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=5.909e^-18)
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

25931 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	Transcript annotation	Binding site annotation
2L	10078242	2L_10078242_SNP [dm3] 2L_10078242_SNP [dm6]	A	G	INTRON CG44153
2L	10470277	2L_10470277_SNP [dm3] 2L_10470277_SNP [dm6]	C	G	INTRON RluA-1
2L	12263056	2L_12263056_SNP [dm3] 2L_12263056_SNP [dm6]	A	G	INTRON aret
2L	12406299	2L_12406299_SNP [dm3] 2L_12406299_SNP [dm6]	A	T	DOWNSTREAM vir-1 INTRON vir-1
2L	14012487	2L_14012487_SNP [dm3] 2L_14012487_SNP [dm6]	G	A	UPSTREAM bgm INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	16001993	2L_16001993_SNP [dm3] 2L_16001993_SNP [dm6]	T	C	DOWNSTREAM CG34167 INTRON beat-Ic EXON CR43825
2L	16015698	2L_16015698_SNP [dm3] 2L_16015698_SNP [dm6]	T	A	INTRON beat-Ic
2L	16016955	2L_16016955_SNP [dm3] 2L_16016955_SNP [dm6]	G	T	INTRON beat-Ic
2L	16017182	2L_16017182_SNP [dm3] 2L_16017182_SNP [dm6]	A	C	INTRON beat-Ic
2L	16018086	2L_16018086_SNP [dm3] 2L_16018086_SNP [dm6]	G	A	INTRON beat-Ic
2L	16021452	2L_16021452_SNP [dm3] 2L_16021452_SNP [dm6]	T	A	INTRON beat-Ic
2L	16021560	2L_16021560_SNP [dm3] 2L_16021560_SNP [dm6]	A	G	INTRON beat-Ic
2L	16021765	2L_16021765_SNP [dm3] 2L_16021765_SNP [dm6]	C	T	INTRON beat-Ic
2L	16022843	2L_16022843_SNP [dm3] 2L_16022843_SNP [dm6]	G	T	INTRON beat-Ic
2L	16023050	2L_16023050_SNP [dm3] 2L_16023050_SNP [dm6]	C	T	INTRON beat-Ic
2L	16023332	2L_16023332_SNP [dm3] 2L_16023332_SNP [dm6]	G	C	INTRON beat-Ic
2L	16023371	2L_16023371_SNP [dm3] 2L_16023371_SNP [dm6]	G	A	INTRON beat-Ic
2L	16023450	2L_16023450_SNP [dm3] 2L_16023450_SNP [dm6]	G	A	INTRON beat-Ic
2L	16027330	2L_16027330_SNP [dm3] 2L_16027330_SNP [dm6]	C	T	INTRON beat-Ic
2L	18138528	2L_18138528_SNP [dm3] 2L_18138528_SNP [dm6]	A	T	UPSTREAM kel DOWNSTREAM Socs36E INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	20244734	2L_20244734_SNP [dm3] 2L_20244734_SNP [dm6]	A	G	INTERGENIC
2L	20265321	2L_20265321_SNP [dm3] 2L_20265321_SNP [dm6]	C	T	UPSTREAM CG17570 INTERGENIC
2L	20266267	2L_20266267_INS [dm3] 2L_20266267_INS [dm6]	T	TCA	INTERGENIC
2L	20602810	2L_20602810_SNP [dm3] 2L_20602810_SNP [dm6]	A	C	DOWNSTREAM CG31677 INTRON CR44909
2L	20611995	2L_20611995_DEL [dm3] 2L_20611995_DEL [dm6]	ATATATATATA...	A	INTRON CR44909
2L	20890441	2L_20890441_SNP [dm3] 2L_20890441_SNP [dm6]	C	T	UPSTREAM sky INTRON sky & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	21056327	2L_21056327_SNP [dm3] 2L_21056327_SNP [dm6]	A	G	NON_SYNONYMOUS_CODING Itgbetanu
2L	8332477	2L_8332477_SNP [dm3] 2L_8332477_SNP [dm6]	C	T	SYNONYMOUS_CODING CG14275
2L	8746438	2L_8746438_SNP [dm3] 2L_8746438_SNP [dm6]	T	A	INTERGENIC
2L	8746486	2L_8746486_SNP [dm3] 2L_8746486_SNP [dm6]	A	T	INTERGENIC
2L	8746489	2L_8746489_SNP [dm3] 2L_8746489_SNP [dm6]	G	T	INTERGENIC
2L	9186538	2L_9186538_SNP [dm3] 2L_9186538_SNP [dm6]	C	T	INTRON tai	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9199928	2L_9199928_SNP [dm3] 2L_9199928_SNP [dm6]	T	G	INTRON tai
2L	9225132	2L_9225132_SNP [dm3] 2L_9225132_SNP [dm6]	C	T	INTRON tai	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	9453519	2L_9453519_INS [dm3] 2L_9453519_INS [dm6]	T	TT	INTRON numb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	9453521	2L_9453521_SNP [dm3] 2L_9453521_SNP [dm6]	T	G	INTRON numb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	9934888	2L_9934888_SNP [dm3] 2L_9934888_SNP [dm6]	T	C	UTR_3_PRIME CG31712
2L	9934895	2L_9934895_SNP [dm3] 2L_9934895_SNP [dm6]	T	C	UTR_3_PRIME CG31712
2R	10578770	2R_10578770_SNP [dm3] 2R_14691265_SNP [dm6]	C	G	INTRON mspo
2R	10589715	2R_10589715_SNP [dm3] 2R_14702210_SNP [dm6]	G	A	INTRON mspo
2R	10914320	2R_10914320_SNP [dm3] 2R_15026815_SNP [dm6]	G	A	INTRON hbs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
2R	12545689	2R_12545689_SNP [dm3] 2R_16658184_SNP [dm6]	A	G	INTRON Picot
2R	12546110	2R_12546110_SNP [dm3] 2R_16658605_SNP [dm6]	G	T	INTRON Picot
2R	12546217	2R_12546217_SNP [dm3] 2R_16658712_SNP [dm6]	T	G	INTRON Picot
2R	12547479	2R_12547479_SNP [dm3] 2R_16659974_SNP [dm6]	T	G	UPSTREAM Picot INTRON Picot
2R	13618071	2R_13618071_SNP [dm3] 2R_17730566_SNP [dm6]	G	T	INTRON CG4984 & 1 other
2R	14730490	2R_14730490_SNP [dm3] 2R_18842985_SNP [dm6]	T	G	SYNONYMOUS_CODING CG15099	TF binding site mE1_TFBS_cad
2R	14962665	2R_14962665_SNP [dm3] 2R_19075160_SNP [dm6]	C	A	INTRON 5-HT1A
2R	14962666	2R_14962666_SNP [dm3] 2R_19075161_SNP [dm6]	C	A	INTRON 5-HT1A
2R	15117861	2R_15117861_SNP [dm3] 2R_19230356_SNP [dm6]	A	T	INTRON cora	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	15294069	2R_15294069_SNP [dm3] 2R_19406564_SNP [dm6]	A	T	DOWNSTREAM hts INTRON hts
2R	16367296	2R_16367296_SNP [dm3] 2R_20479791_SNP [dm6]	A	G	DOWNSTREAM CG12484 INTERGENIC
2R	16377608	2R_16377608_SNP [dm3] 2R_20490103_SNP [dm6]	T	G	DOWNSTREAM CR44643 INTERGENIC
2R	16609987	2R_16609987_SNP [dm3] 2R_20722482_SNP [dm6]	C	T	UPSTREAM CR44660 INTRON dpr
2R	16867487	2R_16867487_SNP [dm3] 2R_20979982_SNP [dm6]	T	C	INTRON CG9313
2R	16942754	2R_16942754_SNP [dm3] 2R_21055249_SNP [dm6]	A	C	INTRON shg	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	16944039	2R_16944039_SNP [dm3] 2R_21056534_SNP [dm6]	C	A	UTR_5_PRIME shg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens mE1_TFBS_Trl
2R	16951437	2R_16951437_SNP [dm3] 2R_21063932_SNP [dm6]	T	G	NON_SYNONYMOUS_CODING Cht12 DOWNSTREAM Cht8
2R	16952513	2R_16952513_SNP [dm3] 2R_21065008_SNP [dm6]	T	G	UPSTREAM Cht12 DOWNSTREAM Cht4 INTERGENIC
2R	16952571	2R_16952571_SNP [dm3] 2R_21065066_SNP [dm6]	A	G	UPSTREAM Cht12 DOWNSTREAM Cht4 INTERGENIC
2R	16952573	2R_16952573_SNP [dm3] 2R_21065068_SNP [dm6]	A	G	UPSTREAM Cht12 DOWNSTREAM Cht4 INTERGENIC
2R	16952586	2R_16952586_SNP [dm3] 2R_21065081_SNP [dm6]	C	A	UPSTREAM Cht12 DOWNSTREAM Cht4 INTERGENIC
2R	16953922	2R_16953922_SNP [dm3] 2R_21066417_SNP [dm6]	T	C	NON_SYNONYMOUS_CODING Cht4 SPLICE_SITE_REGION Cht4	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	16955172	2R_16955172_SNP [dm3] 2R_21067667_SNP [dm6]	T	G	UPSTREAM Cht4 & 1 other DOWNSTREAM Cht9 INTERGENIC
2R	16955201	2R_16955201_DEL [dm3] 2R_21067696_DEL [dm6]	TGAAATACAT	T	UPSTREAM Cht4 & 1 other DOWNSTREAM Cht9 INTERGENIC
2R	16955227	2R_16955227_SNP [dm3] 2R_21067722_SNP [dm6]	C	A	UPSTREAM Cht4 & 1 other DOWNSTREAM Cht9 INTERGENIC
2R	16955244	2R_16955244_SNP [dm3] 2R_21067739_SNP [dm6]	A	T	UPSTREAM Cht4 & 1 other DOWNSTREAM Cht9 INTERGENIC
2R	16955273	2R_16955273_SNP [dm3] 2R_21067768_SNP [dm6]	C	T	UPSTREAM Cht4 & 1 other DOWNSTREAM Cht9 INTERGENIC
2R	17125021	2R_17125021_SNP [dm3] 2R_21237516_SNP [dm6]	A	C	INTRON ASPP
2R	17163596	2R_17163596_SNP [dm3] 2R_21276091_SNP [dm6]	T	A	INTRON Rgk3
2R	20180585	2R_20180585_SNP [dm3] 2R_24293062_SNP [dm6]	C	T	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	2728758	2R_2728758_SNP [dm3] 2R_6841253_SNP [dm6]	G	T	UPSTREAM CR44166 INTERGENIC
2R	2944841	2R_2944841_SNP [dm3] 2R_7057336_SNP [dm6]	G	A	SYNONYMOUS_CODING Tsp42Ep DOWNSTREAM Tsp42Eo & 1 other	TF binding site mE1_TFBS_chinmo
2R	2944931	2R_2944931_SNP [dm3] 2R_7057426_SNP [dm6]	C	A	DOWNSTREAM Tsp42Eo & 1 other INTRON Tsp42Ep	TF binding site mE1_TFBS_chinmo
2R	2953739	2R_2953739_SNP [dm3] 2R_7066234_SNP [dm6]	C	T	DOWNSTREAM Tsp42Er INTERGENIC
2R	2953768	2R_2953768_SNP [dm3] 2R_7066263_SNP [dm6]	G	A	DOWNSTREAM Tsp42Er INTERGENIC
2R	2954708	2R_2954708_SNP [dm3] 2R_7067203_SNP [dm6]	T	A	INTERGENIC	TF binding site mE1_TFBS_cad
2R	2961259	2R_2961259_SNP [dm3] 2R_7073754_SNP [dm6]	G	A	SYNONYMOUS_CODING CG12831
2R	2963151	2R_2963151_SNP [dm3] 2R_7075646_SNP [dm6]	C	T	INTERGENIC
2R	2968730	2R_2968730_SNP [dm3] 2R_7081225_SNP [dm6]	A	T	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	2987229	2R_2987229_SNP [dm3] 2R_7099724_SNP [dm6]	A	G	INTRON esn
2R	2987234	2R_2987234_SNP [dm3] 2R_7099729_SNP [dm6]	G	A	INTRON esn
2R	2995720	2R_2995720_SNP [dm3] 2R_7108215_SNP [dm6]	C	T	INTRON esn
2R	3007692	2R_3007692_SNP [dm3] 2R_7120187_SNP [dm6]	A	C	INTRON esn
2R	3081015	2R_3081015_SNP [dm3] 2R_7193510_SNP [dm6]	A	T	NON_SYNONYMOUS_CODING pk INTRON pk	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5408498	2R_5408498_SNP [dm3] 2R_9520993_SNP [dm6]	T	C	INTRON brp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	6073621	2R_6073621_SNP [dm3] 2R_10186116_SNP [dm6]	T	C	INTRON KCNQ
2R	6073703	2R_6073703_SNP [dm3] 2R_10186198_SNP [dm6]	A	T	INTRON KCNQ
3L	10423569	3L_10423569_SNP [dm3] 3L_10430469_SNP [dm6]	G	C	SYNONYMOUS_CODING Ir67b
3L	11898260	3L_11898260_SNP [dm3] 3L_11905160_SNP [dm6]	A	G	INTRON CG44837
3L	12950264	3L_12950264_SNP [dm3] 3L_12957164_SNP [dm6]	G	C	INTERGENIC
3L	12950269	3L_12950269_SNP [dm3] 3L_12957169_SNP [dm6]	A	T	INTERGENIC
3L	14074673	3L_14074673_SNP [dm3] 3L_14081573_SNP [dm6]	T	G	SYNONYMOUS_CODING btl	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	1733901	3L_1733901_SNP [dm3] 3L_1733901_SNP [dm6]	G	A	SYNONYMOUS_CODING Oseg4	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	17559710	3L_17559710_DEL [dm3] 3L_17566610_DEL [dm6]	CAC	C	UPSTREAM snoRNA:Me28S-A576 INTRON Eip74EF	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	19991045	3L_19991045_SNP [dm3] 3L_19997945_SNP [dm6]	T	C	UTR_3_PRIME CG7433 DOWNSTREAM CG7433 & 1 other
3L	2514490	3L_2514490_SNP [dm3] 3L_2514490_SNP [dm6]	T	A	INTRON Spn	TF binding site mE1_TFBS_sbb
3L	4944798	3L_4944798_SNP [dm3] 3L_4944798_SNP [dm6]	G	A	INTRON Con
3L	4944808	3L_4944808_SNP [dm3] 3L_4944808_SNP [dm6]	A	G	INTRON Con
3L	6093045	3L_6093045_SNP [dm3] 3L_6099945_SNP [dm6]	C	A	INTRON Ets65A

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By genomic position
Variant impact
Gene name

Microbiota_OTU051 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results