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=4.556e^-10)
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_P	0.01371

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.8038	0.094
In_3R_P	6.5431	0.0379

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2620 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	19197180	X_19197180_SNP [dm3] X_19303147_SNP [dm6]	A	T	7.891e^-9	0.005	INTRON CG8051
X	19197185	X_19197185_SNP [dm3] X_19303152_SNP [dm6]	G	C	7.891e^-9	0.005	INTRON CG8051
X	19197275	X_19197275_DEL [dm3] X_19303242_DEL [dm6]	GTAA	G	7.891e^-9	0.005	INTRON CG8051
X	19197213	X_19197213_SNP [dm3] X_19303180_SNP [dm6]	T	A	1.068e^-8	0.005	INTRON CG8051
X	9271054	X_9271054_SNP [dm3] X_9377021_SNP [dm6]	A	T	6.071e^-8	0.023	INTRON mgl
3L	7390249	3L_7390249_SNP [dm3] 3L_7397149_SNP [dm6]	A	C	1.234e^-7	0.033	NON_SYNONYMOUS_CODING CG32379
3L	7390266	3L_7390266_SNP [dm3] 3L_7397166_SNP [dm6]	A	G	1.234e^-7	0.033	NON_SYNONYMOUS_CODING CG32379
2L	2965886	2L_2965886_SNP [dm3] 2L_2965886_SNP [dm6]	A	G	2.150e^-7	0.045	UTR_3_PRIME Rbp9
2L	2265624	2L_2265624_SNP [dm3] 2L_2265624_SNP [dm6]	C	T	2.174e^-7	0.045	UPSTREAM CG34049 INTERGENIC
3L	13518121	3L_13518121_DEL [dm3] 3L_13525021_DEL [dm6]	TGGTT	T	2.597e^-7	0.047	UTR_3_PRIME bru-3
3L	7392890	3L_7392890_SNP [dm3] 3L_7399790_SNP [dm6]	C	T	2.807e^-7	0.047	UTR_3_PRIME CG8562 UPSTREAM CG18417
3L	11418611	3L_11418611_SNP [dm3] 3L_11425511_SNP [dm6]	C	A	3.000e^-7	0.047	SYNONYMOUS_CODING CG7560	TF binding site mE1_TFBS_cad
2R	18474638	2R_18474638_SNP [dm3] 2R_22587133_SNP [dm6]	T	C	4.071e^-7	0.058	INTRON dnr1
X	1380440	X_1380440_SNP [dm3] X_1486407_SNP [dm6]	C	T	4.853e^-7	0.06	UTR_3_PRIME Nmdar2 INTRON inc	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	9344621	2L_9344621_SNP [dm3] 2L_9344621_SNP [dm6]	G	A	4.865e^-7	0.06	UTR_3_PRIME CG3748 DOWNSTREAM CG3748
3L	10221419	3L_10221419_SNP [dm3] 3L_10228319_SNP [dm6]	G	A	6.760e^-7	0.07	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3L	5388358	3L_5388358_SNP [dm3] 3L_5395258_SNP [dm6]	T	C	6.767e^-7	0.07	INTERGENIC
X	9658116	X_9658116_SNP [dm3] X_9764083_SNP [dm6]	C	A	6.856e^-7	0.07	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	7050133	3L_7050133_SNP [dm3] 3L_7057033_SNP [dm6]	G	C	7.164e^-7	0.07	INTERGENIC
X	19197897	X_19197897_SNP [dm3] X_19303864_SNP [dm6]	T	G	9.490e^-7	0.082	SYNONYMOUS_CODING CG8051
3L	3279039	3L_3279039_SNP [dm3] 3L_3279039_SNP [dm6]	G	A	9.698e^-7	0.082	INTERGENIC
2L	15996764	2L_15996764_SNP [dm3] 2L_15996764_SNP [dm6]	T	G	9.698e^-7	0.082	INTERGENIC
3L	12758371	3L_12758371_SNP [dm3] 3L_12765271_SNP [dm6]	C	G	1.064e^-6	0.086	SYNONYMOUS_CODING CG32113	TF binding site mE1_TFBS_cad
2L	7552018	2L_7552018_DEL [dm3] 2L_7552018_DEL [dm6]	TCCCAAG	T	1.334e^-6	0.092	INTRON RapGAP1
2R	20684519	2R_20684519_SNP [dm3] 2R_24796996_SNP [dm6]	G	A	1.347e^-6	0.092	SYNONYMOUS_CODING Orc4 UPSTREAM CG12849	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	20684606	2R_20684606_SNP [dm3] 2R_24797083_SNP [dm6]	T	C	1.347e^-6	0.092	UPSTREAM CG12849 INTRON Orc4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	20684898	2R_20684898_SNP [dm3] 2R_24797375_SNP [dm6]	A	T	1.347e^-6	0.092	UTR_5_PRIME Orc4 UPSTREAM CG12849	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
3L	7392894	3L_7392894_SNP [dm3] 3L_7399794_SNP [dm6]	A	C	1.387e^-6	0.092	UTR_3_PRIME CG8562 UPSTREAM CG18417
X	14802854	X_14802854_SNP [dm3] X_14908821_SNP [dm6]	A	G	1.621e^-6	0.098	SYNONYMOUS_CODING CG9509 INTRON Flo2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	17010742	3R_17010742_SNP [dm3] 3R_21185020_SNP [dm6]	T	G	1.660e^-6	0.098	UTR_5_PRIME SNF4Agamma INTRON SNF4Agamma	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
X	15217450	X_15217450_SNP [dm3] X_15323417_SNP [dm6]	T	G	1.683e^-6	0.098	UPSTREAM Top1 INTRON Top1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	6837443	3L_6837443_SNP [dm3] 3L_6844343_SNP [dm6]	G	T	1.683e^-6	0.098	INTERGENIC
2R	1635175	2R_1635175_SNP [dm3] 2R_5747670_SNP [dm6]	T	A	1.760e^-6	0.099	INTERGENIC	TF binding site mE1_TFBS_cad
3L	7392849	3L_7392849_DEL [dm3] 3L_7399749_DEL [dm6]	CAC	C	1.966e^-6	0.099	UTR_3_PRIME CG8562 UPSTREAM CG18417
3L	3279025	3L_3279025_SNP [dm3] 3L_3279025_SNP [dm6]	C	A	2.048e^-6	0.099	INTERGENIC
X	6664816	X_6664816_SNP [dm3] X_6770783_SNP [dm6]	A	G	2.061e^-6	0.099	UPSTREAM COQ7 DOWNSTREAM shf & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt
2L	1544388	2L_1544388_SNP [dm3] 2L_1544388_SNP [dm6]	A	G	2.098e^-6	0.099	INTERGENIC
3L	7392844	3L_7392844_SNP [dm3] 3L_7399744_SNP [dm6]	A	G	2.117e^-6	0.099	UTR_3_PRIME CG8562 UPSTREAM CG18417
2R	7297083	2R_7297083_SNP [dm3] 2R_11409578_SNP [dm6]	C	A	2.156e^-6	0.099	UPSTREAM CG30026 DOWNSTREAM CG34054 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	2572543	2L_2572543_SNP [dm3] 2L_2572543_SNP [dm6]	A	C	2.168e^-6	0.099	SYNONYMOUS_CODING Cyp309a2 DOWNSTREAM Rad1 & 1 other	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad
2R	9683460	2R_9683460_SNP [dm3] 2R_13795955_SNP [dm6]	T	A	2.226e^-6	0.099	INTRON Cpr50Cb
2R	9683472	2R_9683472_SNP [dm3] 2R_13795967_SNP [dm6]	C	A	2.226e^-6	0.099	INTRON Cpr50Cb
2L	2965922	2L_2965922_SNP [dm3] 2L_2965922_SNP [dm6]	T	C	2.359e^-6	0.099	UTR_3_PRIME Rbp9
3R	7739054	3R_7739054_SNP [dm3] 3R_11913332_SNP [dm6]	G	T	2.537e^-6	0.099	INTRON Cad87A
X	7115622	X_7115622_SNP [dm3] X_7221589_SNP [dm6]	G	T	2.578e^-6	0.099	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	7115758	X_7115758_SNP [dm3] X_7221725_SNP [dm6]	G	A	2.578e^-6	0.099	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	7115780	X_7115780_SNP [dm3] X_7221747_SNP [dm6]	G	A	2.578e^-6	0.099	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	7115786	X_7115786_SNP [dm3] X_7221753_SNP [dm6]	C	A	2.578e^-6	0.099	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	6803228	2R_6803228_SNP [dm3] 2R_10915723_SNP [dm6]	G	C	2.758e^-6	0.099	INTERGENIC
2R	14705610	2R_14705610_MNP [dm3] 2R_18818105_MNP [dm6]	TAG	ATT	2.772e^-6	0.099	INTERGENIC
3L	6837432	3L_6837432_SNP [dm3] 3L_6844332_SNP [dm6]	G	T	2.862e^-6	0.099	INTERGENIC
2R	18476522	2R_18476522_SNP [dm3] 2R_22589017_SNP [dm6]	C	T	2.904e^-6	0.099	INTRON dnr1	TF binding site mE1_TFBS_inv
3L	2083454	3L_2083454_SNP [dm3] 3L_2083454_SNP [dm6]	C	T	2.989e^-6	0.099	SYNONYMOUS_CODING sls INTRON sls	TF binding site mE1_TFBS_HSA
2L	4294740	2L_4294740_SNP [dm3] 2L_4294740_SNP [dm6]	G	C	3.074e^-6	0.099	INTRON tutl	TF binding site mE1_TFBS_chinmo
3L	2891148	3L_2891148_SNP [dm3] 3L_2891148_SNP [dm6]	C	T	3.148e^-6	0.099	INTRON spz5
2L	16409030	2L_16409030_SNP [dm3] 2L_16409030_SNP [dm6]	A	G	3.160e^-6	0.099	INTRON CG5888
2L	1586943	2L_1586943_SNP [dm3] 2L_1586943_SNP [dm6]	G	A	3.165e^-6	0.099	SYNONYMOUS_CODING CG10869 INTRON haf
3L	11434438	3L_11434438_SNP [dm3] 3L_11441338_SNP [dm6]	C	A	3.213e^-6	0.099	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	8394832	3L_8394832_SNP [dm3] 3L_8401732_SNP [dm6]	C	T	3.374e^-6	0.099	SYNONYMOUS_CODING CG7120 DOWNSTREAM mkg-p & 1 other	TF binding site mE1_TFBS_cad
2R	14705596	2R_14705596_SNP [dm3] 2R_18818091_SNP [dm6]	A	C	3.398e^-6	0.099	INTERGENIC
2R	14705598	2R_14705598_DEL [dm3] 2R_18818093_DEL [dm6]	TA	T	3.398e^-6	0.099	INTERGENIC
2R	14705604	2R_14705604_DEL [dm3] 2R_18818099_DEL [dm6]	GTG	A	3.398e^-6	0.099	INTERGENIC
3L	8046491	3L_8046491_SNP [dm3] 3L_8053391_SNP [dm6]	T	C	3.435e^-6	0.099	UTR_3_PRIME nmo DOWNSTREAM nmo & 1 other
2R	6546411	2R_6546411_SNP [dm3] 2R_10658906_SNP [dm6]	T	G	3.442e^-6	0.099	INTERGENIC
2R	14842499	2R_14842499_SNP [dm3] 2R_18954994_SNP [dm6]	A	T	3.442e^-6	0.099	UTR_5_PRIME sano
2L	14565272	2L_14565272_SNP [dm3] 2L_14565272_SNP [dm6]	G	A	3.584e^-6	0.101	INTERGENIC
X	4614645	X_4614645_SNP [dm3] X_4720612_SNP [dm6]	T	A	3.760e^-6	0.104	INTRON Proc-R
2L	1159554	2L_1159554_SNP [dm3] 2L_1159554_SNP [dm6]	T	A	3.993e^-6	0.109	UPSTREAM CR43767 DOWNSTREAM CG5080 INTRON Tango14	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	6665069	X_6665069_SNP [dm3] X_6771036_SNP [dm6]	T	C	4.067e^-6	0.11	UPSTREAM COQ7 DOWNSTREAM shf & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt
3L	11418594	3L_11418594_SNP [dm3] 3L_11425494_SNP [dm6]	A	C	4.180e^-6	0.111	NON_SYNONYMOUS_CODING CG7560	TF binding site mE1_TFBS_cad
3L	3280444	3L_3280444_SNP [dm3] 3L_3280444_SNP [dm6]	A	G	4.273e^-6	0.112	START_GAINED CG12017 UTR_5_PRIME CG12017
3L	8155849	3L_8155849_SNP [dm3] 3L_8162749_SNP [dm6]	A	T	4.371e^-6	0.112	INTRON CG13675
3L	8455475	3L_8455475_SNP [dm3] 3L_8462375_SNP [dm6]	A	T	4.448e^-6	0.112	INTRON Gug	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	2581125	2R_2581125_SNP [dm3] 2R_6693620_SNP [dm6]	C	G	4.448e^-6	0.112	NON_SYNONYMOUS_CODING CG3270 DOWNSTREAM CG9422	TF binding site mE1_TFBS_chinmo
3L	7392852	3L_7392852_SNP [dm3] 3L_7399752_SNP [dm6]	A	T	4.592e^-6	0.114	UTR_3_PRIME CG8562 UPSTREAM CG18417
3L	4133221	3L_4133221_INS [dm3] 3L_4133221_INS [dm6]	A	ATA	4.930e^-6	0.12	INTRON ens	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2265654	2L_2265654_SNP [dm3] 2L_2265654_SNP [dm6]	C	T	4.986e^-6	0.12	UPSTREAM CG34049 INTERGENIC
3L	15834680	3L_15834680_SNP [dm3] 3L_15841580_SNP [dm6]	C	T	5.054e^-6	0.12	INTRON CG32150
2R	14009794	2R_14009794_SNP [dm3] 2R_18122289_SNP [dm6]	G	A	5.095e^-6	0.12	SYNONYMOUS_CODING stau	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	20587062	3L_20587062_SNP [dm3] 3L_20593962_SNP [dm6]	T	C	5.241e^-6	0.122	INTERGENIC
3R	26553502	3R_26553502_SNP [dm3] 3R_30727780_SNP [dm6]	G	T	5.464e^-6	0.126	UTR_3_PRIME CG1340	TF binding site mE1_TFBS_cad
X	1983611	X_1983611_SNP [dm3] X_2089578_SNP [dm6]	G	A	5.586e^-6	0.127	UTR_5_PRIME Unc-76 INTRON Unc-76	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	14905471	2R_14905471_SNP [dm3] 2R_19017966_SNP [dm6]	G	A	5.758e^-6	0.129	INTERGENIC
2L	11192164	2L_11192164_SNP [dm3] 2L_11192164_SNP [dm6]	A	G	5.847e^-6	0.13	INTRON Ca-beta
2L	8340949	2L_8340949_SNP [dm3] 2L_8340949_SNP [dm6]	T	C	5.972e^-6	0.13	SYNONYMOUS_CODING CG14274
3L	5388170	3L_5388170_SNP [dm3] 3L_5395070_SNP [dm6]	A	G	6.056e^-6	0.13	INTERGENIC
2L	7714172	2L_7714172_SNP [dm3] 2L_7714172_SNP [dm6]	A	G	6.057e^-6	0.13	SYNONYMOUS_CODING CG33296 DOWNSTREAM Ntl
3R	17082061	3R_17082061_SNP [dm3] 3R_21256339_SNP [dm6]	C	G	6.177e^-6	0.131	INTRON ETHR
2L	9344630	2L_9344630_SNP [dm3] 2L_9344630_SNP [dm6]	G	T	6.540e^-6	0.134	UTR_3_PRIME CG3748 DOWNSTREAM CG3748
2L	9344639	2L_9344639_SNP [dm3] 2L_9344639_SNP [dm6]	A	C	6.540e^-6	0.134	UTR_3_PRIME CG3748 DOWNSTREAM CG3748
3L	15239122	3L_15239122_SNP [dm3] 3L_15246022_SNP [dm6]	C	T	6.574e^-6	0.134	INTERGENIC
3L	7389703	3L_7389703_SNP [dm3] 3L_7396603_SNP [dm6]	A	C	6.857e^-6	0.137	SYNONYMOUS_CODING CG32379 DOWNSTREAM CG8563	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	8000954	2L_8000954_SNP [dm3] 2L_8000954_SNP [dm6]	G	A	6.884e^-6	0.137	INTRON Wwox
3L	2599006	3L_2599006_SNP [dm3] 3L_2599006_SNP [dm6]	T	G	6.907e^-6	0.137	SYNONYMOUS_CODING CG12182 UTR_5_PRIME CG12182 UPSTREAM CG16985	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_sens mE1_TFBS_Trl
2L	11192334	2L_11192334_SNP [dm3] 2L_11192334_SNP [dm6]	T	A	7.123e^-6	0.139	INTRON Ca-beta
2L	7508200	2L_7508200_SNP [dm3] 2L_7508200_SNP [dm6]	A	T	7.212e^-6	0.139	INTRON RapGAP1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	1904100	3L_1904100_SNP [dm3] 3L_1904100_SNP [dm6]	C	T	7.272e^-6	0.139	INTRON CG1887
2L	13030284	2L_13030284_SNP [dm3] 2L_13030284_SNP [dm6]	C	T	7.348e^-6	0.14	SYNONYMOUS_CODING CG9932	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	7289524	2L_7289524_SNP [dm3] 2L_7289524_SNP [dm6]	T	A	7.476e^-6	0.14	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	15057174	3R_15057174_SNP [dm3] 3R_19231452_SNP [dm6]	G	A	7.539e^-6	0.14	SYNONYMOUS_CODING unc79 DOWNSTREAM CG3773	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Microbiota_OTU028 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results