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=1.229e^-12)
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	0.01736

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	7.1905	0.0275

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

8392 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	5298399	2L_5298399_INS [dm3] 2L_5298399_INS [dm6]	A	AA	5.590e^-16	1.040e^-9	UPSTREAM CR45730 INTRON vri
3R	21608140	3R_21608140_SNP [dm3] 3R_25782418_SNP [dm6]	T	C	1.826e^-15	1.698e^-9	INTERGENIC
2R	4205960	2R_4205960_SNP [dm3] 2R_8318455_SNP [dm6]	A	G	2.495e^-14	1.547e^-8	INTERGENIC
X	21867866	X_21867866_SNP [dm3] X_22466030_SNP [dm6]	T	C	1.580e^-12	7.349e^-7	UPSTREAM CG14619 INTRON CG14619
X	12207510	X_12207510_SNP [dm3] X_12313477_SNP [dm6]	G	A	2.288e^-12	8.512e^-7	INTRON Ten-a
X	12207484	X_12207484_SNP [dm3] X_12313451_SNP [dm6]	G	T	3.941e^-12	1.084e^-6	INTRON Ten-a
3R	22626260	3R_22626260_SNP [dm3] 3R_26800538_SNP [dm6]	A	T	4.662e^-12	1.084e^-6	INTRON Tl
3R	22626282	3R_22626282_DEL [dm3] 3R_26800560_DEL [dm6]	CAACCC	GT	4.662e^-12	1.084e^-6	INTRON Tl
3R	15493540	3R_15493540_SNP [dm3] 3R_19667818_SNP [dm6]	G	T	6.735e^-12	1.392e^-6	INTRON CG7432
3L	15866056	3L_15866056_SNP [dm3] 3L_15872956_SNP [dm6]	A	T	9.400e^-12	1.697e^-6	INTRON pHCl
3L	15012944	3L_15012944_SNP [dm3] 3L_15019844_SNP [dm6]	A	G	1.003e^-11	1.697e^-6	INTRON Sytbeta
2L	6123609	2L_6123609_SNP [dm3] 2L_6123609_SNP [dm6]	C	T	1.393e^-11	2.160e^-6	UTR_3_PRIME stai
3L	14628116	3L_14628116_SNP [dm3] 3L_14635016_SNP [dm6]	C	T	2.515e^-11	3.554e^-6	INTRON dlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
3R	13915897	3R_13915897_DEL [dm3] 3R_18090175_DEL [dm6]	TTCT	T	2.675e^-11	3.554e^-6	UPSTREAM sr INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	10726566	X_10726566_SNP [dm3] X_10832533_SNP [dm6]	A	G	2.914e^-11	3.614e^-6	DOWNSTREAM sbr INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2L	6420123	2L_6420123_SNP [dm3] 2L_6420123_SNP [dm6]	T	C	3.380e^-11	3.729e^-6	SYNONYMOUS_CODING Tig	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	8033741	3L_8033741_SNP [dm3] 3L_8040641_SNP [dm6]	G	C	3.408e^-11	3.729e^-6	INTRON nmo
2R	15942708	2R_15942708_SNP [dm3] 2R_20055203_SNP [dm6]	G	A	5.678e^-11	5.332e^-6	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	6325099	2L_6325099_SNP [dm3] 2L_6325099_SNP [dm6]	A	T	5.769e^-11	5.332e^-6	INTRON PDZ-GEF	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2L	6325160	2L_6325160_SNP [dm3] 2L_6325160_SNP [dm6]	T	G	5.769e^-11	5.332e^-6	INTRON PDZ-GEF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	7681769	2R_7681769_SNP [dm3] 2R_11794264_SNP [dm6]	G	C	6.018e^-11	5.332e^-6	INTRON ths	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_D mE1_TFBS_HSA mE1_TFBS_sens
2L	4014046	2L_4014046_SNP [dm3] 2L_4014046_SNP [dm6]	T	A	1.070e^-10	9.051e^-6	INTERGENIC
3L	15360876	3L_15360876_SNP [dm3] 3L_15367776_SNP [dm6]	A	T	2.043e^-10	1.652e^-5	INTERGENIC
3L	9510270	3L_9510270_DEL [dm3] 3L_9517170_DEL [dm6]	TT	A	2.554e^-10	1.883e^-5	INTRON CG33700
3R	21326483	3R_21326483_SNP [dm3] 3R_25500761_SNP [dm6]	C	T	2.631e^-10	1.883e^-5	INTERGENIC
3R	21326492	3R_21326492_SNP [dm3] 3R_25500770_SNP [dm6]	T	G	2.631e^-10	1.883e^-5	INTERGENIC
2L	2183666	2L_2183666_SNP [dm3] 2L_2183666_SNP [dm6]	T	C	3.159e^-10	2.162e^-5	EXON CR43751	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	21865027	X_21865027_SNP [dm3] X_22463191_SNP [dm6]	T	C	3.254e^-10	2.162e^-5	SYNONYMOUS_CODING CG14619 UTR_5_PRIME CG14619 INTRON CG14619	TF binding site mE1_TFBS_HSA
3L	2837492	3L_2837492_SNP [dm3] 3L_2837492_SNP [dm6]	G	A	3.863e^-10	2.474e^-5	INTRON CG43444
2L	19318279	2L_19318279_SNP [dm3] 2L_19318279_SNP [dm6]	A	T	3.990e^-10	2.474e^-5	INTERGENIC	TF binding site mE1_TFBS_cad
3R	16877950	3R_16877950_SNP [dm3] 3R_21052228_SNP [dm6]	G	A	4.327e^-10	2.597e^-5	NON_SYNONYMOUS_CODING Mvl DOWNSTREAM Mvl
3R	16885832	3R_16885832_SNP [dm3] 3R_21060110_SNP [dm6]	T	G	6.230e^-10	3.622e^-5	UTR_5_PRIME Mvl INTRON Mvl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
2L	5376878	2L_5376878_SNP [dm3] 2L_5376878_SNP [dm6]	G	T	7.984e^-10	4.501e^-5	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	6270408	2L_6270408_SNP [dm3] 2L_6270408_SNP [dm6]	T	A	8.917e^-10	4.637e^-5	UPSTREAM CR42735 INTRON Ddr
X	8277684	X_8277684_SNP [dm3] X_8383651_SNP [dm6]	G	A	8.973e^-10	4.637e^-5	INTERGENIC
X	8277685	X_8277685_SNP [dm3] X_8383652_SNP [dm6]	T	C	8.973e^-10	4.637e^-5	INTERGENIC
3L	4026537	3L_4026537_SNP [dm3] 3L_4026537_SNP [dm6]	C	T	9.301e^-10	4.677e^-5	UPSTREAM Gr64a & 1 other INTERGENIC
2L	3130433	2L_3130433_SNP [dm3] 2L_3130433_SNP [dm6]	T	C	1.030e^-9	5.008e^-5	DOWNSTREAM CG15403 INTRON toc
3L	18934788	3L_18934788_SNP [dm3] 3L_18941688_SNP [dm6]	A	T	1.050e^-9	5.008e^-5	INTRON CG32204
3L	16664595	3L_16664595_SNP [dm3] 3L_16671495_SNP [dm6]	T	C	1.106e^-9	5.145e^-5	UPSTREAM CR45241 DOWNSTREAM zetaCOP INTERGENIC	TF binding site mE1_TFBS_cad
2L	14971220	2L_14971220_DEL [dm3] 2L_14971220_DEL [dm6]	AA	A	1.286e^-9	5.837e^-5	INTRON CG42313
3R	15300939	3R_15300939_SNP [dm3] 3R_19475217_SNP [dm6]	C	T	1.472e^-9	6.518e^-5	INTRON Dys
2L	6324948	2L_6324948_SNP [dm3] 2L_6324948_SNP [dm6]	C	T	1.733e^-9	7.499e^-5	INTRON PDZ-GEF	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	15300930	3R_15300930_SNP [dm3] 3R_19475208_SNP [dm6]	C	T	1.944e^-9	8.218e^-5	INTRON Dys
3L	18606809	3L_18606809_SNP [dm3] 3L_18613709_SNP [dm6]	G	A	2.114e^-9	8.739e^-5	NON_SYNONYMOUS_CODING CG32199 INTRON CG4174 & 1 other
2L	5907372	2L_5907372_SNP [dm3] 2L_5907372_SNP [dm6]	G	T	2.255e^-9	9.120e^-5	INTRON bchs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3R	21194456	3R_21194456_SNP [dm3] 3R_25368734_SNP [dm6]	T	G	2.454e^-9	9.714e^-5	INTRON Fur1
2L	5744474	2L_5744474_SNP [dm3] 2L_5744474_SNP [dm6]	C	T	2.522e^-9	9.775e^-5	INTRON CG11030
2R	15387655	2R_15387655_SNP [dm3] 2R_19500150_SNP [dm6]	G	A	2.740e^-9	1.028e^-4	SYNONYMOUS_CODING CG15120 DOWNSTREAM CG16926
3R	15031852	3R_15031852_SNP [dm3] 3R_19206130_SNP [dm6]	A	C	2.762e^-9	1.028e^-4	INTERGENIC
2L	12296072	2L_12296072_SNP [dm3] 2L_12296072_SNP [dm6]	G	C	2.927e^-9	1.068e^-4	INTRON aret
2R	15035159	2R_15035159_SNP [dm3] 2R_19147654_SNP [dm6]	C	T	3.000e^-9	1.071e^-4	INTRON ena	TF binding site mE1_TFBS_HSA
2L	6886825	2L_6886825_SNP [dm3] 2L_6886825_SNP [dm6]	T	C	3.134e^-9	1.071e^-4	INTRON Nlg2	TF binding site BDTNP1_TFBS_twi
3L	13206390	3L_13206390_INS [dm3] 3L_13213290_INS [dm6]	T	TTT	3.134e^-9	1.071e^-4	UPSTREAM tRNA:CR32127 DOWNSTREAM tRNA:CR32126 INTERGENIC	TF binding site mE1_TFBS_cad
2R	8565902	2R_8565902_SNP [dm3] 2R_12678397_SNP [dm6]	C	T	3.259e^-9	1.071e^-4	INTRON CG42708
3L	7322909	3L_7322909_SNP [dm3] 3L_7329809_SNP [dm6]	C	A	3.290e^-9	1.071e^-4	SYNONYMOUS_CODING mus312 UTR_3_PRIME CG42307 UPSTREAM CG8602 DOWNSTREAM CG42307	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	9253442	2L_9253442_INS [dm3] 2L_9253442_INS [dm6]	G	GTATAGA	3.339e^-9	1.071e^-4	UPSTREAM borr DOWNSTREAM lectin-30A INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3L	18235739	3L_18235739_SNP [dm3] 3L_18242639_SNP [dm6]	C	A	3.397e^-9	1.071e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18235743	3L_18235743_SNP [dm3] 3L_18242643_SNP [dm6]	T	G	3.397e^-9	1.071e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	4206831	2R_4206831_SNP [dm3] 2R_8319326_SNP [dm6]	G	C	3.575e^-9	1.108e^-4	INTERGENIC
3L	15750623	3L_15750623_SNP [dm3] 3L_15757523_SNP [dm6]	C	A	4.289e^-9	1.294e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	20648493	2R_20648493_SNP [dm3] 2R_24760970_SNP [dm6]	A	C	4.448e^-9	1.294e^-4	DOWNSTREAM spz6 INTRON CG3880	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
2R	8566202	2R_8566202_SNP [dm3] 2R_12678697_SNP [dm6]	A	T	4.487e^-9	1.294e^-4	INTRON CG42708
3R	12903014	3R_12903014_SNP [dm3] 3R_17077292_SNP [dm6]	A	T	4.492e^-9	1.294e^-4	INTRON Keap1
3R	16321001	3R_16321001_SNP [dm3] 3R_20495279_SNP [dm6]	G	A	4.522e^-9	1.294e^-4	INTERGENIC
3L	689544	3L_689544_SNP [dm3] 3L_689544_SNP [dm6]	A	G	4.868e^-9	1.352e^-4	SYNONYMOUS_CODING CG32483 UPSTREAM RabX6	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	689571	3L_689571_SNP [dm3] 3L_689571_SNP [dm6]	C	T	4.868e^-9	1.352e^-4	SYNONYMOUS_CODING CG32483 UPSTREAM RabX6	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3R	19175379	3R_19175379_SNP [dm3] 3R_23349657_SNP [dm6]	A	G	5.005e^-9	1.369e^-4	SYNONYMOUS_CODING DNApol-epsilon	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9661271	3R_9661271_SNP [dm3] 3R_13835549_SNP [dm6]	G	A	5.242e^-9	1.393e^-4	INTRON Nsf2
3R	9661326	3R_9661326_SNP [dm3] 3R_13835604_SNP [dm6]	C	A	5.242e^-9	1.393e^-4	INTRON Nsf2	TF binding site mE1_TFBS_cad
3R	19375447	3R_19375447_SNP [dm3] 3R_23549725_SNP [dm6]	A	C	5.450e^-9	1.428e^-4	INTERGENIC
3R	14205913	3R_14205913_INS [dm3] 3R_18380191_INS [dm6]	T	TAGCACGTTTACTGGGAT...	6.188e^-9	1.599e^-4	INTRON CG7675
2L	5100022	2L_5100022_SNP [dm3] 2L_5100022_SNP [dm6]	T	C	6.554e^-9	1.666e^-4	SYNONYMOUS_CODING CG8680 UPSTREAM Msp300 DOWNSTREAM CG4230	TF binding site BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
2R	14602122	2R_14602122_SNP [dm3] 2R_18714617_SNP [dm6]	C	A	6.628e^-9	1.666e^-4	INTERGENIC
3L	10428792	3L_10428792_SNP [dm3] 3L_10435692_SNP [dm6]	T	C	6.853e^-9	1.700e^-4	INTERGENIC
3L	16895072	3L_16895072_SNP [dm3] 3L_16901972_SNP [dm6]	A	G	7.213e^-9	1.743e^-4	SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_inv
3L	16895171	3L_16895171_SNP [dm3] 3L_16902071_SNP [dm6]	G	A	7.213e^-9	1.743e^-4	INTRON Lmpt	TF binding site mE1_TFBS_inv
2R	17850182	2R_17850182_DEL [dm3] 2R_21962677_DEL [dm6]	ATGTA	A	7.358e^-9	1.755e^-4	INTERGENIC
2R	12322079	2R_12322079_SNP [dm3] 2R_16434574_SNP [dm6]	A	C	7.554e^-9	1.779e^-4	SYNONYMOUS_CODING CG7848	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3R	23516657	3R_23516657_SNP [dm3] 3R_27690935_SNP [dm6]	G	T	7.727e^-9	1.797e^-4	INTRON CG12880	TF binding site mE1_TFBS_chinmo
3R	21398042	3R_21398042_DEL [dm3] 3R_25572320_DEL [dm6]	TCCTGGTTGCCCCT...	T	7.892e^-9	1.801e^-4	INTRON msi
3L	8256840	3L_8256840_SNP [dm3] 3L_8263740_SNP [dm6]	C	G	7.939e^-9	1.801e^-4	INTRON Dscam4
X	21880112	X_21880112_SNP [dm3] X_22478276_SNP [dm6]	T	C	8.137e^-9	1.802e^-4	UPSTREAM CG12576 INTRON CG12576
X	21880181	X_21880181_SNP [dm3] X_22478345_SNP [dm6]	G	A	8.137e^-9	1.802e^-4	UPSTREAM CG12576 INTRON CG12576
2R	16925812	2R_16925812_SNP [dm3] 2R_21038307_SNP [dm6]	T	A	8.439e^-9	1.847e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	21194491	3R_21194491_SNP [dm3] 3R_25368769_SNP [dm6]	G	T	9.031e^-9	1.934e^-4	INTRON Fur1
2R	14602986	2R_14602986_SNP [dm3] 2R_18715481_SNP [dm6]	A	G	9.043e^-9	1.934e^-4	INTERGENIC
2L	5385717	2L_5385717_SNP [dm3] 2L_5385717_SNP [dm6]	A	G	9.761e^-9	2.064e^-4	INTERGENIC
2R	12322058	2R_12322058_SNP [dm3] 2R_16434553_SNP [dm6]	C	T	1.045e^-8	2.135e^-4	SYNONYMOUS_CODING CG7848	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3L	12292906	3L_12292906_SNP [dm3] 3L_12299806_SNP [dm6]	G	A	1.056e^-8	2.135e^-4	INTERGENIC
3L	12292924	3L_12292924_SNP [dm3] 3L_12299824_SNP [dm6]	C	G	1.056e^-8	2.135e^-4	INTERGENIC
3L	12292929	3L_12292929_SNP [dm3] 3L_12299829_SNP [dm6]	A	C	1.056e^-8	2.135e^-4	INTERGENIC
2L	12381479	2L_12381479_SNP [dm3] 2L_12381479_SNP [dm6]	T	C	1.110e^-8	2.220e^-4	INTRON bru-2
3R	23837706	3R_23837706_SNP [dm3] 3R_28011984_SNP [dm6]	C	T	1.210e^-8	2.366e^-4	INTERGENIC
3R	24512436	3R_24512436_SNP [dm3] 3R_28686714_SNP [dm6]	A	T	1.210e^-8	2.366e^-4	INTRON CG9990
2L	5288591	2L_5288591_SNP [dm3] 2L_5288591_SNP [dm6]	C	A	1.231e^-8	2.366e^-4	UPSTREAM vri DOWNSTREAM CR44742 EXON CR44743	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14603046	2R_14603046_SNP [dm3] 2R_18715541_SNP [dm6]	G	A	1.234e^-8	2.366e^-4	INTERGENIC
3L	15011771	3L_15011771_SNP [dm3] 3L_15018671_SNP [dm6]	A	G	1.310e^-8	2.461e^-4	INTRON Sytbeta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15011785	3L_15011785_SNP [dm3] 3L_15018685_SNP [dm6]	C	T	1.310e^-8	2.461e^-4	SPLICE_SITE_REGION Sytbeta INTRON Sytbeta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24637329	3R_24637329_SNP [dm3] 3R_28811607_SNP [dm6]	C	T	1.398e^-8	2.588e^-4	UPSTREAM CG1646 & 2 others INTERGENIC	enhancer FlyBase regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx

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By genomic position
Variant impact
Gene name

Microbiota_OTU081 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results