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=1.479e^-13)
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	0.002916

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	10.2972	0.0058

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

6072 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	12031268	3L_12031268_SNP [dm3] 3L_12038168_SNP [dm6]	C	G	7.121e^-17	1.325e^-10	INTRON rols
3L	8451039	3L_8451039_SNP [dm3] 3L_8457939_SNP [dm6]	C	T	5.110e^-13	4.071e^-7	INTRON Gug	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Trl
2R	17866839	2R_17866839_SNP [dm3] 2R_21979334_SNP [dm6]	T	C	6.565e^-13	4.071e^-7	SYNONYMOUS_CODING Gr58b UPSTREAM Gr58a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	5855431	3R_5855431_SNP [dm3] 3R_10029709_SNP [dm6]	G	C	3.357e^-12	1.561e^-6	INTRON Mical
2R	15207702	2R_15207702_INS [dm3] 2R_19320197_INS [dm6]	A	ACATTACA	4.977e^-12	1.852e^-6	INTRON Rgk1
3R	9795836	3R_9795836_SNP [dm3] 3R_13970114_SNP [dm6]	C	T	9.593e^-12	2.974e^-6	SYNONYMOUS_CODING rdx	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11522765	3L_11522765_SNP [dm3] 3L_11529665_SNP [dm6]	T	C	1.492e^-11	3.615e^-6	INTRON Mob2
2R	8176319	2R_8176319_INS [dm3] 2R_12288814_INS [dm6]	A	ATA	1.555e^-11	3.615e^-6	INTRON CG42700
2L	3867675	2L_3867675_SNP [dm3] 2L_3867675_SNP [dm6]	C	T	4.104e^-11	7.993e^-6	UPSTREAM Cep97 DOWNSTREAM CG3964 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2L	12765169	2L_12765169_SNP [dm3] 2L_12765169_SNP [dm6]	T	C	4.296e^-11	7.993e^-6	INTERGENIC
2R	16693092	2R_16693092_SNP [dm3] 2R_20805587_SNP [dm6]	A	G	5.110e^-11	8.644e^-6	INTERGENIC
2L	1707752	2L_1707752_SNP [dm3] 2L_1707752_SNP [dm6]	G	A	6.386e^-11	9.139e^-6	UTR_3_PRIME CG17660 UPSTREAM CR44976 DOWNSTREAM cpb	TF binding site mE1_TFBS_cad
2L	1707753	2L_1707753_SNP [dm3] 2L_1707753_SNP [dm6]	G	A	6.386e^-11	9.139e^-6	UTR_3_PRIME CG17660 UPSTREAM CR44976 DOWNSTREAM cpb	TF binding site mE1_TFBS_cad
2R	14709468	2R_14709468_DEL [dm3] 2R_18821963_DEL [dm6]	CC	C	1.344e^-10	1.786e^-5	DOWNSTREAM CG15097 & 1 other INTRON Phb2	TF binding site mE1_TFBS_cad
2R	15042857	2R_15042857_SNP [dm3] 2R_19155352_SNP [dm6]	A	C	1.574e^-10	1.952e^-5	UTR_5_PRIME ena INTRON ena	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	12765157	2L_12765157_SNP [dm3] 2L_12765157_SNP [dm6]	T	C	1.819e^-10	2.115e^-5	INTERGENIC
3R	17137902	3R_17137902_SNP [dm3] 3R_21312180_SNP [dm6]	T	A	2.244e^-10	2.456e^-5	EXON Hsromega
2R	14952171	2R_14952171_SNP [dm3] 2R_19064666_SNP [dm6]	G	T	2.702e^-10	2.793e^-5	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	17137907	3R_17137907_SNP [dm3] 3R_21312185_SNP [dm6]	G	A	3.253e^-10	3.185e^-5	EXON Hsromega
3L	16768392	3L_16768392_SNP [dm3] 3L_16775292_SNP [dm6]	C	T	3.702e^-10	3.316e^-5	SYNONYMOUS_CODING Nrt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	19895267	X_19895267_SNP [dm3] X_20001234_SNP [dm6]	C	T	3.742e^-10	3.316e^-5	NON_SYNONYMOUS_CODING CG17003	TF binding site mE1_TFBS_chinmo
3L	5285574	3L_5285574_SNP [dm3] 3L_5292474_SNP [dm6]	A	T	4.123e^-10	3.487e^-5	INTERGENIC
2L	6626194	2L_6626194_SNP [dm3] 2L_6626194_SNP [dm6]	G	C	4.802e^-10	3.745e^-5	NON_SYNONYMOUS_CODING Oatp26F DOWNSTREAM CG34345	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	16598389	2L_16598389_SNP [dm3] 2L_16598389_SNP [dm6]	T	G	4.863e^-10	3.745e^-5	INTRON CG42389	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	17894069	X_17894069_SNP [dm3] X_18000036_SNP [dm6]	C	A	5.135e^-10	3.745e^-5	INTRON Sh
3L	16427992	3L_16427992_SNP [dm3] 3L_16434892_SNP [dm6]	T	C	5.233e^-10	3.745e^-5	INTRON CG33158 & 1 other
2R	5635494	2R_5635494_SNP [dm3] 2R_9747989_SNP [dm6]	G	T	6.088e^-10	4.172e^-5	UTR_5_PRIME sqa UPSTREAM CheA46a
X	10860656	X_10860656_SNP [dm3] X_10966623_SNP [dm6]	A	T	6.389e^-10	4.172e^-5	INTRON C901
2L	2070954	2L_2070954_DEL [dm3] 2L_2070954_DEL [dm6]	TCTTTGATTT	T	6.503e^-10	4.172e^-5	INTRON dpr3
2L	171817	2L_171817_SNP [dm3] 2L_171817_SNP [dm6]	G	A	6.995e^-10	4.338e^-5	INTRON spen	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	4928467	X_4928467_SNP [dm3] X_5034434_SNP [dm6]	T	A	7.329e^-10	4.398e^-5	INTRON CR44833
3R	5587282	3R_5587282_SNP [dm3] 3R_9761560_SNP [dm6]	T	A	9.538e^-10	5.545e^-5	UTR_3_PRIME Snap24 DOWNSTREAM CG8417
3L	18655273	3L_18655273_SNP [dm3] 3L_18662173_SNP [dm6]	G	A	1.351e^-9	7.615e^-5	INTRON MYPT-75D
2L	710274	2L_710274_SNP [dm3] 2L_710274_SNP [dm6]	C	T	1.763e^-9	9.647e^-5	UPSTREAM CR44988 INTRON ds
3L	18655225	3L_18655225_SNP [dm3] 3L_18662125_SNP [dm6]	A	T	1.860e^-9	9.886e^-5	INTRON MYPT-75D
2L	20388449	2L_20388449_SNP [dm3] 2L_20388449_SNP [dm6]	G	T	3.182e^-9	1.634e^-4	INTRON CG10947
X	8478150	X_8478150_SNP [dm3] X_8584117_SNP [dm6]	G	A	3.250e^-9	1.634e^-4	NON_SYNONYMOUS_CODING CG12065	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	14206003	3L_14206003_INS [dm3] 3L_14212903_INS [dm6]	T	TGG	3.707e^-9	1.815e^-4	INTRON nuf	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	2085036	2L_2085036_SNP [dm3] 2L_2085036_SNP [dm6]	G	T	3.981e^-9	1.894e^-4	DOWNSTREAM CR44055 INTRON dpr3
3R	2318018	3R_2318018_SNP [dm3] 3R_6492296_SNP [dm6]	G	A	4.100e^-9	1.894e^-4	INTRON CG15186	TF binding site mE1_TFBS_cad
2R	7313871	2R_7313871_DEL [dm3] 2R_11426366_DEL [dm6]	ATAA	A	4.339e^-9	1.894e^-4	INTRON Drip
2R	1024810	2R_1024810_SNP [dm3] 2R_5137305_SNP [dm6]	A	T	4.350e^-9	1.894e^-4	INTERGENIC	transposable element FlyBase
3R	9628976	3R_9628976_INS [dm3] 3R_13803254_INS [dm6]	C	CC	4.377e^-9	1.894e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	19622756	2L_19622756_SNP [dm3] 2L_19622756_SNP [dm6]	T	C	5.997e^-9	2.536e^-4	INTRON Lar
3R	3416388	3R_3416388_SNP [dm3] 3R_7590666_SNP [dm6]	C	T	9.081e^-9	3.755e^-4	INTRON CG34127
2R	11585560	2R_11585560_SNP [dm3] 2R_15698055_SNP [dm6]	C	G	1.077e^-8	4.174e^-4	DOWNSTREAM CG30080 & 2 others INTERGENIC	TF binding site mE1_TFBS_bab1
2R	15209666	2R_15209666_SNP [dm3] 2R_19322161_SNP [dm6]	T	A	1.131e^-8	4.174e^-4	INTRON Rgk1	TF binding site mE1_TFBS_inv
3L	274909	3L_274909_SNP [dm3] 3L_274909_SNP [dm6]	T	C	1.152e^-8	4.174e^-4	UTR_3_PRIME miple2 UPSTREAM ttm2
2L	1714084	2L_1714084_SNP [dm3] 2L_1714084_SNP [dm6]	C	T	1.178e^-8	4.174e^-4	SYNONYMOUS_CODING frtz	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	7749889	X_7749889_SNP [dm3] X_7855856_SNP [dm6]	T	C	1.250e^-8	4.174e^-4	INTERGENIC
3R	1761481	3R_1761481_INS [dm3] 3R_5935759_INS [dm6]	C	CGTCTAA	1.253e^-8	4.174e^-4	INTRON CG34113
3R	1761482	3R_1761482_DEL [dm3] 3R_5935760_DEL [dm6]	TTGCCATTA	T	1.253e^-8	4.174e^-4	INTRON CG34113
X	12060488	X_12060488_SNP [dm3] X_12166455_SNP [dm6]	A	G	1.283e^-8	4.174e^-4	INTRON Ten-a
X	19908450	X_19908450_SNP [dm3] X_20014417_SNP [dm6]	C	T	1.347e^-8	4.174e^-4	UPSTREAM Dop2R INTRON Dop2R
X	19908498	X_19908498_SNP [dm3] X_20014465_SNP [dm6]	T	A	1.485e^-8	4.174e^-4	UPSTREAM Dop2R INTRON Dop2R
2L	15029851	2L_15029851_SNP [dm3] 2L_15029851_SNP [dm6]	C	T	1.490e^-8	4.174e^-4	SYNONYMOUS_CODING GABA-B-R1 DOWNSTREAM CG33310
2L	15031365	2L_15031365_SNP [dm3] 2L_15031365_SNP [dm6]	G	T	1.490e^-8	4.174e^-4	NON_SYNONYMOUS_CODING CG31832 INTRON GABA-B-R1
2L	15031905	2L_15031905_SNP [dm3] 2L_15031905_SNP [dm6]	A	G	1.490e^-8	4.174e^-4	UPSTREAM CG31832 INTRON GABA-B-R1
2L	15031956	2L_15031956_SNP [dm3] 2L_15031956_SNP [dm6]	A	T	1.490e^-8	4.174e^-4	UPSTREAM CG31832 INTRON GABA-B-R1
2L	15031960	2L_15031960_SNP [dm3] 2L_15031960_SNP [dm6]	T	G	1.490e^-8	4.174e^-4	UPSTREAM CG31832 INTRON GABA-B-R1
2L	16609803	2L_16609803_SNP [dm3] 2L_16609803_SNP [dm6]	G	A	1.490e^-8	4.174e^-4	NON_SYNONYMOUS_CODING CG4631 INTRON CG42389
3R	5655791	3R_5655791_SNP [dm3] 3R_9830069_SNP [dm6]	A	T	1.490e^-8	4.174e^-4	INTRON Teh1
3R	5655867	3R_5655867_SNP [dm3] 3R_9830145_SNP [dm6]	T	C	1.490e^-8	4.174e^-4	INTRON Teh1
3R	5865381	3R_5865381_SNP [dm3] 3R_10039659_SNP [dm6]	G	A	1.490e^-8	4.174e^-4	INTRON Mical
3R	5866688	3R_5866688_SNP [dm3] 3R_10040966_SNP [dm6]	T	C	1.490e^-8	4.174e^-4	INTRON Mical
2R	15209632	2R_15209632_SNP [dm3] 2R_19322127_SNP [dm6]	T	G	1.534e^-8	4.174e^-4	INTRON Rgk1	TF binding site mE1_TFBS_inv
X	8809756	X_8809756_SNP [dm3] X_8915723_SNP [dm6]	A	T	1.603e^-8	4.174e^-4	INTRON rdgA
2R	1024229	2R_1024229_SNP [dm3] 2R_5136724_SNP [dm6]	C	T	1.608e^-8	4.174e^-4	INTERGENIC	transposable element FlyBase
2R	1024243	2R_1024243_SNP [dm3] 2R_5136738_SNP [dm6]	C	A	1.608e^-8	4.174e^-4	INTERGENIC	transposable element FlyBase
2R	1027532	2R_1027532_SNP [dm3] 2R_5140027_SNP [dm6]	T	C	1.608e^-8	4.174e^-4	INTERGENIC
2R	1031474	2R_1031474_SNP [dm3] 2R_5143969_SNP [dm6]	C	G	1.608e^-8	4.174e^-4	UPSTREAM Atf6 INTERGENIC	transposable element FlyBase
3L	3468418	3L_3468418_SNP [dm3] 3L_3468418_SNP [dm6]	T	A	1.616e^-8	4.174e^-4	UTR_3_PRIME CG14971 DOWNSTREAM CycJ
2L	12765164	2L_12765164_SNP [dm3] 2L_12765164_SNP [dm6]	T	G	1.787e^-8	4.507e^-4	INTERGENIC
2R	19131156	2R_19131156_SNP [dm3] 2R_23243633_SNP [dm6]	G	T	1.823e^-8	4.507e^-4	DOWNSTREAM yip3 INTERGENIC
2L	4045651	2L_4045651_DEL [dm3] 2L_4045651_DEL [dm6]	TG	T	1.924e^-8	4.507e^-4	INTRON ed	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	4137890	X_4137890_DEL [dm3] X_4243857_DEL [dm6]	AAACAATATTTAA...	A	1.924e^-8	4.507e^-4	DOWNSTREAM Muc4B INTERGENIC
X	4137915	X_4137915_SNP [dm3] X_4243882_SNP [dm6]	A	C	1.924e^-8	4.507e^-4	DOWNSTREAM Muc4B INTERGENIC
3R	22811592	3R_22811592_SNP [dm3] 3R_26985870_SNP [dm6]	G	T	1.935e^-8	4.507e^-4	SYNONYMOUS_CODING CG31075 DOWNSTREAM CG14253	TF binding site mE1_TFBS_cad
X	4137957	X_4137957_DEL [dm3] X_4243924_DEL [dm6]	AGTTCG	A	1.963e^-8	4.507e^-4	DOWNSTREAM Muc4B INTERGENIC
2R	1031975	2R_1031975_SNP [dm3] 2R_5144470_SNP [dm6]	T	A	2.055e^-8	4.507e^-4	UPSTREAM Atf6 INTERGENIC	transposable element FlyBase
3R	23327567	3R_23327567_SNP [dm3] 3R_27501845_SNP [dm6]	T	A	2.085e^-8	4.507e^-4	NON_SYNONYMOUS_CODING CG43139 DOWNSTREAM CG5402
3R	23327635	3R_23327635_SNP [dm3] 3R_27501913_SNP [dm6]	G	C	2.085e^-8	4.507e^-4	NON_SYNONYMOUS_CODING CG43139 DOWNSTREAM CG5402
2R	1020872	2R_1020872_SNP [dm3] 2R_5133367_SNP [dm6]	A	T	2.156e^-8	4.507e^-4	INTERGENIC	transposable element FlyBase
2R	1027138	2R_1027138_SNP [dm3] 2R_5139633_SNP [dm6]	C	A	2.156e^-8	4.507e^-4	INTERGENIC	TF binding site mE1_TFBS_cad
2R	1035997	2R_1035997_SNP [dm3] 2R_5148492_SNP [dm6]	G	A	2.156e^-8	4.507e^-4	NON_SYNONYMOUS_CODING Atf6
2R	1036711	2R_1036711_SNP [dm3] 2R_5149206_SNP [dm6]	T	C	2.156e^-8	4.507e^-4	INTRON Atf6
2R	14489957	2R_14489957_SNP [dm3] 2R_18602452_SNP [dm6]	C	T	2.156e^-8	4.507e^-4	INTRON GEFmeso
X	15641956	X_15641956_SNP [dm3] X_15747923_SNP [dm6]	C	T	2.156e^-8	4.507e^-4	SYNONYMOUS_CODING Tcp-1zeta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	19899677	X_19899677_SNP [dm3] X_20005644_SNP [dm6]	A	T	2.156e^-8	4.507e^-4	UTR_3_PRIME Dop2R
X	8809749	X_8809749_SNP [dm3] X_8915716_SNP [dm6]	A	G	2.292e^-8	4.628e^-4	INTRON rdgA
3L	15373417	3L_15373417_SNP [dm3] 3L_15380317_SNP [dm6]	G	T	2.334e^-8	4.628e^-4	INTERGENIC
3L	11950719	3L_11950719_SNP [dm3] 3L_11957619_SNP [dm6]	G	T	2.366e^-8	4.628e^-4	UTR_5_PRIME CG11570 UPSTREAM CG43294 DOWNSTREAM CG7248
2L	5662627	2L_5662627_SNP [dm3] 2L_5662627_SNP [dm6]	A	T	2.427e^-8	4.628e^-4	UPSTREAM Hsp60C & 1 other INTERGENIC
2R	10867349	2R_10867349_SNP [dm3] 2R_14979844_SNP [dm6]	A	T	2.512e^-8	4.628e^-4	UTR_3_PRIME ckn
X	4137932	X_4137932_SNP [dm3] X_4243899_SNP [dm6]	C	A	2.535e^-8	4.628e^-4	DOWNSTREAM Muc4B INTERGENIC
X	4137949	X_4137949_INS [dm3] X_4243916_INS [dm6]	G	GTT	2.535e^-8	4.628e^-4	DOWNSTREAM Muc4B INTERGENIC
X	4137951	X_4137951_INS [dm3] X_4243918_INS [dm6]	A	AT	2.535e^-8	4.628e^-4	DOWNSTREAM Muc4B INTERGENIC
X	4137954	X_4137954_SNP [dm3] X_4243921_SNP [dm6]	A	T	2.535e^-8	4.628e^-4	DOWNSTREAM Muc4B INTERGENIC
X	4137976	X_4137976_SNP [dm3] X_4243943_SNP [dm6]	G	C	2.535e^-8	4.628e^-4	DOWNSTREAM Muc4B INTERGENIC
3R	10739739	3R_10739739_SNP [dm3] 3R_14914017_SNP [dm6]	G	C	2.546e^-8	4.628e^-4	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU020 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results