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=2.811e^-6)
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_2R_NS	0.02191

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	7.1163	0.0285

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1924 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
X	2436373	X_2436373_SNP [dm3] X_2542340_SNP [dm6]	G	C	2.607e^-7	0.251	INTRON trol	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3R	23538649	3R_23538649_SNP [dm3] 3R_27712927_SNP [dm6]	C	G	2.972e^-7	0.251	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	14633266	2L_14633266_SNP [dm3] 2L_14633266_SNP [dm6]	C	A	5.685e^-7	0.251	INTRON osp
3L	11213323	3L_11213323_SNP [dm3] 3L_11220223_SNP [dm6]	A	C	6.709e^-7	0.251	INTRON CG42671	TF binding site mE1_TFBS_cad
3R	19532231	3R_19532231_SNP [dm3] 3R_23706509_SNP [dm6]	A	G	6.746e^-7	0.251	INTRON CR44052 & 1 other
2L	1231684	2L_1231684_DEL [dm3] 2L_1231684_DEL [dm6]	AA	A	9.361e^-7	0.252	INTERGENIC
3R	19530790	3R_19530790_SNP [dm3] 3R_23705068_SNP [dm6]	C	T	1.002e^-6	0.252	SYNONYMOUS_CODING CG31414 DOWNSTREAM CG31413	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23373731	3R_23373731_DEL [dm3] 3R_27548009_DEL [dm6]	TGTT	T	1.084e^-6	0.252	UTR_3_PRIME Klp98A DOWNSTREAM Gr98d	TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA
X	16343490	X_16343490_SNP [dm3] X_16449457_SNP [dm6]	G	A	1.373e^-6	0.284	UTR_5_PRIME Rbp2 INTRON Rbp2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	12771671	X_12771671_SNP [dm3] X_12877638_SNP [dm6]	T	G	1.745e^-6	0.324	INTRON Pde9
3R	21365747	3R_21365747_DEL [dm3] 3R_25540025_DEL [dm6]	GAGCTATCCGAG...	G	2.243e^-6	0.324	INTRON msi
X	9762803	X_9762803_SNP [dm3] X_9868770_SNP [dm6]	T	C	2.355e^-6	0.324	UPSTREAM CG45060 INTERGENIC
X	18865652	X_18865652_SNP [dm3] X_18971619_SNP [dm6]	G	T	2.769e^-6	0.324	INTRON CG43759
2L	1231760	2L_1231760_SNP [dm3] 2L_1231760_SNP [dm6]	G	T	2.826e^-6	0.324	INTERGENIC
2L	1231767	2L_1231767_DEL [dm3] 2L_1231767_DEL [dm6]	CT	A	2.826e^-6	0.324	INTERGENIC
2R	15468087	2R_15468087_SNP [dm3] 2R_19580582_SNP [dm6]	G	C	2.882e^-6	0.324	INTRON sm
2L	18262485	2L_18262485_SNP [dm3] 2L_18262485_SNP [dm6]	T	G	3.341e^-6	0.324	UPSTREAM CR44901 INTRON CG42750
2R	2833828	2R_2833828_SNP [dm3] 2R_6946323_SNP [dm6]	G	T	3.416e^-6	0.324	DOWNSTREAM tRNA:K2:42Ea INTRON mim & 1 other
3R	19600426	3R_19600426_SNP [dm3] 3R_23774704_SNP [dm6]	G	A	3.967e^-6	0.324	SYNONYMOUS_CODING Nup98-96 UPSTREAM CG10208	TF binding site mE1_TFBS_HSA
2L	10943390	2L_10943390_SNP [dm3] 2L_10943390_SNP [dm6]	A	C	4.004e^-6	0.324	UPSTREAM CR44492 INTRON dpr2 EXON CR44493
3R	27287037	3R_27287037_SNP [dm3] 3R_31461315_SNP [dm6]	C	A	4.018e^-6	0.324	INTRON CG11334
X	8757632	X_8757632_SNP [dm3] X_8863599_SNP [dm6]	C	A	4.019e^-6	0.324	UPSTREAM CG12075 INTRON CG12075
3R	18605557	3R_18605557_DEL [dm3] 3R_22779835_DEL [dm6]	GAGC	CG	4.179e^-6	0.324	UPSTREAM CR43654 INTRON CG7029 EXON CR43654	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25064853	3R_25064853_INS [dm3] 3R_29239131_INS [dm6]	T	TGTAT	4.579e^-6	0.324	UTR_3_PRIME CG31427 UPSTREAM CG11951 INTRON CG31427
2L	16010268	2L_16010268_SNP [dm3] 2L_16010268_SNP [dm6]	C	A	4.707e^-6	0.324	INTRON beat-Ic
2L	15433147	2L_15433147_SNP [dm3] 2L_15433147_SNP [dm6]	G	A	4.757e^-6	0.324	UPSTREAM CG4161 INTERGENIC
2L	15433162	2L_15433162_SNP [dm3] 2L_15433162_SNP [dm6]	G	C	4.757e^-6	0.324	UPSTREAM CG4161 INTERGENIC
3L	3293635	3L_3293635_SNP [dm3] 3L_3293635_SNP [dm6]	A	G	4.881e^-6	0.324	INTRON CG12009
3R	25150265	3R_25150265_SNP [dm3] 3R_29324543_SNP [dm6]	T	C	5.493e^-6	0.352	INTERGENIC
2R	11886156	2R_11886156_SNP [dm3] 2R_15998651_SNP [dm6]	T	G	5.877e^-6	0.354	INTRON ATPCL
2R	9015391	2R_9015391_SNP [dm3] 2R_13127886_SNP [dm6]	A	G	6.194e^-6	0.354	DOWNSTREAM CG3955 INTERGENIC
2L	11942092	2L_11942092_SNP [dm3] 2L_11942092_SNP [dm6]	G	A	6.274e^-6	0.354	INTERGENIC	regulatory region REDfly_CRMs
X	5393192	X_5393192_DEL [dm3] X_5499159_DEL [dm6]	TGGAATTGTT	T	6.511e^-6	0.354	INTERGENIC
X	5393205	X_5393205_SNP [dm3] X_5499172_SNP [dm6]	C	T	6.511e^-6	0.354	INTERGENIC
2L	11219035	2L_11219035_SNP [dm3] 2L_11219035_SNP [dm6]	C	A	6.661e^-6	0.354	INTRON ab	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	26600817	3R_26600817_SNP [dm3] 3R_30775095_SNP [dm6]	C	A	7.174e^-6	0.366	INTRON zfh1	TF binding site mE1_TFBS_cad
X	13689581	X_13689581_SNP [dm3] X_13795548_SNP [dm6]	A	T	7.278e^-6	0.366	DOWNSTREAM CG10996 INTRON inaE
X	5393187	X_5393187_SNP [dm3] X_5499154_SNP [dm6]	C	A	7.754e^-6	0.374	INTERGENIC
X	13971252	X_13971252_INS [dm3] X_14077219_INS [dm6]	A	AA	7.841e^-6	0.374	INTERGENIC	TF binding site mE1_TFBS_HSA
X	3983021	X_3983021_SNP [dm3] X_4088988_SNP [dm6]	C	A	8.927e^-6	0.415	INTRON CG43689	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	11886138	2R_11886138_SNP [dm3] 2R_15998633_SNP [dm6]	A	C	9.769e^-6	0.443	INTRON ATPCL
3L	11213350	3L_11213350_SNP [dm3] 3L_11220250_SNP [dm6]	A	G	1.048e^-5	0.458	INTRON CG42671	TF binding site mE1_TFBS_cad
3R	21670080	3R_21670080_SNP [dm3] 3R_25844358_SNP [dm6]	G	A	1.070e^-5	0.458	EXON CR45653
2L	1231441	2L_1231441_SNP [dm3] 2L_1231441_SNP [dm6]	T	C	1.083e^-5	0.458	INTERGENIC
2R	11886172	2R_11886172_SNP [dm3] 2R_15998667_SNP [dm6]	G	A	1.155e^-5	0.477	INTRON ATPCL
2L	14633263	2L_14633263_DEL [dm3] 2L_14633263_DEL [dm6]	CG	C	1.212e^-5	0.482	INTRON osp
3R	13821503	3R_13821503_SNP [dm3] 3R_17995781_SNP [dm6]	T	A	1.217e^-5	0.482	INTRON cpo
3R	23410655	3R_23410655_SNP [dm3] 3R_27584933_SNP [dm6]	G	A	1.244e^-5	0.482	NON_SYNONYMOUS_CODING raps	TF binding site mE1_TFBS_chinmo
2R	12963726	2R_12963726_DEL [dm3] 2R_17076221_DEL [dm6]	ACA	A	1.274e^-5	0.484	UPSTREAM CG30460 INTRON CG30460	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	677700	3L_677700_SNP [dm3] 3L_677700_SNP [dm6]	T	A	1.324e^-5	0.493	DOWNSTREAM CG17129 INTERGENIC
2R	997991	2R_997991_SNP [dm3] 2R_5110486_SNP [dm6]	T	C	1.449e^-5	0.506	INTERGENIC
3R	19254668	3R_19254668_SNP [dm3] 3R_23428946_SNP [dm6]	G	A	1.488e^-5	0.506	INTRON CG4374	TF binding site BDTNP1_TFBS_prd
X	7473703	X_7473703_SNP [dm3] X_7579670_SNP [dm6]	T	C	1.488e^-5	0.506	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	24035602	3R_24035602_SNP [dm3] 3R_28209880_SNP [dm6]	T	A	1.499e^-5	0.506	INTRON CG34354	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	986092	2R_986092_SNP [dm3] 2R_5098587_SNP [dm6]	C	T	1.517e^-5	0.506	INTERGENIC	transposable element FlyBase
3R	23635755	3R_23635755_SNP [dm3] 3R_27810033_SNP [dm6]	T	G	1.523e^-5	0.506	INTRON CG34353
2R	12822743	2R_12822743_SNP [dm3] 2R_16935238_SNP [dm6]	C	T	1.595e^-5	0.521	INTRON Pkc53E
2L	11942094	2L_11942094_SNP [dm3] 2L_11942094_SNP [dm6]	A	G	1.652e^-5	0.53	INTERGENIC	regulatory region REDfly_CRMs
2R	969917	2R_969917_SNP [dm3] 2R_5082412_SNP [dm6]	C	A	1.755e^-5	0.553	EXON CR43360	TF binding site mE1_TFBS_cad
3L	18658495	3L_18658495_SNP [dm3] 3L_18665395_SNP [dm6]	G	A	1.803e^-5	0.559	INTRON MYPT-75D	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	16010229	2L_16010229_SNP [dm3] 2L_16010229_SNP [dm6]	A	G	1.876e^-5	0.561	INTRON beat-Ic
2L	16010234	2L_16010234_SNP [dm3] 2L_16010234_SNP [dm6]	A	G	1.876e^-5	0.561	INTRON beat-Ic
3L	7746389	3L_7746389_SNP [dm3] 3L_7753289_SNP [dm6]	A	T	1.899e^-5	0.561	INTRON CG32373
2L	12203789	2L_12203789_SNP [dm3] 2L_12203789_SNP [dm6]	A	C	1.963e^-5	0.561	INTRON aret
2L	17056509	2L_17056509_SNP [dm3] 2L_17056509_SNP [dm6]	A	G	1.978e^-5	0.561	INTERGENIC
2L	4486067	2L_4486067_SNP [dm3] 2L_4486067_SNP [dm6]	T	A	1.991e^-5	0.561	SYNONYMOUS_CODING dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	23014876	3R_23014876_SNP [dm3] 3R_27189154_SNP [dm6]	G	T	2.131e^-5	0.564	INTRON Ser	regulatory region REDfly_CRMs
2L	1232900	2L_1232900_SNP [dm3] 2L_1232900_SNP [dm6]	G	A	2.161e^-5	0.564	INTERGENIC
3L	6339966	3L_6339966_SNP [dm3] 3L_6346866_SNP [dm6]	A	G	2.214e^-5	0.564	INTRON CG13300
2R	12962322	2R_12962322_SNP [dm3] 2R_17074817_SNP [dm6]	G	A	2.219e^-5	0.564	INTRON CG30460
3L	18359565	3L_18359565_SNP [dm3] 3L_18366465_SNP [dm6]	T	A	2.221e^-5	0.564	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	17067234	2L_17067234_SNP [dm3] 2L_17067234_SNP [dm6]	T	G	2.222e^-5	0.564	INTERGENIC
2R	2835140	2R_2835140_SNP [dm3] 2R_6947635_SNP [dm6]	T	C	2.229e^-5	0.564	UPSTREAM tRNA:K2:42Ea DOWNSTREAM tRNA:K2:42Eb & 1 other INTRON mim & 1 other
3R	24424135	3R_24424135_SNP [dm3] 3R_28598413_SNP [dm6]	T	A	2.266e^-5	0.564	SYNONYMOUS_CODING Noa36	TF binding site mE1_TFBS_sens
3L	13908933	3L_13908933_SNP [dm3] 3L_13915833_SNP [dm6]	A	T	2.298e^-5	0.564	INTRON Rgl
3R	25444997	3R_25444997_SNP [dm3] 3R_29619275_SNP [dm6]	G	T	2.303e^-5	0.564	START_GAINED CG1907 UTR_5_PRIME CG1907	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	19692709	3L_19692709_SNP [dm3] 3L_19699609_SNP [dm6]	T	A	2.402e^-5	0.566	INTERGENIC
3L	5180899	3L_5180899_SNP [dm3] 3L_5187799_SNP [dm6]	T	A	2.424e^-5	0.566	INTRON shep	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3L	1828827	3L_1828827_SNP [dm3] 3L_1828827_SNP [dm6]	A	T	2.431e^-5	0.566	UTR_5_PRIME Cpr62Ba INTRON Cpr62Ba
X	12850893	X_12850893_SNP [dm3] X_12956860_SNP [dm6]	G	A	2.440e^-5	0.566	INTRON hec
3L	14523237	3L_14523237_SNP [dm3] 3L_14530137_SNP [dm6]	A	T	2.464e^-5	0.566	INTRON bbg
3L	20249843	3L_20249843_SNP [dm3] 3L_20256743_SNP [dm6]	T	C	2.598e^-5	0.569	INTRON rdgC	TF binding site BDTNP1_TFBS_twi
3L	14523243	3L_14523243_SNP [dm3] 3L_14530143_SNP [dm6]	C	G	2.613e^-5	0.569	INTRON bbg
3L	14523259	3L_14523259_SNP [dm3] 3L_14530159_SNP [dm6]	C	A	2.613e^-5	0.569	INTRON bbg
2R	13996299	2R_13996299_SNP [dm3] 2R_18108794_SNP [dm6]	A	C	2.616e^-5	0.569	UPSTREAM CG5756 INTERGENIC
3R	17365784	3R_17365784_SNP [dm3] 3R_21540062_SNP [dm6]	A	C	2.643e^-5	0.569	INTERGENIC
2R	8417564	2R_8417564_SNP [dm3] 2R_12530059_SNP [dm6]	A	C	2.667e^-5	0.569	INTRON fra	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
X	19888635	X_19888635_SNP [dm3] X_19994602_SNP [dm6]	C	T	2.711e^-5	0.569	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	977056	2R_977056_SNP [dm3] 2R_5089551_SNP [dm6]	G	A	2.739e^-5	0.569	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_ttk
3L	7952792	3L_7952792_SNP [dm3] 3L_7959692_SNP [dm6]	A	C	2.753e^-5	0.569	INTERGENIC
2R	12965013	2R_12965013_SNP [dm3] 2R_17077508_SNP [dm6]	C	A	2.791e^-5	0.571	INTRON CG30460
3L	14327479	3L_14327479_SNP [dm3] 3L_14334379_SNP [dm6]	C	T	2.832e^-5	0.572	INTRON fz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	23335935	3R_23335935_SNP [dm3] 3R_27510213_SNP [dm6]	A	G	2.859e^-5	0.572	INTERGENIC
2L	12118083	2L_12118083_SNP [dm3] 2L_12118083_SNP [dm6]	T	G	2.907e^-5	0.575	INTRON CG17211
3L	12263165	3L_12263165_SNP [dm3] 3L_12270065_SNP [dm6]	C	T	3.034e^-5	0.582	UTR_3_PRIME Pbgs DOWNSTREAM CG32100
2R	19208828	2R_19208828_SNP [dm3] 2R_23321305_SNP [dm6]	C	G	3.065e^-5	0.582	DOWNSTREAM CG30416 INTERGENIC
2R	19208831	2R_19208831_SNP [dm3] 2R_23321308_SNP [dm6]	T	C	3.065e^-5	0.582	DOWNSTREAM CG30416 INTERGENIC
2R	19208840	2R_19208840_SNP [dm3] 2R_23321317_SNP [dm6]	G	A	3.065e^-5	0.582	DOWNSTREAM CG30416 INTERGENIC
3L	2771152	3L_2771152_SNP [dm3] 3L_2771152_SNP [dm6]	G	A	3.258e^-5	0.612	INTRON CG9977	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11268852	3R_11268852_SNP [dm3] 3R_15443130_SNP [dm6]	T	A	3.398e^-5	0.619	UTR_3_PRIME AdamTS-A DOWNSTREAM Act88F	TF binding site mE1_TFBS_cad

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By genomic position
Variant impact
Gene name

Microbiota_OTU017 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results