	T	C	1.095e^-5	0.893	INTRON zormin
2R	14273279	2R_14273279_SNP [dm3] 2R_18385774_SNP [dm6]	C	T	1.217e^-5	0.904	UPSTREAM CG15067 & 1 other DOWNSTREAM CG18107 INTERGENIC
3L	21916473	3L_21916473_SNP [dm3] 3L_21923373_SNP [dm6]	A	G	1.239e^-5	0.904	UTR_3_PRIME mub INTRON mub
2L	15859794	2L_15859794_SNP [dm3] 2L_15859794_SNP [dm6]	A	G	1.275e^-5	0.904	INTERGENIC	TF binding site mE1_TFBS_sbb
3R	19227864	3R_19227864_SNP [dm3] 3R_23402142_SNP [dm6]	A	C	1.301e^-5	0.904	UPSTREAM Ir94d DOWNSTREAM CG17380 INTERGENIC
3R	19227859	3R_19227859_SNP [dm3] 3R_23402137_SNP [dm6]	C	A	1.401e^-5	0.904	UPSTREAM Ir94d DOWNSTREAM CG17380 INTERGENIC
2R	14886513	2R_14886513_SNP [dm3] 2R_18999008_SNP [dm6]	T	C	1.492e^-5	0.904	INTRON tn
2R	17220553	2R_17220553_SNP [dm3] 2R_21333048_SNP [dm6]	C	T	1.511e^-5	0.904	SYNONYMOUS_CODING dom UPSTREAM snoRNA:Psi18S-1389a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	10853015	2R_10853015_SNP [dm3] 2R_14965510_SNP [dm6]	A	T	1.528e^-5	0.904	UPSTREAM ckn INTRON ckn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_Trl
2L	3681226	2L_3681226_SNP [dm3] 2L_3681226_SNP [dm6]	A	T	1.542e^-5	0.904	INTRON CG34340
3L	21460609	3L_21460609_SNP [dm3] 3L_21467509_SNP [dm6]	G	A	1.646e^-5	0.911	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10695726	3L_10695726_SNP [dm3] 3L_10702626_SNP [dm6]	A	C	1.667e^-5	0.911	INTERGENIC
3R	7334298	3R_7334298_SNP [dm3] 3R_11508576_SNP [dm6]	G	C	1.700e^-5	0.911	INTERGENIC
2L	2805620	2L_2805620_SNP [dm3] 2L_2805620_SNP [dm6]	G	A	1.795e^-5	0.912	INTRON daw	TF binding site mE1_TFBS_Trl
2R	9976074	2R_9976074_SNP [dm3] 2R_14088569_SNP [dm6]	C	T	1.818e^-5	0.912	INTRON Prosap
3L	21612312	3L_21612312_SNP [dm3] 3L_21619212_SNP [dm6]	C	T	1.892e^-5	0.912	DOWNSTREAM CG7166 INTRON CG11307	TF binding site mE1_TFBS_HSA
3R	16230634	3R_16230634_SNP [dm3] 3R_20404912_SNP [dm6]	C	G	1.897e^-5	0.912	INTRON Gfrl
2R	9976072	2R_9976072_SNP [dm3] 2R_14088567_SNP [dm6]	C	A	1.989e^-5	0.913	INTRON Prosap
2L	5582238	2L_5582238_SNP [dm3] 2L_5582238_SNP [dm6]	G	T	1.997e^-5	0.913	INTERGENIC
2L	5296159	2L_5296159_SNP [dm3] 2L_5296159_SNP [dm6]	A	G	2.098e^-5	0.92	INTRON vri
3R	10187071	3R_10187071_SNP [dm3] 3R_14361349_SNP [dm6]	C	A	2.162e^-5	0.92	UTR_5_PRIME CG31320 INTRON NK7.1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	5151102	3R_5151102_SNP [dm3] 3R_9325380_SNP [dm6]	G	A	2.239e^-5	0.92	INTRON CG8861
3L	3749170	3L_3749170_DEL [dm3] 3L_3749170_DEL [dm6]	AA	A	2.286e^-5	0.92	INTRON CG32264
3R	12809881	3R_12809881_SNP [dm3] 3R_16984159_SNP [dm6]	T	G	2.294e^-5	0.92	INTRON CG18622	TF binding site mE1_TFBS_cad
2L	14787342	2L_14787342_SNP [dm3] 2L_14787342_SNP [dm6]	C	A	2.353e^-5	0.92	INTERGENIC
2R	17467033	2R_17467033_SNP [dm3] 2R_21579528_SNP [dm6]	A	C	2.479e^-5	0.92	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	19646959	X_19646959_SNP [dm3] X_19752926_SNP [dm6]	G	A	2.494e^-5	0.92	INTRON Pmp70	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt
X	16171867	X_16171867_SNP [dm3] X_16277834_SNP [dm6]	A	T	2.638e^-5	0.92	UPSTREAM eas DOWNSTREAM Prosalpha4 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	17220034	2R_17220034_SNP [dm3] 2R_21332529_SNP [dm6]	A	T	2.921e^-5	0.92	SYNONYMOUS_CODING dom DOWNSTREAM snoRNA:Me28S-A2589c	TF binding site mE1_TFBS_cad
3L	517362	3L_517362_SNP [dm3] 3L_517362_SNP [dm6]	T	A	2.942e^-5	0.92	INTRON klar
3R	19062061	3R_19062061_SNP [dm3] 3R_23236339_SNP [dm6]	A	T	3.024e^-5	0.92	INTRON CG4467
2L	10956528	2L_10956528_SNP [dm3] 2L_10956528_SNP [dm6]	T	G	3.040e^-5	0.92	INTRON dpr2
2R	14890425	2R_14890425_SNP [dm3] 2R_19002920_SNP [dm6]	C	T	3.048e^-5	0.92	UTR_3_PRIME tn INTRON tn
3R	24579135	3R_24579135_SNP [dm3] 3R_28753413_SNP [dm6]	C	T	3.125e^-5	0.92	INTERGENIC
3L	18034476	3L_18034476_SNP [dm3] 3L_18041376_SNP [dm6]	T	C	3.285e^-5	0.92	INTRON Eip75B & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
2R	18643452	2R_18643452_SNP [dm3] 2R_22755947_SNP [dm6]	A	G	3.315e^-5	0.92	UPSTREAM CR30267 DOWNSTREAM CG13526 INTRON CG42260	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	14417449	2R_14417449_INS [dm3] 2R_18529944_INS [dm6]	A	AA	3.473e^-5	0.92	INTRON CG10924	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15874214	3L_15874214_SNP [dm3] 3L_15881114_SNP [dm6]	T	A	3.511e^-5	0.92	INTRON pHCl
2L	2585992	2L_2585992_SNP [dm3] 2L_2585992_SNP [dm6]	A	C	3.694e^-5	0.92	UPSTREAM Drp1 INTERGENIC	TF binding site mE1_TFBS_HSA
3R	18958333	3R_18958333_SNP [dm3] 3R_23132611_SNP [dm6]	G	A	3.883e^-5	0.92	INTRON hh	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	17358511	3R_17358511_DEL [dm3] 3R_21532789_DEL [dm6]	TTATGTAAAG	T	3.902e^-5	0.92	INTRON CR43372
2R	9052468	2R_9052468_SNP [dm3] 2R_13164963_SNP [dm6]	G	A	3.943e^-5	0.92	INTRON GLaz
3R	7329746	3R_7329746_SNP [dm3] 3R_11504024_SNP [dm6]	T	C	4.237e^-5	0.92	INTRON dpr5
3R	23145161	3R_23145161_SNP [dm3] 3R_27319439_SNP [dm6]	T	C	4.321e^-5	0.92	DOWNSTREAM CR44287 INTRON CG3339	TF binding site mE1_TFBS_chinmo
2R	12809569	2R_12809569_SNP [dm3] 2R_16922064_SNP [dm6]	T	G	4.333e^-5	0.92	INTERGENIC
2L	14787326	2L_14787326_SNP [dm3] 2L_14787326_SNP [dm6]	C	T	4.358e^-5	0.92	INTERGENIC
3L	3193101	3L_3193101_SNP [dm3] 3L_3193101_SNP [dm6]	C	T	4.491e^-5	0.92	UTR_5_PRIME Hsp83 UPSTREAM Hsp83 & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	2408859	2R_2408859_SNP [dm3] 2R_6521354_SNP [dm6]	A	T	4.533e^-5	0.92	INTRON jing
3L	6974392	3L_6974392_SNP [dm3] 3L_6981292_SNP [dm6]	A	C	4.575e^-5	0.92	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	11433230	3L_11433230_SNP [dm3] 3L_11440130_SNP [dm6]	C	T	4.580e^-5	0.92	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12799626	2R_12799626_SNP [dm3] 2R_16912121_SNP [dm6]	T	C	4.607e^-5	0.92	INTERGENIC
X	15498914	X_15498914_INS [dm3] X_15604881_INS [dm6]	T	GA	4.613e^-5	0.92	UTR_3_PRIME sog	TF binding site BDTNP1_TFBS_dl
2L	15567434	2L_15567434_SNP [dm3] 2L_15567434_SNP [dm6]	A	C	4.628e^-5	0.92	INTRON kek3
2L	15567435	2L_15567435_SNP [dm3] 2L_15567435_SNP [dm6]	G	A	4.628e^-5	0.92	INTRON kek3
3L	8865817	3L_8865817_SNP [dm3] 3L_8872717_SNP [dm6]	A	G	4.663e^-5	0.92	INTRON dally	TF binding site BDTNP1_TFBS_twi
X	19646998	X_19646998_SNP [dm3] X_19752965_SNP [dm6]	A	G	4.674e^-5	0.92	INTRON Pmp70	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt mE1_TFBS_sens
3L	22591076	3L_22591076_SNP [dm3] 3L_22597976_SNP [dm6]	A	C	4.686e^-5	0.92	INTRON CG14459
3R	19840221	3R_19840221_SNP [dm3] 3R_24014499_SNP [dm6]	A	T	4.731e^-5	0.92	INTRON KrT95D
3R	19228229	3R_19228229_SNP [dm3] 3R_23402507_SNP [dm6]	A	G	4.791e^-5	0.92	UPSTREAM Ir94d DOWNSTREAM CG17380 INTERGENIC
2R	10914693	2R_10914693_SNP [dm3] 2R_15027188_SNP [dm6]	C	T	4.817e^-5	0.92	INTRON hbs	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	18227469	2L_18227469_SNP [dm3] 2L_18227469_SNP [dm6]	T	C	4.827e^-5	0.92	INTRON CG42750
3L	8474200	3L_8474200_SNP [dm3] 3L_8481100_SNP [dm6]	G	A	4.846e^-5	0.92	INTRON CG43163	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	21623173	3L_21623173_SNP [dm3] 3L_21630073_SNP [dm6]	A	G	4.921e^-5	0.92	DOWNSTREAM MED1 INTRON MED1
3L	3769838	3L_3769838_SNP [dm3] 3L_3769838_SNP [dm6]	T	A	4.931e^-5	0.92	INTRON CG32264
2R	5292972	2R_5292972_SNP [dm3] 2R_9405467_SNP [dm6]	G	A	4.989e^-5	0.92	INTRON wun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	15567445	2L_15567445_SNP [dm3] 2L_15567445_SNP [dm6]	A	T	5.048e^-5	0.92	INTRON kek3
3R	16581131	3R_16581131_SNP [dm3] 3R_20755409_SNP [dm6]	G	A	5.068e^-5	0.92	SYNONYMOUS_CODING CG42322 UTR_3_PRIME CG42322	TF binding site mE1_TFBS_inv
3R	2625682	3R_2625682_DEL [dm3] 3R_6799960_DEL [dm6]	TT	T	5.105e^-5	0.92	INTRON Dfd	regulatory region FlyBase REDfly_CRMs TF binding site mE1_TFBS_cnc
2L	4154259	2L_4154259_SNP [dm3] 2L_4154259_SNP [dm6]	C	A	5.153e^-5	0.92	INTERGENIC
3L	21602306	3L_21602306_SNP [dm3] 3L_21609206_SNP [dm6]	A	C	5.157e^-5	0.92	INTRON TfAP-2
3L	1825378	3L_1825378_SNP [dm3] 3L_1825378_SNP [dm6]	A	T	5.167e^-5	0.92	INTRON Cpr62Ba
3L	9746241	3L_9746241_DEL [dm3] 3L_9753141_DEL [dm6]	TGTTGCT	T	5.179e^-5	0.92	CODON_DELETION CG42268
2R	14887846	2R_14887846_SNP [dm3] 2R_19000341_SNP [dm6]	C	T	5.335e^-5	0.92	INTRON tn
3R	10187046	3R_10187046_SNP [dm3] 3R_14361324_SNP [dm6]	A	T	5.478e^-5	0.92	UTR_5_PRIME CG31320 INTRON NK7.1	TF binding site mE1_TFBS_HSA
X	3811411	X_3811411_SNP [dm3] X_3917378_SNP [dm6]	A	T	5.480e^-5	0.92	INTRON CG42541
X	19231182	X_19231182_SNP [dm3] X_19337149_SNP [dm6]	G	A	5.508e^-5	0.92	INTRON nAChRalpha7	TF binding site BDTNP1_TFBS_dl
2R	4799005	2R_4799005_SNP [dm3] 2R_8911500_SNP [dm6]	A	G	5.626e^-5	0.92	NON_SYNONYMOUS_CODING Pgi DOWNSTREAM CG30349	TF binding site mE1_TFBS_cad
3R	2600402	3R_2600402_SNP [dm3] 3R_6774680_SNP [dm6]	A	G	5.684e^-5	0.92	INTRON CR42721	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

pc_Defecation_Paerug phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results