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=9.051e^-14)
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

Covariate	χ²	p-value	Significance
wolba	3.7185	0.0538

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2162 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	1504711	3L_1504711_SNP [dm3] 3L_1504711_SNP [dm6]	A	G	1.185e^-6	0.499	SYNONYMOUS_CODING cue INTRON Psa	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	12353497	X_12353497_INS [dm3] X_12459464_INS [dm6]	G	GT	1.460e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353505	X_12353505_SNP [dm3] X_12459472_SNP [dm6]	C	G	1.460e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353530	X_12353530_SNP [dm3] X_12459497_SNP [dm6]	C	T	1.604e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353460	X_12353460_SNP [dm3] X_12459427_SNP [dm6]	A	G	1.799e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353328	X_12353328_DEL [dm3] X_12459295_DEL [dm6]	CCATATTATCCA...	C	2.274e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353312	X_12353312_SNP [dm3] X_12459279_SNP [dm6]	G	T	2.597e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
2L	6113198	2L_6113198_INS [dm3] 2L_6113198_INS [dm6]	A	AGC	2.676e^-6	0.499	INTRON stai
X	12353424	X_12353424_SNP [dm3] X_12459391_SNP [dm6]	G	A	2.749e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353504	X_12353504_SNP [dm3] X_12459471_SNP [dm6]	C	A	2.770e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	12353418	X_12353418_SNP [dm3] X_12459385_SNP [dm6]	A	T	3.115e^-6	0.499	DOWNSTREAM Rab40 INTERGENIC
X	14037617	X_14037617_SNP [dm3] X_14143584_SNP [dm6]	C	T	3.218e^-6	0.499	INTERGENIC
3L	17428403	3L_17428403_SNP [dm3] 3L_17435303_SNP [dm6]	A	T	4.286e^-6	0.523	SYNONYMOUS_CODING CG12229 INTRON CG32176	TF binding site mE1_TFBS_sens
2L	6113211	2L_6113211_SNP [dm3] 2L_6113211_SNP [dm6]	C	A	4.450e^-6	0.523	INTRON stai
X	12353522	X_12353522_SNP [dm3] X_12459489_SNP [dm6]	C	A	4.501e^-6	0.523	DOWNSTREAM Rab40 INTERGENIC
2L	7170554	2L_7170554_SNP [dm3] 2L_7170554_SNP [dm6]	A	T	4.906e^-6	0.523	INTERGENIC
3L	10641161	3L_10641161_SNP [dm3] 3L_10648061_SNP [dm6]	C	T	5.565e^-6	0.523	INTRON CG32066
2L	3401638	2L_3401638_SNP [dm3] 2L_3401638_SNP [dm6]	G	T	5.790e^-6	0.523	INTERGENIC
X	12353511	X_12353511_SNP [dm3] X_12459478_SNP [dm6]	C	T	6.258e^-6	0.523	DOWNSTREAM Rab40 INTERGENIC
3R	1554423	3R_1554423_SNP [dm3] 3R_5728701_SNP [dm6]	C	T	6.265e^-6	0.523	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi transposable element FlyBase
3L	1171292	3L_1171292_SNP [dm3] 3L_1171292_SNP [dm6]	C	T	6.436e^-6	0.523	INTRON bab2	regulatory region REDfly_CRMs
X	12646218	X_12646218_SNP [dm3] X_12752185_SNP [dm6]	G	C	6.623e^-6	0.523	EXON CR44619	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
X	12353495	X_12353495_SNP [dm3] X_12459462_SNP [dm6]	C	T	6.857e^-6	0.523	DOWNSTREAM Rab40 INTERGENIC
2L	6113210	2L_6113210_SNP [dm3] 2L_6113210_SNP [dm6]	A	C	6.913e^-6	0.523	INTRON stai
3L	1520090	3L_1520090_SNP [dm3] 3L_1520090_SNP [dm6]	C	T	7.193e^-6	0.523	SYNONYMOUS_CODING Psa	TF binding site mE1_TFBS_cad
X	12646225	X_12646225_SNP [dm3] X_12752192_SNP [dm6]	C	G	7.595e^-6	0.523	EXON CR44619	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
X	12353474	X_12353474_SNP [dm3] X_12459441_SNP [dm6]	T	A	9.412e^-6	0.523	DOWNSTREAM Rab40 INTERGENIC
3R	13150606	3R_13150606_SNP [dm3] 3R_17324884_SNP [dm6]	G	A	9.976e^-6	0.523	INTRON beat-IIa
2L	7956330	2L_7956330_SNP [dm3] 2L_7956330_SNP [dm6]	C	T	1.001e^-5	0.523	INTRON Snoo	TF binding site mE1_TFBS_inv
2L	18201222	2L_18201222_SNP [dm3] 2L_18201222_SNP [dm6]	G	A	1.041e^-5	0.523	DOWNSTREAM CR43413 INTRON CG42750
2L	18201230	2L_18201230_SNP [dm3] 2L_18201230_SNP [dm6]	A	T	1.041e^-5	0.523	DOWNSTREAM CR43413 INTRON CG42750
2R	6366396	2R_6366396_DEL [dm3] 2R_10478891_DEL [dm6]	GTGTTCTG	G	1.084e^-5	0.523	UPSTREAM whd DOWNSTREAM trsn & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2L	14350942	2L_14350942_SNP [dm3] 2L_14350942_SNP [dm6]	T	C	1.170e^-5	0.523	INTRON l_2_34Fc
3R	23717166	3R_23717166_SNP [dm3] 3R_27891444_SNP [dm6]	T	G	1.204e^-5	0.523	INTRON CG34353
2L	2792727	2L_2792727_INS [dm3] 2L_2792727_INS [dm6]	T	TT	1.208e^-5	0.523	UTR_3_PRIME Syt1 INTRON Syt1
3R	1599143	3R_1599143_SNP [dm3] 3R_5773421_SNP [dm6]	G	A	1.211e^-5	0.523	INTRON CG2082
3L	12474106	3L_12474106_SNP [dm3] 3L_12481006_SNP [dm6]	T	A	1.218e^-5	0.523	INTRON CG10663
3L	12474107	3L_12474107_SNP [dm3] 3L_12481007_SNP [dm6]	C	T	1.218e^-5	0.523	INTRON CG10663
2L	16340521	2L_16340521_SNP [dm3] 2L_16340521_SNP [dm6]	A	G	1.229e^-5	0.523	NON_SYNONYMOUS_CODING CG44405 UPSTREAM CG42266	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	19071623	X_19071623_SNP [dm3] X_19177590_SNP [dm6]	C	T	1.288e^-5	0.523	NON_SYNONYMOUS_CODING CG7556
3L	1814842	3L_1814842_SNP [dm3] 3L_1814842_SNP [dm6]	A	T	1.296e^-5	0.523	INTRON GV1
X	20864704	X_20864704_SNP [dm3] X_20993677_SNP [dm6]	C	A	1.305e^-5	0.523	INTERGENIC
3R	19710424	3R_19710424_SNP [dm3] 3R_23884702_SNP [dm6]	G	A	1.321e^-5	0.523	INTRON Pli
2R	10898349	2R_10898349_SNP [dm3] 2R_15010844_SNP [dm6]	T	A	1.325e^-5	0.523	UPSTREAM hbs INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk
3L	1520249	3L_1520249_SNP [dm3] 3L_1520249_SNP [dm6]	T	C	1.341e^-5	0.523	SYNONYMOUS_CODING Psa	TF binding site mE1_TFBS_cad
3L	11924163	3L_11924163_SNP [dm3] 3L_11931063_SNP [dm6]	G	A	1.370e^-5	0.523	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12353397	X_12353397_SNP [dm3] X_12459364_SNP [dm6]	A	T	1.372e^-5	0.523	DOWNSTREAM Rab40 INTERGENIC
2R	14556492	2R_14556492_SNP [dm3] 2R_18668987_SNP [dm6]	T	A	1.378e^-5	0.523	INTRON edl
3R	1554417	3R_1554417_SNP [dm3] 3R_5728695_SNP [dm6]	G	T	1.383e^-5	0.523	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi transposable element FlyBase
3L	14060675	3L_14060675_SNP [dm3] 3L_14067575_SNP [dm6]	C	T	1.489e^-5	0.523	INTRON CG32138
3L	11924134	3L_11924134_DEL [dm3] 3L_11931034_DEL [dm6]	TACAAT	T	1.493e^-5	0.523	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10179802	3L_10179802_DEL [dm3] 3L_10186702_DEL [dm6]	CCCAA	C	1.541e^-5	0.523	UPSTREAM dpr10 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	10238155	3R_10238155_SNP [dm3] 3R_14412433_SNP [dm6]	A	G	1.546e^-5	0.523	INTRON cv-c	TF binding site mE1_TFBS_inv
2R	2424244	2R_2424244_SNP [dm3] 2R_6536739_SNP [dm6]	T	C	1.568e^-5	0.523	INTRON jing
3R	13150582	3R_13150582_SNP [dm3] 3R_17324860_SNP [dm6]	C	T	1.574e^-5	0.523	INTRON beat-IIa
X	12353382	X_12353382_SNP [dm3] X_12459349_SNP [dm6]	A	T	1.613e^-5	0.523	DOWNSTREAM Rab40 INTERGENIC
X	12353384	X_12353384_SNP [dm3] X_12459351_SNP [dm6]	C	G	1.613e^-5	0.523	DOWNSTREAM Rab40 INTERGENIC
X	12353992	X_12353992_SNP [dm3] X_12459959_SNP [dm6]	T	C	1.632e^-5	0.523	UTR_3_PRIME Rab40
X	12353266	X_12353266_SNP [dm3] X_12459233_SNP [dm6]	G	A	1.731e^-5	0.535	DOWNSTREAM Rab40 INTERGENIC
X	12353268	X_12353268_SNP [dm3] X_12459235_SNP [dm6]	T	C	1.731e^-5	0.535	DOWNSTREAM Rab40 INTERGENIC
3L	574042	3L_574042_SNP [dm3] 3L_574042_SNP [dm6]	G	T	1.804e^-5	0.535	INTRON hipk	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	13804469	2L_13804469_SNP [dm3] 2L_13804469_SNP [dm6]	A	G	1.858e^-5	0.535	INTRON CAH1
X	21466619	X_21466619_DEL [dm3] X_21595592_DEL [dm6]	ACAC	A	1.878e^-5	0.535	INTERGENIC
X	12353301	X_12353301_DEL [dm3] X_12459268_DEL [dm6]	TG	C	1.976e^-5	0.535	DOWNSTREAM Rab40 INTERGENIC
2R	2424254	2R_2424254_SNP [dm3] 2R_6536749_SNP [dm6]	G	C	1.983e^-5	0.535	INTRON jing
3L	1520162	3L_1520162_SNP [dm3] 3L_1520162_SNP [dm6]	G	A	2.033e^-5	0.535	SYNONYMOUS_CODING Psa	TF binding site mE1_TFBS_cad
3L	1520652	3L_1520652_SNP [dm3] 3L_1520652_SNP [dm6]	C	T	2.033e^-5	0.535	SYNONYMOUS_CODING Psa	TF binding site mE1_TFBS_cad
3L	1520838	3L_1520838_SNP [dm3] 3L_1520838_SNP [dm6]	G	A	2.033e^-5	0.535	INTRON Psa	TF binding site mE1_TFBS_cad
3L	1521552	3L_1521552_SNP [dm3] 3L_1521552_SNP [dm6]	G	A	2.033e^-5	0.535	SYNONYMOUS_CODING Psa	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	7955589	2L_7955589_SNP [dm3] 2L_7955589_SNP [dm6]	A	T	2.041e^-5	0.535	INTRON Snoo
2L	7955593	2L_7955593_SNP [dm3] 2L_7955593_SNP [dm6]	A	T	2.041e^-5	0.535	INTRON Snoo
2R	9380805	2R_9380805_SNP [dm3] 2R_13493300_SNP [dm6]	T	G	2.218e^-5	0.565	INTRON bbc	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	1615752	2R_1615752_SNP [dm3] 2R_5728247_SNP [dm6]	T	A	2.232e^-5	0.565	UPSTREAM ap INTERGENIC
2R	10468428	2R_10468428_SNP [dm3] 2R_14580923_SNP [dm6]	G	A	2.249e^-5	0.565	INTRON ttv
X	2332359	X_2332359_SNP [dm3] X_2438326_SNP [dm6]	C	T	2.309e^-5	0.573	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5223822	2R_5223822_DEL [dm3] 2R_9336317_DEL [dm6]	TGCT	T	2.453e^-5	0.589	INTRON CG13954 & 1 other
2R	5223828	2R_5223828_INS [dm3] 2R_9336323_INS [dm6]	T	TG	2.453e^-5	0.589	INTRON CG13954 & 1 other
X	12353603	X_12353603_SNP [dm3] X_12459570_SNP [dm6]	C	A	2.475e^-5	0.589	DOWNSTREAM Rab40 INTERGENIC
2L	11183909	2L_11183909_SNP [dm3] 2L_11183909_SNP [dm6]	A	C	2.532e^-5	0.589	INTRON Ca-beta
2L	6113255	2L_6113255_SNP [dm3] 2L_6113255_SNP [dm6]	T	A	2.564e^-5	0.589	INTRON stai
2L	18871893	2L_18871893_SNP [dm3] 2L_18871893_SNP [dm6]	G	A	2.574e^-5	0.589	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	20785223	X_20785223_SNP [dm3] X_20914196_SNP [dm6]	T	A	2.627e^-5	0.589	INTRON shakB
2R	16173100	2R_16173100_SNP [dm3] 2R_20285595_SNP [dm6]	A	G	2.660e^-5	0.589	SPLICE_SITE_REGION CG16868 INTRON CG16868	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	9248864	3R_9248864_SNP [dm3] 3R_13423142_SNP [dm6]	A	G	2.682e^-5	0.589	DOWNSTREAM Ir87a INTERGENIC
3L	6321402	3L_6321402_SNP [dm3] 3L_6328302_SNP [dm6]	A	G	2.691e^-5	0.589	NON_SYNONYMOUS_CODING Or65c
2L	12395279	2L_12395279_SNP [dm3] 2L_12395279_SNP [dm6]	C	A	2.756e^-5	0.596	INTRON bru-2
3R	9248835	3R_9248835_SNP [dm3] 3R_13423113_SNP [dm6]	T	G	2.877e^-5	0.599	SYNONYMOUS_CODING Ir87a
X	12353347	X_12353347_SNP [dm3] X_12459314_SNP [dm6]	T	C	2.881e^-5	0.599	DOWNSTREAM Rab40 INTERGENIC
3L	16506931	3L_16506931_SNP [dm3] 3L_16513831_SNP [dm6]	T	C	2.892e^-5	0.599	INTRON CG43373
2L	6011338	2L_6011338_DEL [dm3] 2L_6011338_DEL [dm6]	TT	T	2.895e^-5	0.599	UPSTREAM CG9098 INTRON CG9098	TF binding site mE1_TFBS_Trl
2L	7956586	2L_7956586_SNP [dm3] 2L_7956586_SNP [dm6]	T	C	2.936e^-5	0.6	INTRON Snoo	TF binding site mE1_TFBS_inv
3R	24944288	3R_24944288_SNP [dm3] 3R_29118566_SNP [dm6]	A	G	3.048e^-5	0.612	UTR_3_PRIME yem DOWNSTREAM Atg14	TF binding site mE1_TFBS_chinmo
2R	16173112	2R_16173112_SNP [dm3] 2R_20285607_SNP [dm6]	T	A	3.089e^-5	0.612	INTRON CG16868	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	16506926	3L_16506926_SNP [dm3] 3L_16513826_SNP [dm6]	C	G	3.139e^-5	0.612	INTRON CG43373
3L	16809873	3L_16809873_SNP [dm3] 3L_16816773_SNP [dm6]	T	G	3.163e^-5	0.612	INTRON nudC & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	15436601	X_15436601_SNP [dm3] X_15542568_SNP [dm6]	A	G	3.172e^-5	0.612	INTRON Ac13E
2L	18201152	2L_18201152_SNP [dm3] 2L_18201152_SNP [dm6]	C	T	3.191e^-5	0.612	DOWNSTREAM CR43413 INTRON CG42750
3L	577515	3L_577515_SNP [dm3] 3L_577515_SNP [dm6]	G	A	3.311e^-5	0.619	UTR_3_PRIME hipk
2L	10124488	2L_10124488_SNP [dm3] 2L_10124488_SNP [dm6]	C	T	3.322e^-5	0.619	INTRON CG44153 & 1 other
3L	13545035	3L_13545035_SNP [dm3] 3L_13551935_SNP [dm6]	C	T	3.356e^-5	0.619	INTRON bru-3

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By genomic position
Variant impact
Gene name

Microbiota_OTU068 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results