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=6.734e^-3)
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

1298 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	11361515	2L_11361515_SNP [dm3] 2L_11361515_SNP [dm6]	A	G	1.976e^-6	0.885	INTRON salr	regulatory region REDfly_CRMs
3R	13588263	3R_13588263_INS [dm3] 3R_17762541_INS [dm6]	G	GTCG	2.029e^-6	0.885	UTR_5_PRIME TyrR UPSTREAM TyrR
3R	24217371	3R_24217371_SNP [dm3] 3R_28391649_SNP [dm6]	C	A	3.376e^-6	0.885	INTERGENIC
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	4.510e^-6	0.885	INTRON Glut1
3R	9151822	3R_9151822_SNP [dm3] 3R_13326100_SNP [dm6]	T	C	6.537e^-6	0.885	INTERGENIC
3R	16739456	3R_16739456_SNP [dm3] 3R_20913734_SNP [dm6]	C	T	6.554e^-6	0.885	UPSTREAM snoRNA:CG31191-a & 1 other DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	6.993e^-6	0.885	INTRON salr	regulatory region REDfly_CRMs
3R	26119375	3R_26119375_SNP [dm3] 3R_30293653_SNP [dm6]	T	A	7.462e^-6	0.885	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3911257	X_3911257_SNP [dm3] X_4017224_SNP [dm6]	G	A	9.644e^-6	0.885	INTERGENIC
X	2794934	X_2794934_SNP [dm3] X_2900901_SNP [dm6]	A	C	1.049e^-5	0.885	INTRON kirre
3R	11618479	3R_11618479_SNP [dm3] 3R_15792757_SNP [dm6]	G	C	1.100e^-5	0.885	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_Ubx
3R	13588248	3R_13588248_SNP [dm3] 3R_17762526_SNP [dm6]	G	A	1.174e^-5	0.885	UTR_5_PRIME TyrR UPSTREAM TyrR
3R	26119383	3R_26119383_SNP [dm3] 3R_30293661_SNP [dm6]	G	C	1.225e^-5	0.885	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	1383873	3L_1383873_SNP [dm3] 3L_1383873_SNP [dm6]	A	C	1.264e^-5	0.885	INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_HSA
X	3911217	X_3911217_SNP [dm3] X_4017184_SNP [dm6]	C	A	1.343e^-5	0.885	INTERGENIC
X	3911229	X_3911229_SNP [dm3] X_4017196_SNP [dm6]	T	G	1.343e^-5	0.885	INTERGENIC
2L	11360994	2L_11360994_SNP [dm3] 2L_11360994_SNP [dm6]	G	C	1.376e^-5	0.885	INTRON salr	regulatory region REDfly_CRMs
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	1.397e^-5	0.885	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	1.397e^-5	0.885	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	1.397e^-5	0.885	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	1.397e^-5	0.885	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	1.397e^-5	0.885	INTERGENIC
X	3911242	X_3911242_DEL [dm3] X_4017209_DEL [dm6]	TAATATCAGT	T	1.538e^-5	0.885	INTERGENIC
3R	11618443	3R_11618443_SNP [dm3] 3R_15792721_SNP [dm6]	A	G	1.699e^-5	0.885	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx
3L	12834135	3L_12834135_SNP [dm3] 3L_12841035_SNP [dm6]	G	T	1.817e^-5	0.885	INTRON CG10960	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
X	11139011	X_11139011_SNP [dm3] X_11244978_SNP [dm6]	C	G	1.853e^-5	0.885	INTRON CG44422
2L	8010191	2L_8010191_SNP [dm3] 2L_8010191_SNP [dm6]	G	A	1.915e^-5	0.885	SYNONYMOUS_CODING CG34010 UPSTREAM CG12560	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	3911227	X_3911227_SNP [dm3] X_4017194_SNP [dm6]	A	T	1.983e^-5	0.885	INTERGENIC
3L	9088728	3L_9088728_SNP [dm3] 3L_9095628_SNP [dm6]	C	T	2.049e^-5	0.885	DOWNSTREAM CG32032 INTERGENIC
3R	26119373	3R_26119373_SNP [dm3] 3R_30293651_SNP [dm6]	G	C	2.153e^-5	0.885	INTRON hdc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	15737816	3L_15737816_SNP [dm3] 3L_15744716_SNP [dm6]	A	T	2.162e^-5	0.885	INTERGENIC
3R	24807557	3R_24807557_SNP [dm3] 3R_28981835_SNP [dm6]	C	T	2.172e^-5	0.885	INTERGENIC
3L	17335883	3L_17335883_SNP [dm3] 3L_17342783_SNP [dm6]	G	A	2.355e^-5	0.885	INTRON brv2
3L	13541893	3L_13541893_INS [dm3] 3L_13548793_INS [dm6]	C	CGGACAC	2.383e^-5	0.885	INTRON bru-3
3R	9196465	3R_9196465_SNP [dm3] 3R_13370743_SNP [dm6]	C	A	2.449e^-5	0.885	DOWNSTREAM CheA87a INTRON Lip3
3R	9196475	3R_9196475_SNP [dm3] 3R_13370753_SNP [dm6]	T	C	2.449e^-5	0.885	DOWNSTREAM CheA87a INTRON Lip3
2R	5318902	2R_5318902_INS [dm3] 2R_9431397_INS [dm6]	A	ATACA	2.451e^-5	0.885	INTRON Pdk
3L	7986579	3L_7986579_MNP [dm3] 3L_7993479_MNP [dm6]	GTT	TAG	2.465e^-5	0.885	INTRON nmo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
X	12940092	X_12940092_SNP [dm3] X_13046059_SNP [dm6]	T	G	2.538e^-5	0.885	INTRON rad
3L	7061417	3L_7061417_SNP [dm3] 3L_7068317_SNP [dm6]	G	A	2.550e^-5	0.885	SYNONYMOUS_CODING CG32391 DOWNSTREAM CG14823 INTRON CG8641
X	4519489	X_4519489_SNP [dm3] X_4625456_SNP [dm6]	C	T	2.592e^-5	0.885	SYNONYMOUS_CODING peb	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	9196104	3R_9196104_SNP [dm3] 3R_13370382_SNP [dm6]	G	A	2.759e^-5	0.885	SYNONYMOUS_CODING Lip3 DOWNSTREAM CheA87a
2R	6379235	2R_6379235_SNP [dm3] 2R_10491730_SNP [dm6]	C	T	2.889e^-5	0.885	UTR_3_PRIME lola INTRON lola
2R	6508001	2R_6508001_SNP [dm3] 2R_10620496_SNP [dm6]	A	C	2.889e^-5	0.885	INTRON CG11883
2L	14359817	2L_14359817_SNP [dm3] 2L_14359817_SNP [dm6]	T	C	2.953e^-5	0.885	SYNONYMOUS_CODING Pgant35A EXON CR43463	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	5376612	3L_5376612_DEL [dm3] 3L_5383512_DEL [dm6]	CTGT	A	2.964e^-5	0.885	UPSTREAM Ir64a INTERGENIC
3L	1605240	3L_1605240_SNP [dm3] 3L_1605240_SNP [dm6]	A	C	2.992e^-5	0.885	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170
2R	6452247	2R_6452247_SNP [dm3] 2R_10564742_SNP [dm6]	C	T	3.015e^-5	0.885	INTRON psq	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	19388879	3L_19388879_SNP [dm3] 3L_19395779_SNP [dm6]	G	C	3.118e^-5	0.885	INTRON CG32206
3L	14642055	3L_14642055_SNP [dm3] 3L_14648955_SNP [dm6]	A	T	3.221e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642058	3L_14642058_SNP [dm3] 3L_14648958_SNP [dm6]	G	A	3.221e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642078	3L_14642078_MNP [dm3] 3L_14648978_MNP [dm6]	GGG	AAA	3.221e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	19388797	3L_19388797_SNP [dm3] 3L_19395697_SNP [dm6]	A	G	3.312e^-5	0.885	INTRON CG32206
3L	2622009	3L_2622009_SNP [dm3] 3L_2622009_SNP [dm6]	A	T	3.386e^-5	0.885	INTRON Pxn
3L	9088629	3L_9088629_SNP [dm3] 3L_9095529_SNP [dm6]	C	G	3.507e^-5	0.885	DOWNSTREAM CG32032 INTERGENIC
3R	10604335	3R_10604335_SNP [dm3] 3R_14778613_SNP [dm6]	G	A	3.565e^-5	0.885	INTRON jvl
3R	25365859	3R_25365859_SNP [dm3] 3R_29540137_SNP [dm6]	T	A	3.704e^-5	0.885	INTERGENIC	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	9088625	3L_9088625_SNP [dm3] 3L_9095525_SNP [dm6]	C	T	3.770e^-5	0.885	DOWNSTREAM CG32032 INTERGENIC
3L	8246620	3L_8246620_SNP [dm3] 3L_8253520_SNP [dm6]	A	T	3.880e^-5	0.885	INTRON Dscam4
3R	9385445	3R_9385445_SNP [dm3] 3R_13559723_SNP [dm6]	T	A	3.932e^-5	0.885	INTERGENIC
3R	9385447	3R_9385447_SNP [dm3] 3R_13559725_SNP [dm6]	C	T	3.932e^-5	0.885	INTERGENIC
X	14382716	X_14382716_SNP [dm3] X_14488683_SNP [dm6]	T	C	4.173e^-5	0.885	INTERGENIC
2L	15343669	2L_15343669_SNP [dm3] 2L_15343669_SNP [dm6]	A	T	4.191e^-5	0.885	INTERGENIC
2L	15343684	2L_15343684_MNP [dm3] 2L_15343684_MNP [dm6]	GTT	ACA	4.191e^-5	0.885	INTERGENIC
2L	15343691	2L_15343691_DEL [dm3] 2L_15343691_DEL [dm6]	CAC	A	4.191e^-5	0.885	INTERGENIC
2R	11059590	2R_11059590_SNP [dm3] 2R_15172085_SNP [dm6]	T	C	4.287e^-5	0.885	INTRON igl
2R	6508603	2R_6508603_SNP [dm3] 2R_10621098_SNP [dm6]	T	G	4.287e^-5	0.885	INTRON CG11883
3R	24366641	3R_24366641_SNP [dm3] 3R_28540919_SNP [dm6]	G	A	4.326e^-5	0.885	UPSTREAM Ppn INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12135321	2L_12135321_SNP [dm3] 2L_12135321_SNP [dm6]	T	G	4.473e^-5	0.885	INTERGENIC
3L	16433813	3L_16433813_SNP [dm3] 3L_16440713_SNP [dm6]	G	A	4.561e^-5	0.885	INTRON CG33158 & 1 other
3L	20070404	3L_20070404_SNP [dm3] 3L_20077304_SNP [dm6]	G	T	4.578e^-5	0.885	INTRON sNPF-R
3R	12384171	3R_12384171_SNP [dm3] 3R_16558449_SNP [dm6]	C	T	4.789e^-5	0.885	INTRON CG42342
3L	14642038	3L_14642038_SNP [dm3] 3L_14648938_SNP [dm6]	T	A	4.994e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	17993103	3R_17993103_SNP [dm3] 3R_22167381_SNP [dm6]	G	C	5.257e^-5	0.885	INTRON SKIP	TF binding site mE1_TFBS_Kr
2L	9014159	2L_9014159_SNP [dm3] 2L_9014159_SNP [dm6]	C	T	5.346e^-5	0.885	UPSTREAM Rcd-1r DOWNSTREAM CG13102 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	24316014	3R_24316014_SNP [dm3] 3R_28490292_SNP [dm6]	T	A	5.393e^-5	0.885	INTRON Dhc98D
2R	10687961	2R_10687961_DEL [dm3] 2R_14800456_DEL [dm6]	GG	G	5.404e^-5	0.885	INTRON kn	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
3R	16738656	3R_16738656_INS [dm3] 3R_20912934_INS [dm6]	T	TCT	5.440e^-5	0.885	UPSTREAM snoRNA:CG31191-a DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	5935829	3L_5935829_SNP [dm3] 3L_5942729_SNP [dm6]	G	A	5.452e^-5	0.885	INTRON CG33993
3L	16433911	3L_16433911_SNP [dm3] 3L_16440811_SNP [dm6]	A	T	5.505e^-5	0.885	INTRON CG33158 & 1 other
3L	16433660	3L_16433660_SNP [dm3] 3L_16440560_SNP [dm6]	A	C	5.602e^-5	0.885	INTRON CG33158 & 1 other
3L	7904156	3L_7904156_SNP [dm3] 3L_7911056_SNP [dm6]	G	T	5.765e^-5	0.885	INTRON pbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	9986084	2L_9986084_SNP [dm3] 2L_9986084_SNP [dm6]	G	A	5.773e^-5	0.885	INTRON bib	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	6470230	2R_6470230_SNP [dm3] 2R_10582725_SNP [dm6]	T	A	5.982e^-5	0.885	UPSTREAM psq INTRON psq	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2R	6470328	2R_6470328_SNP [dm3] 2R_10582823_SNP [dm6]	C	T	5.982e^-5	0.885	UPSTREAM psq INTRON psq	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
2R	6470331	2R_6470331_SNP [dm3] 2R_10582826_SNP [dm6]	A	G	5.982e^-5	0.885	UPSTREAM psq INTRON psq	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
2R	6470398	2R_6470398_DEL [dm3] 2R_10582893_DEL [dm6]	TT	T	5.982e^-5	0.885	UPSTREAM psq INTRON psq	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2R	6470408	2R_6470408_SNP [dm3] 2R_10582903_SNP [dm6]	T	A	5.982e^-5	0.885	UPSTREAM psq INTRON psq	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
X	6320110	X_6320110_SNP [dm3] X_6426077_SNP [dm6]	T	A	5.984e^-5	0.885	INTRON CG42340
3R	16739498	3R_16739498_SNP [dm3] 3R_20913776_SNP [dm6]	T	C	6.001e^-5	0.885	UPSTREAM snoRNA:CG31191-a & 1 other DOWNSTREAM CR44106 INTRON CG31191	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	17955756	X_17955756_DEL [dm3] X_18061723_DEL [dm6]	CCCGC	C	6.139e^-5	0.885	INTRON Sh
3R	18178125	3R_18178125_SNP [dm3] 3R_22352403_SNP [dm6]	C	T	6.149e^-5	0.885	NON_SYNONYMOUS_CODING rdhB
2L	5249270	2L_5249270_SNP [dm3] 2L_5249270_SNP [dm6]	T	A	6.187e^-5	0.885	INTRON tkv	TF binding site mE1_TFBS_cnc
3L	14642130	3L_14642130_INS [dm3] 3L_14649030_INS [dm6]	T	TTGT	6.281e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	13626819	3R_13626819_SNP [dm3] 3R_17801097_SNP [dm6]	G	T	6.287e^-5	0.885	DOWNSTREAM CG17806 INTRON CG17803
3L	14642070	3L_14642070_SNP [dm3] 3L_14648970_SNP [dm6]	C	T	6.344e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642095	3L_14642095_SNP [dm3] 3L_14648995_SNP [dm6]	T	A	6.344e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642098	3L_14642098_SNP [dm3] 3L_14648998_SNP [dm6]	A	T	6.344e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642110	3L_14642110_SNP [dm3] 3L_14649010_SNP [dm6]	T	C	6.344e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642039	3L_14642039_SNP [dm3] 3L_14648939_SNP [dm6]	T	G	6.386e^-5	0.885	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

productivity1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results