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=1.383e^-16)
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

14929 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	15772424	3L_15772424_SNP [dm3] 3L_15779324_SNP [dm6]	G	A	0	0	INTERGENIC
3L	23941852	3L_23941852_SNP [dm3] 3L_23948752_SNP [dm6]	G	T	0	0	INTRON CG40470
3L	23948927	3L_23948927_SNP [dm3] 3L_23955827_SNP [dm6]	A	T	0	0	INTRON CG40470
3L	23953498	3L_23953498_SNP [dm3] 3L_23960398_SNP [dm6]	T	A	0	0	INTRON CG40470
3L	23953546	3L_23953546_SNP [dm3] 3L_23960446_SNP [dm6]	C	A	0	0	INTRON CG40470
3L	23980145	3L_23980145_SNP [dm3] 3L_23987045_SNP [dm6]	A	G	0	0	UPSTREAM CG40470 INTERGENIC
3L	23980172	3L_23980172_SNP [dm3] 3L_23987072_SNP [dm6]	G	A	0	0	UPSTREAM CG40470 INTERGENIC
3L	24000392	3L_24000392_SNP [dm3] 3L_24007292_SNP [dm6]	A	G	0	0	INTERGENIC
3L	24000403	3L_24000403_SNP [dm3] 3L_24007303_SNP [dm6]	T	C	0	0	INTERGENIC
3L	24000667	3L_24000667_SNP [dm3] 3L_24007567_SNP [dm6]	C	G	0	0	INTERGENIC
3L	24001354	3L_24001354_SNP [dm3] 3L_24008254_SNP [dm6]	G	T	0	0	INTERGENIC
3L	24029261	3L_24029261_SNP [dm3] 3L_24036161_SNP [dm6]	G	A	0	0	DOWNSTREAM CG40045 INTERGENIC
3L	24035050	3L_24035050_SNP [dm3] 3L_24041950_SNP [dm6]	G	A	0	0	INTERGENIC
3L	24050464	3L_24050464_DEL [dm3] 3L_24057364_DEL [dm6]	ACTGTG	A	0	0	INTERGENIC
3L	24057576	3L_24057576_SNP [dm3] 3L_24064476_SNP [dm6]	C	T	0	0	INTERGENIC
3R	11998292	3R_11998292_SNP [dm3] 3R_16172570_SNP [dm6]	G	T	0	0	DOWNSTREAM CG6006 INTRON CG8925
3R	12009329	3R_12009329_SNP [dm3] 3R_16183607_SNP [dm6]	C	A	0	0	INTRON CG8927
3R	26893651	3R_26893651_INS [dm3] 3R_31067929_INS [dm6]	T	TGGA	0	0	INTRON Sox100B
2L	16015788	2L_16015788_SNP [dm3] 2L_16015788_SNP [dm6]	A	T	5.642e^-67	4.564e^-62	INTRON beat-Ic
3L	1551401	3L_1551401_SNP [dm3] 3L_1551401_SNP [dm6]	C	T	5.642e^-67	4.564e^-62	INTRON Cct1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	1551404	3L_1551404_SNP [dm3] 3L_1551404_SNP [dm6]	G	A	5.642e^-67	4.564e^-62	INTRON Cct1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	1551446	3L_1551446_INS [dm3] 3L_1551446_INS [dm6]	G	GTAG	5.642e^-67	4.564e^-62	INTRON Cct1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	8877836	X_8877836_SNP [dm3] X_8983803_SNP [dm6]	G	C	5.642e^-67	4.564e^-62	SYNONYMOUS_CODING CG12662 INTRON rdgA & 1 other
X	17170921	X_17170921_SNP [dm3] X_17276888_SNP [dm6]	A	T	5.982e^-66	4.460e^-61	INTRON f
2R	9266598	2R_9266598_SNP [dm3] 2R_13379093_SNP [dm6]	C	T	5.994e^-66	4.460e^-61	INTERGENIC
3R	26894999	3R_26894999_SNP [dm3] 3R_31069277_SNP [dm6]	C	T	6.916e^-65	4.949e^-60	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11886128	2R_11886128_INS [dm3] 2R_15998623_INS [dm6]	T	TT	6.739e^-64	4.643e^-59	INTRON ATPCL
2L	17375814	2L_17375814_SNP [dm3] 2L_17375814_SNP [dm6]	C	T	7.274e^-64	4.834e^-59	INTRON Lrch	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	3239182	2L_3239182_SNP [dm3] 2L_3239182_SNP [dm6]	A	T	7.772e^-63	4.986e^-58	INTERGENIC
X	17171228	X_17171228_SNP [dm3] X_17277195_SNP [dm6]	G	A	8.312e^-63	5.023e^-58	INTRON f
3R	26896054	3R_26896054_SNP [dm3] 3R_31070332_SNP [dm6]	A	T	8.370e^-63	5.023e^-58	INTRON Sox100B	TF binding site BDTNP1_TFBS_twi
X	17171224	X_17171224_SNP [dm3] X_17277191_SNP [dm6]	C	T	8.762e^-62	5.094e^-57	INTRON f
2L	6770735	2L_6770735_SNP [dm3] 2L_6770735_SNP [dm6]	C	T	5.015e^-22	2.827e^-17	INTRON CG11321
X	19309901	X_19309901_SNP [dm3] X_19415868_SNP [dm6]	T	G	5.947e^-22	3.254e^-17	INTRON kek5
2R	18906079	2R_18906079_SNP [dm3] 2R_23018556_SNP [dm6]	C	T	3.251e^-20	1.728e^-15	INTRON twi & 1 other
3L	23995369	3L_23995369_SNP [dm3] 3L_24002269_SNP [dm6]	T	A	7.774e^-20	4.017e^-15	INTERGENIC
3L	23970313	3L_23970313_SNP [dm3] 3L_23977213_SNP [dm6]	G	T	1.531e^-19	7.408e^-15	INTRON CG40470
3L	23993445	3L_23993445_SNP [dm3] 3L_24000345_SNP [dm6]	T	C	1.547e^-19	7.408e^-15	INTERGENIC
3L	23979086	3L_23979086_SNP [dm3] 3L_23985986_SNP [dm6]	C	T	1.553e^-19	7.408e^-15	INTRON CG40470
3L	23969634	3L_23969634_SNP [dm3] 3L_23976534_SNP [dm6]	T	C	3.102e^-19	1.443e^-14	INTRON CG40470
X	11842270	X_11842270_SNP [dm3] X_11948237_SNP [dm6]	T	A	1.162e^-18	5.271e^-14	INTRON cac
2L	10956848	2L_10956848_SNP [dm3] 2L_10956848_SNP [dm6]	T	A	1.488e^-18	6.436e^-14	INTRON dpr2
2L	10956853	2L_10956853_SNP [dm3] 2L_10956853_SNP [dm6]	C	A	1.488e^-18	6.436e^-14	INTRON dpr2
2R	11886138	2R_11886138_SNP [dm3] 2R_15998633_SNP [dm6]	A	C	2.898e^-18	1.225e^-13	INTRON ATPCL
2L	18212638	2L_18212638_SNP [dm3] 2L_18212638_SNP [dm6]	C	T	3.994e^-18	1.651e^-13	INTRON CG42750
2R	11886172	2R_11886172_SNP [dm3] 2R_15998667_SNP [dm6]	G	A	5.422e^-18	2.193e^-13	INTRON ATPCL
3L	4727462	3L_4727462_SNP [dm3] 3L_4727462_SNP [dm6]	A	C	6.269e^-17	2.474e^-12	INTRON RhoGEF64C
3L	1482100	3L_1482100_DEL [dm3] 3L_1482100_DEL [dm6]	TTCGTTCGGGACAAT...	T	6.382e^-17	2.474e^-12	INTRON stet	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_chinmo
2R	1337553	2R_1337553_SNP [dm3] 2R_5450048_SNP [dm6]	T	A	8.330e^-17	3.103e^-12	INTRON laccase2
X	8899167	X_8899167_SNP [dm3] X_9005134_SNP [dm6]	G	T	8.340e^-17	3.103e^-12	INTRON rdgA & 1 other
2L	20550969	2L_20550969_SNP [dm3] 2L_20550969_SNP [dm6]	A	G	1.195e^-16	3.913e^-12	INTERGENIC
3L	24002578	3L_24002578_DEL [dm3] 3L_24009478_DEL [dm6]	ACTCTATGCA	A	1.278e^-16	3.913e^-12	DOWNSTREAM CR40053 INTERGENIC
3L	24029932	3L_24029932_SNP [dm3] 3L_24036832_SNP [dm6]	A	T	1.278e^-16	3.913e^-12	DOWNSTREAM CG40045 INTERGENIC
3L	24029934	3L_24029934_DEL [dm3] 3L_24036834_DEL [dm6]	TTTATTTTATCACTCTTTAC...	T	1.278e^-16	3.913e^-12	DOWNSTREAM CG40045 INTERGENIC
3L	24030096	3L_24030096_DEL [dm3] 3L_24036996_DEL [dm6]	GATCG	G	1.278e^-16	3.913e^-12	INTERGENIC
3L	24033498	3L_24033498_SNP [dm3] 3L_24040398_SNP [dm6]	C	T	1.278e^-16	3.913e^-12	INTERGENIC
3L	24033547	3L_24033547_SNP [dm3] 3L_24040447_SNP [dm6]	C	T	1.278e^-16	3.913e^-12	INTERGENIC
3L	24042150	3L_24042150_SNP [dm3] 3L_24049050_SNP [dm6]	T	C	1.278e^-16	3.913e^-12	INTERGENIC
3L	24042180	3L_24042180_SNP [dm3] 3L_24049080_SNP [dm6]	A	G	1.278e^-16	3.913e^-12	INTERGENIC
3L	24042907	3L_24042907_DEL [dm3] 3L_24049807_DEL [dm6]	ACAACTTAAAATGACTCTAT...	A	1.278e^-16	3.913e^-12	INTERGENIC
3L	4309376	3L_4309376_SNP [dm3] 3L_4309376_SNP [dm6]	C	T	1.283e^-16	3.913e^-12	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	26765978	3R_26765978_SNP [dm3] 3R_30940256_SNP [dm6]	C	T	1.374e^-16	4.122e^-12	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	26927184	3R_26927184_DEL [dm3] 3R_31101462_DEL [dm6]	AATGATATAGGCGTGT...	A	1.492e^-16	4.366e^-12	UPSTREAM CG15553 INTERGENIC
3L	15773740	3L_15773740_SNP [dm3] 3L_15780640_SNP [dm6]	C	T	1.525e^-16	4.366e^-12	INTERGENIC
3L	15773741	3L_15773741_SNP [dm3] 3L_15780641_SNP [dm6]	C	A	1.525e^-16	4.366e^-12	INTERGENIC
3R	26923441	3R_26923441_DEL [dm3] 3R_31097719_DEL [dm6]	GTCTTTTACTACTTTG...	G	1.711e^-16	4.824e^-12	UPSTREAM CG11317 INTERGENIC
3L	24044561	3L_24044561_SNP [dm3] 3L_24051461_SNP [dm6]	A	G	2.238e^-16	6.215e^-12	INTERGENIC
3R	22556493	3R_22556493_SNP [dm3] 3R_26730771_SNP [dm6]	G	A	2.618e^-16	6.682e^-12	DOWNSTREAM CG14246 INTERGENIC
3R	26922271	3R_26922271_SNP [dm3] 3R_31096549_SNP [dm6]	A	T	2.807e^-16	6.682e^-12	INTRON CG11317
3R	26922912	3R_26922912_SNP [dm3] 3R_31097190_SNP [dm6]	C	A	2.807e^-16	6.682e^-12	START_GAINED CG11317 UTR_5_PRIME CG11317
2L	12101353	2L_12101353_SNP [dm3] 2L_12101353_SNP [dm6]	A	G	2.838e^-16	6.682e^-12	SYNONYMOUS_CODING Patsas DOWNSTREAM Ced-12
2L	14752808	2L_14752808_SNP [dm3] 2L_14752808_SNP [dm6]	A	T	2.838e^-16	6.682e^-12	INTERGENIC
2L	3239019	2L_3239019_SNP [dm3] 2L_3239019_SNP [dm6]	G	A	2.838e^-16	6.682e^-12	INTERGENIC
2L	3239077	2L_3239077_SNP [dm3] 2L_3239077_SNP [dm6]	G	C	2.838e^-16	6.682e^-12	INTERGENIC
2R	14063413	2R_14063413_SNP [dm3] 2R_18175908_SNP [dm6]	G	T	2.838e^-16	6.682e^-12	UTR_3_PRIME CG5726 DOWNSTREAM CG10916	TF binding site mE1_TFBS_cad
2R	17945307	2R_17945307_SNP [dm3] 2R_22057802_SNP [dm6]	G	A	2.838e^-16	6.682e^-12	UPSTREAM CG13500 INTERGENIC	TF binding site mE1_TFBS_cad
2R	17945308	2R_17945308_SNP [dm3] 2R_22057803_SNP [dm6]	G	A	2.838e^-16	6.682e^-12	UPSTREAM CG13500 INTERGENIC	TF binding site mE1_TFBS_cad
3R	23086254	3R_23086254_SNP [dm3] 3R_27260532_SNP [dm6]	T	G	2.838e^-16	6.682e^-12	SYNONYMOUS_CODING woc UPSTREAM woc EXON CR44049	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	17170978	X_17170978_DEL [dm3] X_17276945_DEL [dm6]	CAATCAT	C	2.838e^-16	6.682e^-12	INTRON f
2L	16241999	2L_16241999_SNP [dm3] 2L_16241999_SNP [dm6]	G	A	2.891e^-16	6.724e^-12	UTR_5_PRIME CG42818 DOWNSTREAM CG42817
2L	16124739	2L_16124739_SNP [dm3] 2L_16124739_SNP [dm6]	G	A	2.998e^-16	6.886e^-12	INTERGENIC
3L	24002365	3L_24002365_SNP [dm3] 3L_24009265_SNP [dm6]	T	A	3.846e^-16	8.678e^-12	DOWNSTREAM CR40053 INTERGENIC
3L	24005202	3L_24005202_SNP [dm3] 3L_24012102_SNP [dm6]	G	A	3.905e^-16	8.678e^-12	UPSTREAM CR40053 INTERGENIC
3L	24029826	3L_24029826_SNP [dm3] 3L_24036726_SNP [dm6]	A	G	3.918e^-16	8.678e^-12	DOWNSTREAM CG40045 INTERGENIC
2L	17331787	2L_17331787_SNP [dm3] 2L_17331787_SNP [dm6]	C	T	4.702e^-16	1.009e^-11	INTERGENIC
X	19285386	X_19285386_SNP [dm3] X_19391353_SNP [dm6]	T	C	4.718e^-16	1.009e^-11	INTRON kek5
X	17171165	X_17171165_SNP [dm3] X_17277132_SNP [dm6]	T	A	4.827e^-16	1.009e^-11	INTRON f
X	17171167	X_17171167_INS [dm3] X_17277134_INS [dm6]	G	ATACATTACATTTATACATT...	4.827e^-16	1.009e^-11	INTRON f
3L	3511253	3L_3511253_SNP [dm3] 3L_3511253_SNP [dm6]	C	T	4.828e^-16	1.009e^-11	SYNONYMOUS_CODING ImpE2 DOWNSTREAM CG42324	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	15773067	3L_15773067_SNP [dm3] 3L_15779967_SNP [dm6]	T	C	4.967e^-16	1.015e^-11	INTERGENIC
2R	17945532	2R_17945532_SNP [dm3] 2R_22058027_SNP [dm6]	G	A	4.974e^-16	1.015e^-11	UPSTREAM CG13500 DOWNSTREAM CG13501 INTERGENIC
3R	26916827	3R_26916827_SNP [dm3] 3R_31091105_SNP [dm6]	G	A	5.126e^-16	1.015e^-11	UTR_3_PRIME CG11317
2L	14752746	2L_14752746_SNP [dm3] 2L_14752746_SNP [dm6]	A	G	5.182e^-16	1.015e^-11	INTERGENIC
2L	3239345	2L_3239345_SNP [dm3] 2L_3239345_SNP [dm6]	C	G	5.182e^-16	1.015e^-11	INTERGENIC
3L	3797845	3L_3797845_SNP [dm3] 3L_3797845_SNP [dm6]	C	A	5.182e^-16	1.015e^-11	INTRON CG32264
3L	15772307	3L_15772307_SNP [dm3] 3L_15779207_SNP [dm6]	C	T	5.589e^-16	1.083e^-11	INTERGENIC
2L	1347497	2L_1347497_SNP [dm3] 2L_1347497_SNP [dm6]	A	T	7.979e^-16	1.507e^-11	INTERGENIC
2L	18239300	2L_18239300_SNP [dm3] 2L_18239300_SNP [dm6]	T	A	8.054e^-16	1.507e^-11	INTRON CG42750
3R	23088373	3R_23088373_SNP [dm3] 3R_27262651_SNP [dm6]	C	G	8.189e^-16	1.507e^-11	NON_SYNONYMOUS_CODING woc DOWNSTREAM CR44049	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	26899420	3R_26899420_SNP [dm3] 3R_31073698_SNP [dm6]	G	A	8.351e^-16	1.507e^-11	INTRON Sox100B

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By genomic position
Variant impact
Gene name

Microbiota_OTU091 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results