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=3.678e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_Mo	0.01798

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	2.7305	0.0984

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1830 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
X	14748016	X_14748016_SNP [dm3] X_14853983_SNP [dm6]	C	A	3.006e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
2R	6622403	2R_6622403_SNP [dm3] 2R_10734898_SNP [dm6]	C	T	3.113e^-6	0.787	UPSTREAM CG7220 INTRON CG7220
2L	5459601	2L_5459601_SNP [dm3] 2L_5459601_SNP [dm6]	T	C	3.393e^-6	0.787	INTERGENIC	TF binding site BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	14748120	X_14748120_SNP [dm3] X_14854087_SNP [dm6]	A	G	3.515e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748327	X_14748327_SNP [dm3] X_14854294_SNP [dm6]	A	T	3.515e^-6	0.787	DOWNSTREAM CG9519 INTRON Flo2
2R	6622249	2R_6622249_INS [dm3] 2R_10734744_INS [dm6]	A	AA	6.878e^-6	0.787	UPSTREAM CG7220 INTRON CG7220
2R	6622252	2R_6622252_MNP [dm3] 2R_10734747_MNP [dm6]	TAC	GTA	6.878e^-6	0.787	UPSTREAM CG7220 INTRON CG7220
2R	6622259	2R_6622259_SNP [dm3] 2R_10734754_SNP [dm6]	C	G	6.878e^-6	0.787	UPSTREAM CG7220 INTRON CG7220
2R	10529846	2R_10529846_SNP [dm3] 2R_14642341_SNP [dm6]	T	G	6.891e^-6	0.787	INTERGENIC
2R	10529851	2R_10529851_SNP [dm3] 2R_14642346_SNP [dm6]	A	G	6.891e^-6	0.787	INTERGENIC
X	14748166	X_14748166_SNP [dm3] X_14854133_SNP [dm6]	G	T	8.915e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748179	X_14748179_SNP [dm3] X_14854146_SNP [dm6]	A	T	8.915e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748180	X_14748180_SNP [dm3] X_14854147_SNP [dm6]	C	T	8.915e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14747991	X_14747991_SNP [dm3] X_14853958_SNP [dm6]	T	C	9.603e^-6	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748377	X_14748377_SNP [dm3] X_14854344_SNP [dm6]	T	C	9.930e^-6	0.787	UTR_3_PRIME CG9519 INTRON Flo2
X	14747941	X_14747941_SNP [dm3] X_14853908_SNP [dm6]	T	A	1.057e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14747743	X_14747743_SNP [dm3] X_14853710_SNP [dm6]	A	G	1.102e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
3R	19204995	3R_19204995_SNP [dm3] 3R_23379273_SNP [dm6]	A	G	1.217e^-5	0.787	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	2908434	X_2908434_SNP [dm3] X_3014401_SNP [dm6]	G	A	1.250e^-5	0.787	INTRON kirre
3L	11925572	3L_11925572_SNP [dm3] 3L_11932472_SNP [dm6]	T	G	1.307e^-5	0.787	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	26077306	3R_26077306_SNP [dm3] 3R_30251584_SNP [dm6]	A	G	1.344e^-5	0.787	DOWNSTREAM CG34299 INTRON CG9682	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
X	5483492	X_5483492_SNP [dm3] X_5589459_SNP [dm6]	G	A	1.368e^-5	0.787	INTERGENIC	TF binding site mE1_TFBS_inv
3R	10915767	3R_10915767_DEL [dm3] 3R_15090045_DEL [dm6]	ATAGATTCAATTCTACA...	A	1.379e^-5	0.787	INTRON CG6966	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	14748028	X_14748028_SNP [dm3] X_14853995_SNP [dm6]	G	T	1.400e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
3R	11900713	3R_11900713_SNP [dm3] 3R_16074991_SNP [dm6]	A	T	1.416e^-5	0.787	SYNONYMOUS_CODING Mhcl INTRON Mhcl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17926749	2R_17926749_SNP [dm3] 2R_22039244_SNP [dm6]	A	G	1.454e^-5	0.787	INTRON CG34370
3R	26077305	3R_26077305_SNP [dm3] 3R_30251583_SNP [dm6]	A	T	1.684e^-5	0.787	DOWNSTREAM CG34299 INTRON CG9682	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
3L	18083332	3L_18083332_SNP [dm3] 3L_18090232_SNP [dm6]	T	G	1.687e^-5	0.787	INTRON CG13698
3L	7449822	3L_7449822_SNP [dm3] 3L_7456722_SNP [dm6]	A	G	1.767e^-5	0.787	SYNONYMOUS_CODING ppk26
3L	7449825	3L_7449825_SNP [dm3] 3L_7456725_SNP [dm6]	C	T	1.767e^-5	0.787	SYNONYMOUS_CODING ppk26
X	14746199	X_14746199_SNP [dm3] X_14852166_SNP [dm6]	C	T	1.783e^-5	0.787	SYNONYMOUS_CODING CG9521 INTRON Flo2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	18700052	3R_18700052_SNP [dm3] 3R_22874330_SNP [dm6]	G	C	1.814e^-5	0.787	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	2908522	X_2908522_SNP [dm3] X_3014489_SNP [dm6]	G	A	1.814e^-5	0.787	INTRON kirre
2R	2024404	2R_2024404_INS [dm3] 2R_6136899_INS [dm6]	A	AA	1.890e^-5	0.787	UPSTREAM CG14589 INTRON EcR
3L	11925809	3L_11925809_SNP [dm3] 3L_11932709_SNP [dm6]	A	G	2.065e^-5	0.787	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	20286602	X_20286602_SNP [dm3] X_20415575_SNP [dm6]	G	A	2.127e^-5	0.787	UPSTREAM Obp19a INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10137081	3L_10137081_SNP [dm3] 3L_10143981_SNP [dm6]	C	T	2.139e^-5	0.787	INTERGENIC
X	12336269	X_12336269_SNP [dm3] X_12442236_SNP [dm6]	A	G	2.158e^-5	0.787	INTRON Pkcdelta
2L	5462385	2L_5462385_INS [dm3] 2L_5462385_INS [dm6]	T	TCTCGT	2.161e^-5	0.787	INTRON mid	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
3L	11926621	3L_11926621_SNP [dm3] 3L_11933521_SNP [dm6]	C	G	2.181e^-5	0.787	SPLICE_SITE_REGION byn INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7266250	2R_7266250_SNP [dm3] 2R_11378745_SNP [dm6]	C	A	2.228e^-5	0.787	INTRON Tsp47F
2R	2024692	2R_2024692_SNP [dm3] 2R_6137187_SNP [dm6]	T	A	2.240e^-5	0.787	UPSTREAM CG14589 INTRON EcR
3R	20377587	3R_20377587_SNP [dm3] 3R_24551865_SNP [dm6]	T	C	2.321e^-5	0.787	INTRON Esyt2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	15334321	3R_15334321_SNP [dm3] 3R_19508599_SNP [dm6]	G	T	2.361e^-5	0.787	UPSTREAM Dys INTRON Dys	TF binding site mE1_TFBS_Trl
2R	14170739	2R_14170739_SNP [dm3] 2R_18283234_SNP [dm6]	A	G	2.484e^-5	0.787	SYNONYMOUS_CODING sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	14170753	2R_14170753_SNP [dm3] 2R_18283248_SNP [dm6]	A	C	2.484e^-5	0.787	SPLICE_SITE_REGION sbb INTRON sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	2024617	2R_2024617_INS [dm3] 2R_6137112_INS [dm6]	T	TTAT	2.545e^-5	0.787	UPSTREAM CG14589 INTRON EcR
3L	11925983	3L_11925983_SNP [dm3] 3L_11932883_SNP [dm6]	T	C	2.672e^-5	0.787	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	13259722	X_13259722_SNP [dm3] X_13365689_SNP [dm6]	T	C	2.789e^-5	0.787	SYNONYMOUS_CODING Syt12	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14747757	X_14747757_SNP [dm3] X_14853724_SNP [dm6]	T	C	2.797e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
2R	17472391	2R_17472391_SNP [dm3] 2R_21584886_SNP [dm6]	C	A	2.912e^-5	0.787	NON_SYNONYMOUS_CODING CG30222 UTR_3_PRIME CG30222
2R	17472400	2R_17472400_SNP [dm3] 2R_21584895_SNP [dm6]	T	C	2.912e^-5	0.787	SYNONYMOUS_CODING CG30222 UTR_3_PRIME CG30222
X	3003793	X_3003793_SNP [dm3] X_3109760_SNP [dm6]	C	T	3.007e^-5	0.787	INTRON kirre
3L	22831215	3L_22831215_SNP [dm3] 3L_22838115_SNP [dm6]	C	A	3.137e^-5	0.787	UTR_3_PRIME CG11226	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
X	14750834	X_14750834_SNP [dm3] X_14856801_SNP [dm6]	A	T	3.146e^-5	0.787	UPSTREAM CG9519 INTRON Flo2
X	12336300	X_12336300_SNP [dm3] X_12442267_SNP [dm6]	A	T	3.196e^-5	0.787	INTRON Pkcdelta
X	12336260	X_12336260_SNP [dm3] X_12442227_SNP [dm6]	A	C	3.378e^-5	0.787	INTRON Pkcdelta
3L	11388928	3L_11388928_SNP [dm3] 3L_11395828_SNP [dm6]	A	G	3.396e^-5	0.787	DOWNSTREAM CG11726 INTERGENIC
3R	26099225	3R_26099225_SNP [dm3] 3R_30273503_SNP [dm6]	C	G	3.491e^-5	0.787	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	14747963	X_14747963_SNP [dm3] X_14853930_SNP [dm6]	A	T	3.495e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	2249372	X_2249372_SNP [dm3] X_2355339_SNP [dm6]	A	G	3.549e^-5	0.787	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl
2L	11609712	2L_11609712_SNP [dm3] 2L_11609712_SNP [dm6]	T	C	3.607e^-5	0.787	DOWNSTREAM spag4 INTRON kek2	TF binding site mE1_TFBS_inv
X	6828122	X_6828122_SNP [dm3] X_6934089_SNP [dm6]	C	G	3.703e^-5	0.787	INTRON CG14431
2R	10529806	2R_10529806_SNP [dm3] 2R_14642301_SNP [dm6]	T	C	3.705e^-5	0.787	INTERGENIC
3L	22839348	3L_22839348_SNP [dm3] 3L_22846248_SNP [dm6]	G	C	3.711e^-5	0.787	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12336250	X_12336250_SNP [dm3] X_12442217_SNP [dm6]	A	C	3.892e^-5	0.787	INTRON Pkcdelta
2R	2060042	2R_2060042_SNP [dm3] 2R_6172537_SNP [dm6]	G	A	3.894e^-5	0.787	UPSTREAM tRNA:K2:42Ad DOWNSTREAM tRNA:CR30316 INTERGENIC	regulatory region REDfly_CRMs
2R	10454281	2R_10454281_SNP [dm3] 2R_14566776_SNP [dm6]	G	C	3.926e^-5	0.787	INTRON ttv
2L	16497934	2L_16497934_SNP [dm3] 2L_16497934_SNP [dm6]	T	G	4.019e^-5	0.787	INTRON Tpr2
3R	11901121	3R_11901121_SNP [dm3] 3R_16075399_SNP [dm6]	A	G	4.030e^-5	0.787	SYNONYMOUS_CODING Mhcl INTRON Mhcl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11359686	3L_11359686_SNP [dm3] 3L_11366586_SNP [dm6]	T	G	4.243e^-5	0.787	DOWNSTREAM CR45036 INTERGENIC	TF binding site mE1_TFBS_inv
2R	6575248	2R_6575248_SNP [dm3] 2R_10687743_SNP [dm6]	A	G	4.258e^-5	0.787	INTRON stan
2R	6575273	2R_6575273_SNP [dm3] 2R_10687768_SNP [dm6]	G	A	4.258e^-5	0.787	INTRON stan
X	14747995	X_14747995_SNP [dm3] X_14853962_SNP [dm6]	G	A	4.353e^-5	0.787	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14746220	X_14746220_SNP [dm3] X_14852187_SNP [dm6]	C	G	4.355e^-5	0.787	SYNONYMOUS_CODING CG9521 INTRON Flo2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	14746250	X_14746250_SNP [dm3] X_14852217_SNP [dm6]	T	C	4.355e^-5	0.787	SYNONYMOUS_CODING CG9521 INTRON Flo2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	22839638	3L_22839638_SNP [dm3] 3L_22846538_SNP [dm6]	G	C	4.416e^-5	0.787	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	15309269	3R_15309269_SNP [dm3] 3R_19483547_SNP [dm6]	C	T	4.421e^-5	0.787	INTRON Dys
X	12336255	X_12336255_SNP [dm3] X_12442222_SNP [dm6]	T	C	4.444e^-5	0.787	INTRON Pkcdelta
2R	8177294	2R_8177294_SNP [dm3] 2R_12289789_SNP [dm6]	T	C	4.452e^-5	0.787	UPSTREAM CG42700 INTRON CG42700
2R	8177295	2R_8177295_SNP [dm3] 2R_12289790_SNP [dm6]	T	C	4.452e^-5	0.787	UPSTREAM CG42700 INTRON CG42700
X	14747090	X_14747090_SNP [dm3] X_14853057_SNP [dm6]	A	G	4.800e^-5	0.787	SYNONYMOUS_CODING CG9521 INTRON Flo2
3L	19917857	3L_19917857_DEL [dm3] 3L_19924757_DEL [dm6]	TA	G	5.205e^-5	0.787	UPSTREAM Grasp65 DOWNSTREAM CG7770 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	778267	3L_778267_SNP [dm3] 3L_778267_SNP [dm6]	C	T	5.220e^-5	0.787	INTERGENIC
3L	22840382	3L_22840382_SNP [dm3] 3L_22847282_SNP [dm6]	G	T	5.237e^-5	0.787	DOWNSTREAM tRNA:CR32460 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	19295211	2L_19295211_SNP [dm3] 2L_19295211_SNP [dm6]	A	G	5.291e^-5	0.787	INTERGENIC
3L	14037571	3L_14037571_SNP [dm3] 3L_14044471_SNP [dm6]	T	C	5.342e^-5	0.787	SYNONYMOUS_CODING blue DOWNSTREAM Hsc70Cb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8381886	3L_8381886_SNP [dm3] 3L_8388786_SNP [dm6]	T	A	5.377e^-5	0.787	NON_SYNONYMOUS_CODING ImpE1	TF binding site mE1_TFBS_cad
3R	6721222	3R_6721222_SNP [dm3] 3R_10895500_SNP [dm6]	C	A	5.426e^-5	0.787	UTR_3_PRIME Leash DOWNSTREAM CR45577	TF binding site mE1_TFBS_HSA mE1_TFBS_run
3R	6721449	3R_6721449_SNP [dm3] 3R_10895727_SNP [dm6]	A	T	5.426e^-5	0.787	UTR_3_PRIME Leash DOWNSTREAM CR45577	TF binding site mE1_TFBS_HSA mE1_TFBS_run
3R	15333095	3R_15333095_SNP [dm3] 3R_19507373_SNP [dm6]	T	A	5.457e^-5	0.787	INTRON Dys
3R	6725942	3R_6725942_SNP [dm3] 3R_10900220_SNP [dm6]	A	T	5.457e^-5	0.787	INTERGENIC
3R	6711687	3R_6711687_SNP [dm3] 3R_10885965_SNP [dm6]	C	T	5.535e^-5	0.787	UTR_5_PRIME Leash UPSTREAM CG14696	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	2565606	X_2565606_SNP [dm3] X_2671573_SNP [dm6]	T	C	5.546e^-5	0.787	INTRON sgg
X	2249375	X_2249375_DEL [dm3] X_2355342_DEL [dm6]	AATT	A	5.634e^-5	0.787	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl
X	2565595	X_2565595_SNP [dm3] X_2671562_SNP [dm6]	T	C	5.656e^-5	0.787	INTRON sgg
2R	9728400	2R_9728400_SNP [dm3] 2R_13840895_SNP [dm6]	G	C	5.673e^-5	0.787	NON_SYNONYMOUS_CODING CG6357 DOWNSTREAM Syngr
2R	17297680	2R_17297680_SNP [dm3] 2R_21410175_SNP [dm6]	A	C	5.710e^-5	0.787	INTRON Sdc
3L	4412923	3L_4412923_SNP [dm3] 3L_4412923_SNP [dm6]	G	C	5.786e^-5	0.787	INTRON DOR
2R	8178119	2R_8178119_SNP [dm3] 2R_12290614_SNP [dm6]	A	G	5.817e^-5	0.787	UPSTREAM CG42700 INTRON CG42700

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By genomic position
Variant impact
Gene name

daughters2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results