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=5.564e^-8)
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_2L_t	0.007002

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	13.5479	0.0011

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
2L	14550370	2L_14550370_SNP [dm3] 2L_14550370_SNP [dm6]	T	C	2.275e^-7	0.427	DOWNSTREAM CR44853 INTERGENIC	TF binding site mE1_TFBS_cad
2L	21006971	2L_21006971_SNP [dm3] 2L_21006971_SNP [dm6]	A	G	1.140e^-6	0.765	INTRON CG42238
3R	8103861	3R_8103861_SNP [dm3] 3R_12278139_SNP [dm6]	T	A	1.599e^-6	0.765	INTRON svp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
3R	8102682	3R_8102682_SNP [dm3] 3R_12276960_SNP [dm6]	G	A	2.102e^-6	0.765	INTRON svp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8102707	3R_8102707_SNP [dm3] 3R_12276985_SNP [dm6]	T	C	2.102e^-6	0.765	INTRON svp
X	13182667	X_13182667_SNP [dm3] X_13288634_SNP [dm6]	T	C	2.514e^-6	0.765	DOWNSTREAM CG15743 INTRON CG15744	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
3L	9989057	3L_9989057_SNP [dm3] 3L_9995957_SNP [dm6]	C	T	3.171e^-6	0.765	INTRON dpr6
2L	6145354	2L_6145354_SNP [dm3] 2L_6145354_SNP [dm6]	G	A	3.314e^-6	0.765	DOWNSTREAM CG13991 INTERGENIC
X	13182675	X_13182675_SNP [dm3] X_13288642_SNP [dm6]	T	C	4.494e^-6	0.765	DOWNSTREAM CG15743 INTRON CG15744	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2L	8883344	2L_8883344_SNP [dm3] 2L_8883344_SNP [dm6]	C	T	4.603e^-6	0.765	INTERGENIC
3L	7149700	3L_7149700_SNP [dm3] 3L_7156600_SNP [dm6]	C	T	5.841e^-6	0.765	UTR_5_PRIME corn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	18836900	3L_18836900_SNP [dm3] 3L_18843800_SNP [dm6]	G	A	7.026e^-6	0.765	INTRON Indy
2L	14001545	2L_14001545_SNP [dm3] 2L_14001545_SNP [dm6]	G	A	7.484e^-6	0.765	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3R	14333003	3R_14333003_SNP [dm3] 3R_18507281_SNP [dm6]	G	T	7.540e^-6	0.765	UPSTREAM fru INTRON fru	TF binding site mE1_TFBS_HSA
2L	8883300	2L_8883300_SNP [dm3] 2L_8883300_SNP [dm6]	G	A	7.610e^-6	0.765	INTERGENIC
X	4448450	X_4448450_SNP [dm3] X_4554417_SNP [dm6]	G	C	7.700e^-6	0.765	UPSTREAM CG11444 INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4442442	2L_4442442_SNP [dm3] 2L_4442442_SNP [dm6]	G	A	7.749e^-6	0.765	UTR_5_PRIME CG15432 UPSTREAM Sfp24F DOWNSTREAM morgue INTRON CG15432	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
2L	7226594	2L_7226594_DEL [dm3] 2L_7226594_DEL [dm6]	GG	G	7.768e^-6	0.765	UTR_3_PRIME Ndae1 INTRON Ndae1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
3R	8105599	3R_8105599_SNP [dm3] 3R_12279877_SNP [dm6]	A	T	8.024e^-6	0.765	INTRON svp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
2L	14001501	2L_14001501_SNP [dm3] 2L_14001501_SNP [dm6]	T	C	8.489e^-6	0.765	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2L	14001563	2L_14001563_SNP [dm3] 2L_14001563_SNP [dm6]	G	C	8.560e^-6	0.765	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2R	10526790	2R_10526790_SNP [dm3] 2R_14639285_SNP [dm6]	G	T	9.387e^-6	0.776	NON_SYNONYMOUS_CODING CG42715 DOWNSTREAM CG43236 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	14001547	2L_14001547_SNP [dm3] 2L_14001547_SNP [dm6]	G	A	1.082e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
X	6137389	X_6137389_SNP [dm3] X_6243356_SNP [dm6]	G	A	1.093e^-5	0.776	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9143032	2R_9143032_INS [dm3] 2R_13255527_INS [dm6]	T	TATTT	1.099e^-5	0.776	UPSTREAM CR44343 INTERGENIC
X	6137091	X_6137091_SNP [dm3] X_6243058_SNP [dm6]	G	A	1.118e^-5	0.776	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8102838	3R_8102838_SNP [dm3] 3R_12277116_SNP [dm6]	T	C	1.150e^-5	0.776	INTRON svp
3L	9974615	3L_9974615_SNP [dm3] 3L_9981515_SNP [dm6]	T	C	1.191e^-5	0.776	INTRON dpr6
X	16897236	X_16897236_DEL [dm3] X_17003203_DEL [dm6]	ACTCGA	A	1.252e^-5	0.776	INTRON CG45002
3L	18372301	3L_18372301_SNP [dm3] 3L_18379201_SNP [dm6]	C	A	1.263e^-5	0.776	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2L	8069478	2L_8069478_SNP [dm3] 2L_8069478_SNP [dm6]	C	T	1.330e^-5	0.776	SYNONYMOUS_CODING poe	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	14001569	2L_14001569_SNP [dm3] 2L_14001569_SNP [dm6]	C	T	1.363e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2L	14001536	2L_14001536_SNP [dm3] 2L_14001536_SNP [dm6]	G	C	1.385e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	8876305	3L_8876305_SNP [dm3] 3L_8883205_SNP [dm6]	A	C	1.491e^-5	0.776	INTRON dally
3L	7568737	3L_7568737_SNP [dm3] 3L_7575637_SNP [dm6]	A	G	1.630e^-5	0.776	INTERGENIC
X	16751460	X_16751460_SNP [dm3] X_16857427_SNP [dm6]	T	C	1.682e^-5	0.776	INTRON CG13003
2L	18568499	2L_18568499_SNP [dm3] 2L_18568499_SNP [dm6]	A	G	1.704e^-5	0.776	INTRON Pde11
2L	16232387	2L_16232387_SNP [dm3] 2L_16232387_SNP [dm6]	T	G	1.748e^-5	0.776	INTRON CG42817	TF binding site BDTNP1_TFBS_slp1
3L	1129068	3L_1129068_DEL [dm3] 3L_1129068_DEL [dm6]	AG	A	1.753e^-5	0.776	INTERGENIC	regulatory region REDfly_CRMs
3L	8876245	3L_8876245_SNP [dm3] 3L_8883145_SNP [dm6]	C	T	1.772e^-5	0.776	INTRON dally
X	6311352	X_6311352_INS [dm3] X_6417319_INS [dm6]	T	TAA	1.774e^-5	0.776	INTERGENIC
3R	13639450	3R_13639450_SNP [dm3] 3R_17813728_SNP [dm6]	A	G	1.926e^-5	0.776	INTRON tinc	TF binding site mE1_TFBS_HSA
2L	14299698	2L_14299698_SNP [dm3] 2L_14299698_SNP [dm6]	C	T	1.977e^-5	0.776	INTRON wb
2R	9108046	2R_9108046_SNP [dm3] 2R_13220541_SNP [dm6]	A	T	2.031e^-5	0.776	UPSTREAM CG4646 DOWNSTREAM Fsn INTRON CG17059	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
2L	4699900	2L_4699900_SNP [dm3] 2L_4699900_SNP [dm6]	C	A	2.044e^-5	0.776	DOWNSTREAM Taf12L INTRON CG34351
X	5471376	X_5471376_SNP [dm3] X_5577343_SNP [dm6]	T	C	2.049e^-5	0.776	INTERGENIC
2R	14883286	2R_14883286_DEL [dm3] 2R_18995781_DEL [dm6]	ATAGGCTTGA	A	2.065e^-5	0.776	DOWNSTREAM snoRNA:abba-a INTRON tn
3L	7583305	3L_7583305_SNP [dm3] 3L_7590205_SNP [dm6]	G	A	2.087e^-5	0.776	SYNONYMOUS_CODING CG7716
3L	18091808	3L_18091808_SNP [dm3] 3L_18098708_SNP [dm6]	A	T	2.097e^-5	0.776	INTRON CG13698
3L	9396652	3L_9396652_SNP [dm3] 3L_9403552_SNP [dm6]	A	T	2.250e^-5	0.776	INTERGENIC
3L	18836861	3L_18836861_SNP [dm3] 3L_18843761_SNP [dm6]	G	A	2.319e^-5	0.776	DOWNSTREAM CR32027 INTRON Indy
3R	14832816	3R_14832816_SNP [dm3] 3R_19007094_SNP [dm6]	C	A	2.324e^-5	0.776	INTRON gukh
X	6137319	X_6137319_SNP [dm3] X_6243286_SNP [dm6]	T	G	2.416e^-5	0.776	SYNONYMOUS_CODING Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	13996612	X_13996612_SNP [dm3] X_14102579_SNP [dm6]	T	C	2.462e^-5	0.776	DOWNSTREAM tRNA:S4:12Ee INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	14001533	2L_14001533_SNP [dm3] 2L_14001533_SNP [dm6]	T	C	2.570e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3R	9970736	3R_9970736_SNP [dm3] 3R_14145014_SNP [dm6]	G	A	2.650e^-5	0.776	INTERGENIC
3L	9228609	3L_9228609_SNP [dm3] 3L_9235509_SNP [dm6]	C	G	2.677e^-5	0.776	NON_SYNONYMOUS_CODING CG4483
2L	19097106	2L_19097106_SNP [dm3] 2L_19097106_SNP [dm6]	G	T	2.701e^-5	0.776	INTRON Lim3
X	4448456	X_4448456_SNP [dm3] X_4554423_SNP [dm6]	G	A	2.806e^-5	0.776	UPSTREAM CG11444 INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1582237	3L_1582237_SNP [dm3] 3L_1582237_SNP [dm6]	A	G	2.811e^-5	0.776	INTRON CG13917
X	14881902	X_14881902_SNP [dm3] X_14987869_SNP [dm6]	A	C	2.875e^-5	0.776	INTRON eag	TF binding site BDTNP1_TFBS_dl
3R	8110711	3R_8110711_DEL [dm3] 3R_12284989_DEL [dm6]	AA	A	2.880e^-5	0.776	INTRON svp
X	6136089	X_6136089_SNP [dm3] X_6242056_SNP [dm6]	G	A	2.917e^-5	0.776	INTRON Rbcn-3A	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	12031173	2L_12031173_SNP [dm3] 2L_12031173_SNP [dm6]	A	G	2.955e^-5	0.776	INTRON dmGlut
2L	14001556	2L_14001556_SNP [dm3] 2L_14001556_SNP [dm6]	A	C	2.968e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	18836857	3L_18836857_SNP [dm3] 3L_18843757_SNP [dm6]	A	G	2.991e^-5	0.776	DOWNSTREAM CR32027 INTRON Indy
3R	25622095	3R_25622095_SNP [dm3] 3R_29796373_SNP [dm6]	G	A	2.995e^-5	0.776	SYNONYMOUS_CODING CG7837 DOWNSTREAM sro	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	15553812	2L_15553812_INS [dm3] 2L_15553812_INS [dm6]	T	TG	3.003e^-5	0.776	INTRON kek3
X	13996614	X_13996614_INS [dm3] X_14102581_INS [dm6]	T	TGT	3.049e^-5	0.776	DOWNSTREAM tRNA:S4:12Ee INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	5103923	2R_5103923_INS [dm3] 2R_9216418_INS [dm6]	A	AGTGCGTTG	3.085e^-5	0.776	INTERGENIC
2L	7696878	2L_7696878_SNP [dm3] 2L_7696878_SNP [dm6]	T	A	3.187e^-5	0.776	INTRON Tep2
2L	17432405	2L_17432405_SNP [dm3] 2L_17432405_SNP [dm6]	G	A	3.314e^-5	0.776	INTRON Dif
2L	9547699	2L_9547699_SNP [dm3] 2L_9547699_SNP [dm6]	C	G	3.370e^-5	0.776	DOWNSTREAM jp & 1 other INTERGENIC
2L	14001513	2L_14001513_SNP [dm3] 2L_14001513_SNP [dm6]	G	A	3.399e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2R	20052058	2R_20052058_SNP [dm3] 2R_24164535_SNP [dm6]	G	A	3.406e^-5	0.776	INTRON CG3328	TF binding site mE1_TFBS_chinmo
3R	14549466	3R_14549466_INS [dm3] 3R_18723744_INS [dm6]	A	AGA	3.423e^-5	0.776	INTRON Cha
2L	13631696	2L_13631696_DEL [dm3] 2L_13631696_DEL [dm6]	TCGTTCATTCGTGTT...	T	3.434e^-5	0.776	DOWNSTREAM CR43410 INTRON kuz
3L	18836662	3L_18836662_SNP [dm3] 3L_18843562_SNP [dm6]	G	A	3.469e^-5	0.776	DOWNSTREAM CR32027 INTRON Indy
3L	18269289	3L_18269289_SNP [dm3] 3L_18276189_SNP [dm6]	T	G	3.568e^-5	0.776	INTERGENIC
3L	2284102	3L_2284102_DEL [dm3] 3L_2284102_DEL [dm6]	GTTGG	G	3.595e^-5	0.776	INTRON MsR2
2L	7392700	2L_7392700_SNP [dm3] 2L_7392700_SNP [dm6]	G	C	3.605e^-5	0.776	INTRON CG5160
3L	18099093	3L_18099093_SNP [dm3] 3L_18105993_SNP [dm6]	A	T	3.610e^-5	0.776	UTR_5_PRIME CG13698 UPSTREAM mRpS26	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	9108073	2R_9108073_SNP [dm3] 2R_13220568_SNP [dm6]	T	A	3.612e^-5	0.776	UPSTREAM CG4646 DOWNSTREAM Fsn INTRON CG17059	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
X	4448398	X_4448398_INS [dm3] X_4554365_INS [dm6]	T	TT	3.617e^-5	0.776	UTR_5_PRIME CG11444 UPSTREAM CG11444 INTRON CR32773	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14883273	2R_14883273_SNP [dm3] 2R_18995768_SNP [dm6]	G	A	3.654e^-5	0.776	DOWNSTREAM snoRNA:abba-a INTRON tn
X	12421798	X_12421798_SNP [dm3] X_12527765_SNP [dm6]	C	T	3.659e^-5	0.776	INTRON CG43921	TF binding site BDTNP1_TFBS_dl
X	13253153	X_13253153_INS [dm3] X_13359120_INS [dm6]	T	TT	3.682e^-5	0.776	UPSTREAM Syt12 INTERGENIC
3R	19700476	3R_19700476_SNP [dm3] 3R_23874754_SNP [dm6]	A	G	3.747e^-5	0.776	INTRON Pli	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	8116880	3R_8116880_SNP [dm3] 3R_12291158_SNP [dm6]	G	C	3.907e^-5	0.776	INTRON svp	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
3L	7489554	3L_7489554_DEL [dm3] 3L_7496454_DEL [dm6]	GG	G	3.961e^-5	0.776	UPSTREAM Cyp4d8 DOWNSTREAM CG8539 INTERGENIC
2L	14001538	2L_14001538_SNP [dm3] 2L_14001538_SNP [dm6]	T	A	4.047e^-5	0.776	UPSTREAM rk INTERGENIC	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2L	11005123	2L_11005123_SNP [dm3] 2L_11005123_SNP [dm6]	G	A	4.093e^-5	0.776	UPSTREAM RpL9 INTRON Nup154	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	10248356	3R_10248356_SNP [dm3] 3R_14422634_SNP [dm6]	T	C	4.108e^-5	0.776	UPSTREAM CR44176 DOWNSTREAM natalisin INTRON cv-c
2R	1373350	2R_1373350_SNP [dm3] 2R_5485845_SNP [dm6]	T	C	4.116e^-5	0.776	INTRON CG30440
3R	8111456	3R_8111456_SNP [dm3] 3R_12285734_SNP [dm6]	T	C	4.130e^-5	0.776	INTRON svp
3L	7489527	3L_7489527_SNP [dm3] 3L_7496427_SNP [dm6]	C	T	4.192e^-5	0.776	UPSTREAM Cyp4d8 DOWNSTREAM CG8539 INTERGENIC
2L	6695664	2L_6695664_SNP [dm3] 2L_6695664_SNP [dm6]	C	T	4.257e^-5	0.776	INTRON Tsp
2R	9897964	2R_9897964_SNP [dm3] 2R_14010459_SNP [dm6]	A	T	4.287e^-5	0.776	START_GAINED mam UTR_5_PRIME mam	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8020902	3R_8020902_SNP [dm3] 3R_12195180_SNP [dm6]	C	A	4.402e^-5	0.776	UPSTREAM CG43450 & 1 other INTERGENIC
3R	8017386	3R_8017386_SNP [dm3] 3R_12191664_SNP [dm6]	G	A	4.402e^-5	0.776	INTERGENIC	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_6_10_C26_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results