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=1.668e^-11)
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_3R_K	0.09342

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

7199 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
3L	1216141	3L_1216141_SNP [dm3] 3L_1216141_SNP [dm6]	C	T	2.968e^-11	2.487e^-5	INTRON mwh	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_inv
2L	7358791	2L_7358791_SNP [dm3] 2L_7358791_SNP [dm6]	A	C	3.201e^-11	2.487e^-5	INTERGENIC
2L	7358790	2L_7358790_SNP [dm3] 2L_7358790_SNP [dm6]	A	T	4.771e^-11	2.487e^-5	INTERGENIC
2R	1603531	2R_1603531_SNP [dm3] 2R_5716026_SNP [dm6]	A	G	5.622e^-11	2.487e^-5	INTRON ap	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	15893993	2R_15893993_SNP [dm3] 2R_20006488_SNP [dm6]	G	T	6.683e^-11	2.487e^-5	UPSTREAM CR44628 INTERGENIC
2R	15886544	2R_15886544_SNP [dm3] 2R_19999039_SNP [dm6]	G	A	1.209e^-10	3.748e^-5	INTERGENIC
2R	6927412	2R_6927412_SNP [dm3] 2R_11039907_SNP [dm6]	T	C	1.721e^-10	4.058e^-5	INTRON luna	TF binding site mE1_TFBS_chinmo
2L	7358831	2L_7358831_SNP [dm3] 2L_7358831_SNP [dm6]	G	T	1.849e^-10	4.058e^-5	INTERGENIC
2R	1610618	2R_1610618_DEL [dm3] 2R_5723113_DEL [dm6]	ACAACTTGACGATC...	A	1.963e^-10	4.058e^-5	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3L	18561260	3L_18561260_SNP [dm3] 3L_18568160_SNP [dm6]	T	C	2.947e^-10	5.482e^-5	INTRON AstC-R1
2L	6356630	2L_6356630_SNP [dm3] 2L_6356630_SNP [dm6]	C	T	7.536e^-10	1.263e^-4	DOWNSTREAM CG9500 & 1 other INTERGENIC	TF binding site mE1_TFBS_bab1
2L	14153560	2L_14153560_SNP [dm3] 2L_14153560_SNP [dm6]	A	T	1.010e^-9	1.263e^-4	INTRON CG17341
2L	7851869	2L_7851869_SNP [dm3] 2L_7851869_SNP [dm6]	A	T	1.366e^-9	1.263e^-4	INTRON CG14535
3L	1204756	3L_1204756_SNP [dm3] 3L_1204756_SNP [dm6]	C	A	1.474e^-9	1.263e^-4	UTR_5_PRIME CG9119 INTRON mwh	TF binding site mE1_TFBS_cad
3L	7097178	3L_7097178_SNP [dm3] 3L_7104078_SNP [dm6]	C	T	1.609e^-9	1.263e^-4	INTRON form3
3L	15265363	3L_15265363_SNP [dm3] 3L_15272263_SNP [dm6]	C	G	1.796e^-9	1.263e^-4	INTERGENIC
3L	15265373	3L_15265373_SNP [dm3] 3L_15272273_SNP [dm6]	T	C	1.796e^-9	1.263e^-4	INTERGENIC
3L	15265374	3L_15265374_SNP [dm3] 3L_15272274_SNP [dm6]	A	T	1.796e^-9	1.263e^-4	INTERGENIC
3L	15265376	3L_15265376_SNP [dm3] 3L_15272276_SNP [dm6]	A	C	1.796e^-9	1.263e^-4	INTERGENIC
3L	15265382	3L_15265382_SNP [dm3] 3L_15272282_SNP [dm6]	A	T	1.796e^-9	1.263e^-4	INTERGENIC
2R	1601950	2R_1601950_SNP [dm3] 2R_5714445_SNP [dm6]	C	T	1.901e^-9	1.263e^-4	INTRON ap
2R	1605964	2R_1605964_SNP [dm3] 2R_5718459_SNP [dm6]	G	A	1.901e^-9	1.263e^-4	INTRON ap
2R	1610634	2R_1610634_SNP [dm3] 2R_5723129_SNP [dm6]	A	T	1.901e^-9	1.263e^-4	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	1610638	2R_1610638_SNP [dm3] 2R_5723133_SNP [dm6]	A	T	1.901e^-9	1.263e^-4	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	1610646	2R_1610646_SNP [dm3] 2R_5723141_SNP [dm6]	A	T	1.901e^-9	1.263e^-4	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	1610648	2R_1610648_SNP [dm3] 2R_5723143_SNP [dm6]	G	C	1.901e^-9	1.263e^-4	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	1621814	2R_1621814_SNP [dm3] 2R_5734309_SNP [dm6]	T	C	1.901e^-9	1.263e^-4	INTERGENIC	regulatory region REDfly_CRMs
2R	5586543	2R_5586543_SNP [dm3] 2R_9699038_SNP [dm6]	G	A	1.901e^-9	1.263e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	15265380	3L_15265380_SNP [dm3] 3L_15272280_SNP [dm6]	C	A	2.021e^-9	1.284e^-4	INTERGENIC
X	4662483	X_4662483_SNP [dm3] X_4768450_SNP [dm6]	G	A	2.070e^-9	1.284e^-4	DOWNSTREAM CG15472 INTERGENIC
2L	12812522	2L_12812522_SNP [dm3] 2L_12812522_SNP [dm6]	C	T	2.488e^-9	1.303e^-4	INTERGENIC
2R	1610635	2R_1610635_SNP [dm3] 2R_5723130_SNP [dm6]	A	G	2.541e^-9	1.303e^-4	INTRON ap	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	1607161	2R_1607161_SNP [dm3] 2R_5719656_SNP [dm6]	G	A	2.585e^-9	1.303e^-4	INTRON ap
2R	1599351	2R_1599351_SNP [dm3] 2R_5711846_SNP [dm6]	C	A	2.621e^-9	1.303e^-4	INTRON ap	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15265358	3L_15265358_SNP [dm3] 3L_15272258_SNP [dm6]	G	A	2.645e^-9	1.303e^-4	INTERGENIC
2R	1611790	2R_1611790_SNP [dm3] 2R_5724285_SNP [dm6]	A	T	2.651e^-9	1.303e^-4	INTRON ap	transposable element FlyBase
2R	1622111	2R_1622111_SNP [dm3] 2R_5734606_SNP [dm6]	C	A	2.651e^-9	1.303e^-4	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_sens
2R	1601746	2R_1601746_SNP [dm3] 2R_5714241_SNP [dm6]	T	A	2.660e^-9	1.303e^-4	INTRON ap	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	1619156	2R_1619156_SNP [dm3] 2R_5731651_SNP [dm6]	C	T	2.947e^-9	1.362e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	1619258	2R_1619258_SNP [dm3] 2R_5731753_SNP [dm6]	C	T	2.947e^-9	1.362e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	7851870	2L_7851870_SNP [dm3] 2L_7851870_SNP [dm6]	T	A	3.024e^-9	1.362e^-4	INTRON CG14535
2L	11877308	2L_11877308_SNP [dm3] 2L_11877308_SNP [dm6]	G	T	3.075e^-9	1.362e^-4	UPSTREAM Pde1c INTRON Pde1c	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	16792194	2L_16792194_SNP [dm3] 2L_16792194_SNP [dm6]	A	G	3.185e^-9	1.378e^-4	NON_SYNONYMOUS_CODING CG17928
2L	18566732	2L_18566732_SNP [dm3] 2L_18566732_SNP [dm6]	A	G	3.335e^-9	1.410e^-4	INTRON Pde11
2R	1613085	2R_1613085_SNP [dm3] 2R_5725580_SNP [dm6]	T	G	3.447e^-9	1.423e^-4	INTRON ap	TF binding site BDTNP1_TFBS_dl mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA
2R	1617381	2R_1617381_SNP [dm3] 2R_5729876_SNP [dm6]	G	A	3.518e^-9	1.423e^-4	INTERGENIC	transposable element FlyBase
2L	16792157	2L_16792157_SNP [dm3] 2L_16792157_SNP [dm6]	G	A	4.395e^-9	1.740e^-4	NON_SYNONYMOUS_CODING CG17928
2L	20001012	2L_20001012_SNP [dm3] 2L_20001012_SNP [dm6]	T	C	4.948e^-9	1.918e^-4	UPSTREAM CR44908 INTRON CG43861
2L	12481326	2L_12481326_SNP [dm3] 2L_12481326_SNP [dm6]	T	C	6.286e^-9	2.387e^-4	INTRON bun	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	1618552	2R_1618552_SNP [dm3] 2R_5731047_SNP [dm6]	G	T	6.860e^-9	2.552e^-4	INTERGENIC
3L	9402701	3L_9402701_SNP [dm3] 3L_9409601_SNP [dm6]	G	A	7.478e^-9	2.728e^-4	SYNONYMOUS_CODING CG4022	TF binding site BDTNP1_TFBS_dl
X	2290361	X_2290361_SNP [dm3] X_2396328_SNP [dm6]	C	T	7.729e^-9	2.765e^-4	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	1631289	2R_1631289_INS [dm3] 2R_5743784_INS [dm6]	T	TTTTTAAGTAAGTT...	1.049e^-8	3.682e^-4	INTERGENIC	regulatory region REDfly_CRMs
X	4441679	X_4441679_SNP [dm3] X_4547646_SNP [dm6]	C	T	1.152e^-8	3.968e^-4	SYNONYMOUS_CODING Usf INTRON CR32773
2L	9347766	2L_9347766_SNP [dm3] 2L_9347766_SNP [dm6]	C	T	1.268e^-8	4.289e^-4	DOWNSTREAM CR44802 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2L	9130853	2L_9130853_DEL [dm3] 2L_9130853_DEL [dm6]	AAACA	A	1.448e^-8	4.812e^-4	INTRON CG32982
3L	5646654	3L_5646654_SNP [dm3] 3L_5653554_SNP [dm6]	C	T	1.632e^-8	5.325e^-4	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	5646660	3L_5646660_SNP [dm3] 3L_5653560_SNP [dm6]	A	G	2.252e^-8	7.222e^-4	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	1602753	2R_1602753_SNP [dm3] 2R_5715248_SNP [dm6]	T	C	2.290e^-8	7.222e^-4	INTRON ap	TF binding site mE1_TFBS_cad
2R	11809964	2R_11809964_SNP [dm3] 2R_15922459_SNP [dm6]	G	C	2.414e^-8	7.486e^-4	UPSTREAM sli DOWNSTREAM bdg INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_bab1 mE1_TFBS_HSA
3L	20996530	3L_20996530_DEL [dm3] 3L_21003430_DEL [dm6]	TGTTAGATT	T	2.675e^-8	8.157e^-4	INTRON skd
2R	17421211	2R_17421211_SNP [dm3] 2R_21533706_SNP [dm6]	C	T	2.758e^-8	8.275e^-4	INTRON Egfr
2R	1617709	2R_1617709_SNP [dm3] 2R_5730204_SNP [dm6]	T	A	3.049e^-8	9.003e^-4	INTERGENIC	transposable element FlyBase
3L	5277029	3L_5277029_SNP [dm3] 3L_5283929_SNP [dm6]	G	C	3.148e^-8	9.151e^-4	INTERGENIC
3L	5646353	3L_5646353_SNP [dm3] 3L_5653253_SNP [dm6]	A	G	3.485e^-8	9.974e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sbb
2L	9347663	2L_9347663_INS [dm3] 2L_9347663_INS [dm6]	T	TATGGAATT	3.795e^-8	0.001	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_kn
2R	7789298	2R_7789298_SNP [dm3] 2R_11901793_SNP [dm6]	C	G	3.808e^-8	0.001	DOWNSTREAM Zip48C INTRON MCPH1	TF binding site mE1_TFBS_sens
3R	13072274	3R_13072274_SNP [dm3] 3R_17246552_SNP [dm6]	G	C	4.157e^-8	0.001	INTRON beat-IIb
2R	1609104	2R_1609104_SNP [dm3] 2R_5721599_SNP [dm6]	G	T	4.392e^-8	0.001	INTRON ap
X	17124610	X_17124610_DEL [dm3] X_17230577_DEL [dm6]	AGCTCCA	A	4.461e^-8	0.001	CODON_DELETION CG10597	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	7619262	2L_7619262_SNP [dm3] 2L_7619262_SNP [dm6]	G	T	4.527e^-8	0.001	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_sens
3R	15694236	3R_15694236_SNP [dm3] 3R_19868514_SNP [dm6]	A	G	4.631e^-8	0.001	SYNONYMOUS_CODING CG4562 UTR_3_PRIME CG4562	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	20376633	3R_20376633_SNP [dm3] 3R_24550911_SNP [dm6]	G	T	4.670e^-8	0.001	INTRON Esyt2
3L	11725208	3L_11725208_SNP [dm3] 3L_11732108_SNP [dm6]	A	G	4.805e^-8	0.001	UPSTREAM CG32087 DOWNSTREAM CG32088 INTERGENIC
2L	10602765	2L_10602765_DEL [dm3] 2L_10602765_DEL [dm6]	TGTGAGTTGAACTACG...	T	5.037e^-8	0.001	INTRON Trim9
2R	9944708	2R_9944708_SNP [dm3] 2R_14057203_SNP [dm6]	C	T	5.056e^-8	0.001	SPLICE_SITE_REGION mam INTRON mam	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11725207	3L_11725207_SNP [dm3] 3L_11732107_SNP [dm6]	G	A	5.137e^-8	0.001	UPSTREAM CG32087 DOWNSTREAM CG32088 INTERGENIC
X	1758369	X_1758369_SNP [dm3] X_1864336_SNP [dm6]	G	A	5.160e^-8	0.001	SYNONYMOUS_CODING CG14814	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	1540226	2L_1540226_DEL [dm3] 2L_1540226_DEL [dm6]	TAT	T	5.259e^-8	0.001	INTERGENIC
2L	6346585	2L_6346585_SNP [dm3] 2L_6346585_SNP [dm6]	C	G	5.675e^-8	0.001	UTR_3_PRIME CG9497 DOWNSTREAM Cpr
X	2570839	X_2570839_SNP [dm3] X_2676806_SNP [dm6]	C	G	6.381e^-8	0.001	DOWNSTREAM sgg & 1 other INTRON sgg
2R	9882561	2R_9882561_SNP [dm3] 2R_13995056_SNP [dm6]	A	G	6.433e^-8	0.001	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2R	13763673	2R_13763673_INS [dm3] 2R_17876168_INS [dm6]	T	TC	7.389e^-8	0.002	INTRON Elk
3L	15265364	3L_15265364_SNP [dm3] 3L_15272264_SNP [dm6]	A	T	7.771e^-8	0.002	INTERGENIC
3L	15265365	3L_15265365_DEL [dm3] 3L_15272265_DEL [dm6]	AAAA	A	7.771e^-8	0.002	INTERGENIC
2R	8653575	2R_8653575_SNP [dm3] 2R_12766070_SNP [dm6]	G	C	7.911e^-8	0.002	INTERGENIC
2L	5789439	2L_5789439_SNP [dm3] 2L_5789439_SNP [dm6]	A	G	7.949e^-8	0.002	INTRON CG9171	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	14245124	X_14245124_SNP [dm3] X_14351091_SNP [dm6]	T	C	8.071e^-8	0.002	INTRON dpr8
2R	7469415	2R_7469415_SNP [dm3] 2R_11581910_SNP [dm6]	G	T	8.331e^-8	0.002	NON_SYNONYMOUS_CODING tou UTR_5_PRIME tou INTRON tou	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	1317183	2R_1317183_SNP [dm3] 2R_5429678_SNP [dm6]	C	G	8.453e^-8	0.002	INTRON laccase2	transposable element FlyBase
2L	7855791	2L_7855791_SNP [dm3] 2L_7855791_SNP [dm6]	T	C	9.190e^-8	0.002	UPSTREAM CG14535 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	7855792	2L_7855792_SNP [dm3] 2L_7855792_SNP [dm6]	A	T	9.190e^-8	0.002	UPSTREAM CG14535 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	10602623	2L_10602623_SNP [dm3] 2L_10602623_SNP [dm6]	T	A	9.820e^-8	0.002	INTRON Trim9
2L	15359139	2L_15359139_SNP [dm3] 2L_15359139_SNP [dm6]	C	A	9.832e^-8	0.002	INTERGENIC
X	11179566	X_11179566_SNP [dm3] X_11285533_SNP [dm6]	G	A	9.921e^-8	0.002	INTRON CG44422
2R	1604088	2R_1604088_SNP [dm3] 2R_5716583_SNP [dm6]	C	A	1.001e^-7	0.002	INTRON ap	TF binding site mE1_TFBS_cad
2R	1605534	2R_1605534_SNP [dm3] 2R_5718029_SNP [dm6]	G	A	1.001e^-7	0.002	INTRON ap	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	5555719	2R_5555719_SNP [dm3] 2R_9668214_SNP [dm6]	C	T	1.001e^-7	0.002	INTRON Mmp2
2R	5555859	2R_5555859_SNP [dm3] 2R_9668354_SNP [dm6]	A	C	1.001e^-7	0.002	INTRON Mmp2
X	14245116	X_14245116_SNP [dm3] X_14351083_SNP [dm6]	A	G	1.061e^-7	0.002	INTRON dpr8

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By genomic position
Variant impact
Gene name

Microbiota_OTU173 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results