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=8.775e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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

1641 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
2R	17362257	2R_17362257_SNP [dm3] 2R_21474752_SNP [dm6]	A	C	2.069e^-6	0.995	INTRON Sdc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_zfh1
X	19506217	X_19506217_SNP [dm3] X_19612184_SNP [dm6]	G	C	4.242e^-6	0.995	SYNONYMOUS_CODING Tyler UTR_5_PRIME Shawn DOWNSTREAM CG14207	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	5611942	2L_5611942_SNP [dm3] 2L_5611942_SNP [dm6]	C	T	5.582e^-6	0.995	INTRON CG14010
2R	12364306	2R_12364306_INS [dm3] 2R_16476801_INS [dm6]	A	AA	7.086e^-6	0.995	INTERGENIC
3L	2520444	3L_2520444_SNP [dm3] 3L_2520444_SNP [dm6]	G	A	7.887e^-6	0.995	INTRON Spn
X	20411217	X_20411217_SNP [dm3] X_20540190_SNP [dm6]	A	G	8.036e^-6	0.995	INTRON RunxB	TF binding site mE1_TFBS_inv
3L	19905217	3L_19905217_SNP [dm3] 3L_19912117_SNP [dm6]	A	T	8.255e^-6	0.995	NON_SYNONYMOUS_CODING Prp3 DOWNSTREAM Mtr3	TF binding site mE1_TFBS_sens
2L	4232747	2L_4232747_SNP [dm3] 2L_4232747_SNP [dm6]	G	T	8.654e^-6	0.995	INTERGENIC
2L	4232446	2L_4232446_SNP [dm3] 2L_4232446_SNP [dm6]	G	T	9.106e^-6	0.995	INTERGENIC
3R	20591010	3R_20591010_SNP [dm3] 3R_24765288_SNP [dm6]	A	G	1.189e^-5	0.995	UPSTREAM AstA INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2L	8710724	2L_8710724_SNP [dm3] 2L_8710724_SNP [dm6]	C	A	1.329e^-5	0.995	SPLICE_SITE_REGION raw INTRON raw	TF binding site mE1_TFBS_chinmo
2L	4232625	2L_4232625_SNP [dm3] 2L_4232625_SNP [dm6]	C	T	1.344e^-5	0.995	INTERGENIC
2R	10933700	2R_10933700_SNP [dm3] 2R_15046195_SNP [dm6]	G	A	1.391e^-5	0.995	INTERGENIC
X	5316852	X_5316852_SNP [dm3] X_5422819_SNP [dm6]	A	G	1.499e^-5	0.995	SYNONYMOUS_CODING CG4165	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	9274487	2R_9274487_SNP [dm3] 2R_13386982_SNP [dm6]	G	A	1.501e^-5	0.995	INTERGENIC
2L	16527082	2L_16527082_SNP [dm3] 2L_16527082_SNP [dm6]	C	T	1.596e^-5	0.995	INTRON CG5953	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
X	20411243	X_20411243_SNP [dm3] X_20540216_SNP [dm6]	C	T	1.726e^-5	0.995	INTRON RunxB	TF binding site mE1_TFBS_inv
3L	2123124	3L_2123124_SNP [dm3] 3L_2123124_SNP [dm6]	A	T	1.755e^-5	0.995	INTRON zormin
2R	1996356	2R_1996356_SNP [dm3] 2R_6108851_SNP [dm6]	A	C	1.804e^-5	0.995	INTRON EcR
2R	9410382	2R_9410382_SNP [dm3] 2R_13522877_SNP [dm6]	C	T	1.834e^-5	0.995	NON_SYNONYMOUS_CODING CG13331 INTRON Vmat	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	18051776	3L_18051776_SNP [dm3] 3L_18058676_SNP [dm6]	C	T	2.054e^-5	0.995	SYNONYMOUS_CODING Eip75B	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9761533	2R_9761533_SNP [dm3] 2R_13874028_SNP [dm6]	C	T	2.156e^-5	0.995	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad
2L	4232509	2L_4232509_SNP [dm3] 2L_4232509_SNP [dm6]	T	A	2.296e^-5	0.995	INTERGENIC
X	15285687	X_15285687_SNP [dm3] X_15391654_SNP [dm6]	G	T	2.301e^-5	0.995	INTRON Cngl
2R	16420966	2R_16420966_SNP [dm3] 2R_20533461_SNP [dm6]	T	C	2.394e^-5	0.995	UPSTREAM CG18067 DOWNSTREAM CR44651 INTRON CG30154	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	9761500	2R_9761500_SNP [dm3] 2R_13873995_SNP [dm6]	T	C	2.399e^-5	0.995	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad
3R	13109751	3R_13109751_SNP [dm3] 3R_17284029_SNP [dm6]	C	T	2.426e^-5	0.995	SYNONYMOUS_CODING CG31418 UPSTREAM CG31419	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	5680379	X_5680379_SNP [dm3] X_5786346_SNP [dm6]	C	A	2.440e^-5	0.995	INTRON CG42699
X	4565701	X_4565701_SNP [dm3] X_4671668_SNP [dm6]	C	T	2.567e^-5	0.995	INTRON rap
3R	13606760	3R_13606760_SNP [dm3] 3R_17781038_SNP [dm6]	A	G	2.642e^-5	0.995	UPSTREAM CG43102 INTRON CG43102
3L	18002813	3L_18002813_SNP [dm3] 3L_18009713_SNP [dm6]	T	C	2.643e^-5	0.995	INTRON Eip75B
3R	25021116	3R_25021116_SNP [dm3] 3R_29195394_SNP [dm6]	T	G	2.665e^-5	0.995	UPSTREAM CG14509 INTERGENIC
3R	17140163	3R_17140163_SNP [dm3] 3R_21314441_SNP [dm6]	A	T	2.775e^-5	0.995	EXON Hsromega
3L	6698033	3L_6698033_SNP [dm3] 3L_6704933_SNP [dm6]	C	A	2.874e^-5	0.995	UTR_5_PRIME CG8519
3L	18052499	3L_18052499_SNP [dm3] 3L_18059399_SNP [dm6]	G	C	2.915e^-5	0.995	NON_SYNONYMOUS_CODING Eip75B	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
3L	20883357	3L_20883357_SNP [dm3] 3L_20890257_SNP [dm6]	A	G	2.950e^-5	0.995	INTERGENIC
2R	9761569	2R_9761569_SNP [dm3] 2R_13874064_SNP [dm6]	C	G	3.018e^-5	0.995	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad
3R	20914733	3R_20914733_SNP [dm3] 3R_25089011_SNP [dm6]	G	T	3.216e^-5	0.995	INTERGENIC
3R	12047260	3R_12047260_DEL [dm3] 3R_16221538_DEL [dm6]	TGTGTGTGT	T	3.227e^-5	0.995	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	25021113	3R_25021113_SNP [dm3] 3R_29195391_SNP [dm6]	T	A	3.588e^-5	0.995	UPSTREAM CG14509 INTERGENIC
3R	25021101	3R_25021101_DEL [dm3] 3R_29195379_DEL [dm6]	ATTATATATAT...	A	3.618e^-5	0.995	UPSTREAM CG14509 INTERGENIC
3L	10769640	3L_10769640_SNP [dm3] 3L_10776540_SNP [dm6]	C	A	3.626e^-5	0.995	INTERGENIC	TF binding site mE1_TFBS_Trl
3L	3385002	3L_3385002_SNP [dm3] 3L_3385002_SNP [dm6]	T	G	3.718e^-5	0.995	INTERGENIC
3R	13606790	3R_13606790_SNP [dm3] 3R_17781068_SNP [dm6]	A	G	3.821e^-5	0.995	UPSTREAM CG43102 INTRON CG43102
3L	20854655	3L_20854655_SNP [dm3] 3L_20861555_SNP [dm6]	T	G	3.871e^-5	0.995	INTRON CG32432
3L	1606816	3L_1606816_SNP [dm3] 3L_1606816_SNP [dm6]	T	C	3.981e^-5	0.995	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	13891963	3R_13891963_SNP [dm3] 3R_18066241_SNP [dm6]	G	A	4.182e^-5	0.995	INTERGENIC
3L	6374266	3L_6374266_SNP [dm3] 3L_6381166_SNP [dm6]	G	T	4.210e^-5	0.995	INTERGENIC
X	20390304	X_20390304_SNP [dm3] X_20519277_SNP [dm6]	C	G	4.212e^-5	0.995	INTRON Tak1
X	20390310	X_20390310_SNP [dm3] X_20519283_SNP [dm6]	G	A	4.212e^-5	0.995	INTRON Tak1
3R	14457158	3R_14457158_SNP [dm3] 3R_18631436_SNP [dm6]	G	T	4.238e^-5	0.995	INTRON qin & 1 other
3L	8626033	3L_8626033_SNP [dm3] 3L_8632933_SNP [dm6]	T	C	4.241e^-5	0.995	SYNONYMOUS_CODING Cdc6 INTRON Zasp66	TF binding site mE1_TFBS_sens
2R	16325255	2R_16325255_DEL [dm3] 2R_20437750_DEL [dm6]	GGAATACG	G	4.374e^-5	0.995	INTRON CG12484
X	5639855	X_5639855_SNP [dm3] X_5745822_SNP [dm6]	A	G	4.538e^-5	0.995	INTRON IntS6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl
X	5093904	X_5093904_SNP [dm3] X_5199871_SNP [dm6]	T	A	4.612e^-5	0.995	INTRON rg & 1 other
3R	22106228	3R_22106228_SNP [dm3] 3R_26280506_SNP [dm6]	G	T	4.637e^-5	0.995	INTERGENIC
2R	7566798	2R_7566798_SNP [dm3] 2R_11679293_SNP [dm6]	T	A	4.678e^-5	0.995	UTR_5_PRIME Roc2 UPSTREAM Buffy	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	17024451	2R_17024451_SNP [dm3] 2R_21136946_SNP [dm6]	G	A	4.723e^-5	0.995	INTRON Magi	TF binding site mE1_TFBS_sens
2L	9186351	2L_9186351_SNP [dm3] 2L_9186351_SNP [dm6]	A	T	4.823e^-5	0.995	INTRON tai	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19383160	2R_19383160_SNP [dm3] 2R_23495637_SNP [dm6]	G	A	4.839e^-5	0.995	INTERGENIC
2L	9845842	2L_9845842_SNP [dm3] 2L_9845842_SNP [dm6]	G	A	4.841e^-5	0.995	INTRON nAChRalpha6
2L	4233467	2L_4233467_SNP [dm3] 2L_4233467_SNP [dm6]	C	T	4.861e^-5	0.995	INTERGENIC
3R	13385559	3R_13385559_SNP [dm3] 3R_17559837_SNP [dm6]	A	G	4.868e^-5	0.995	SYNONYMOUS_CODING Hmx	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	4870901	X_4870901_SNP [dm3] X_4976868_SNP [dm6]	T	C	4.907e^-5	0.995	INTRON CR44833
3L	10185557	3L_10185557_SNP [dm3] 3L_10192457_SNP [dm6]	G	A	4.948e^-5	0.995	DOWNSTREAM ect INTRON ect
2R	10802507	2R_10802507_SNP [dm3] 2R_14915002_SNP [dm6]	C	A	5.045e^-5	0.995	INTRON CG10249
X	6254734	X_6254734_SNP [dm3] X_6360701_SNP [dm6]	A	T	5.053e^-5	0.995	UTR_3_PRIME kdn DOWNSTREAM swaPsi	TF binding site BDTNP1_TFBS_dl
X	9049282	X_9049282_SNP [dm3] X_9155249_SNP [dm6]	T	C	5.140e^-5	0.995	UPSTREAM His3.3B INTRON His3.3B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc
3R	12247520	3R_12247520_INS [dm3] 3R_16421798_INS [dm6]	A	AATAGTA	5.251e^-5	0.995	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi
X	5640422	X_5640422_SNP [dm3] X_5746389_SNP [dm6]	A	T	5.596e^-5	0.995	UPSTREAM IntS6 INTRON IntS6	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
X	19502657	X_19502657_SNP [dm3] X_19608624_SNP [dm6]	T	C	5.655e^-5	0.995	INTRON CG14207	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	21004769	3R_21004769_DEL [dm3] 3R_25179047_DEL [dm6]	AGGTGCAGTTTTAGGCTTAA...	A	5.667e^-5	0.995	INTRON lobo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	18004394	3L_18004394_SNP [dm3] 3L_18011294_SNP [dm6]	C	A	5.719e^-5	0.995	INTRON Eip75B	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	4860275	X_4860275_SNP [dm3] X_4966242_SNP [dm6]	T	G	5.739e^-5	0.995	INTRON CR44833	regulatory region REDfly_CRMs
2R	16994592	2R_16994592_SNP [dm3] 2R_21107087_SNP [dm6]	C	T	5.756e^-5	0.995	INTRON ktub
X	12653734	X_12653734_SNP [dm3] X_12759701_SNP [dm6]	T	A	5.839e^-5	0.995	DOWNSTREAM CG12717 INTRON ade5	TF binding site mE1_TFBS_inv
X	19507082	X_19507082_SNP [dm3] X_19613049_SNP [dm6]	A	G	5.895e^-5	0.995	NON_SYNONYMOUS_CODING Tyler UTR_5_PRIME Shawn UTR_3_PRIME Tyler UPSTREAM Shawn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
3R	13110469	3R_13110469_SNP [dm3] 3R_17284747_SNP [dm6]	G	T	5.932e^-5	0.995	NON_SYNONYMOUS_CODING CG31419 DOWNSTREAM CG31418
3R	25021257	3R_25021257_SNP [dm3] 3R_29195535_SNP [dm6]	A	C	5.961e^-5	0.995	UPSTREAM CG14509 INTERGENIC
3R	3483475	3R_3483475_SNP [dm3] 3R_7657753_SNP [dm6]	A	G	6.271e^-5	0.995	UPSTREAM Nlg1 INTERGENIC
3R	3483422	3R_3483422_SNP [dm3] 3R_7657700_SNP [dm6]	A	C	6.304e^-5	0.995	UPSTREAM Nlg1 INTERGENIC
3L	10185657	3L_10185657_SNP [dm3] 3L_10192557_SNP [dm6]	C	T	6.354e^-5	0.995	DOWNSTREAM ect INTRON ect
3R	23783282	3R_23783282_SNP [dm3] 3R_27957560_SNP [dm6]	A	G	6.364e^-5	0.995	SYNONYMOUS_CODING CG4884 UTR_3_PRIME CG42487 DOWNSTREAM CG5527	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	7595460	2L_7595460_SNP [dm3] 2L_7595460_SNP [dm6]	G	T	6.484e^-5	0.995	INTERGENIC
3R	20600728	3R_20600728_SNP [dm3] 3R_24775006_SNP [dm6]	G	C	6.517e^-5	0.995	INTRON CG42331
3L	3795336	3L_3795336_SNP [dm3] 3L_3795336_SNP [dm6]	A	G	6.554e^-5	0.995	UPSTREAM CG32264 INTRON CG32264
2R	15287207	2R_15287207_SNP [dm3] 2R_19399702_SNP [dm6]	A	C	6.596e^-5	0.995	UTR_3_PRIME hts UPSTREAM CR43430 INTRON hts
2L	1841571	2L_1841571_SNP [dm3] 2L_1841571_SNP [dm6]	G	A	6.651e^-5	0.995	UPSTREAM CR44074 INTRON wry
X	5361099	X_5361099_SNP [dm3] X_5467066_SNP [dm6]	T	A	6.686e^-5	0.995	INTRON SPR
2L	15564812	2L_15564812_SNP [dm3] 2L_15564812_SNP [dm6]	G	T	6.692e^-5	0.995	INTRON kek3
3R	13606812	3R_13606812_SNP [dm3] 3R_17781090_SNP [dm6]	C	G	6.773e^-5	0.995	UPSTREAM CG43102 INTRON CG43102
2R	14516091	2R_14516091_SNP [dm3] 2R_18628586_SNP [dm6]	C	T	6.796e^-5	0.995	SYNONYMOUS_CODING Eip55E DOWNSTREAM Sec6	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	13606761	3R_13606761_SNP [dm3] 3R_17781039_SNP [dm6]	C	A	6.841e^-5	0.995	UPSTREAM CG43102 INTRON CG43102
X	5532353	X_5532353_SNP [dm3] X_5638320_SNP [dm6]	T	G	6.886e^-5	0.995	UPSTREAM CG42492 INTRON CG42492	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	11508310	3L_11508310_SNP [dm3] 3L_11515210_SNP [dm6]	A	T	6.904e^-5	0.995	INTRON CG7512
2L	4232110	2L_4232110_SNP [dm3] 2L_4232110_SNP [dm6]	C	T	6.930e^-5	0.995	INTERGENIC
2L	4232121	2L_4232121_SNP [dm3] 2L_4232121_SNP [dm6]	G	T	6.930e^-5	0.995	INTERGENIC
2L	7333613	2L_7333613_SNP [dm3] 2L_7333613_SNP [dm6]	C	T	7.046e^-5	0.995	UPSTREAM Wnt6 INTERGENIC
3R	12375763	3R_12375763_SNP [dm3] 3R_16550041_SNP [dm6]	G	T	7.138e^-5	0.995	INTRON CG42342
X	9049428	X_9049428_SNP [dm3] X_9155395_SNP [dm6]	A	G	7.347e^-5	0.995	UPSTREAM His3.3B INTRON His3.3B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc

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By genomic position
Variant impact
Gene name

PC3_Nutri_Score_High phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results