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=1.664e^-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

1496 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
3L	21968126	3L_21968126_SNP [dm3] 3L_21975026_SNP [dm6]	T	A	2.622e^-6	0.711	INTRON CG7470
3L	21968129	3L_21968129_SNP [dm3] 3L_21975029_SNP [dm6]	T	C	2.622e^-6	0.711	INTRON CG7470
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	2.622e^-6	0.711	INTRON CG7470
2R	18600700	2R_18600700_SNP [dm3] 2R_22713195_SNP [dm6]	T	C	2.668e^-6	0.711	SYNONYMOUS_CODING CG30268 DOWNSTREAM CG30275
3L	21968433	3L_21968433_SNP [dm3] 3L_21975333_SNP [dm6]	A	G	4.100e^-6	0.711	INTRON CG7470
X	12388124	X_12388124_SNP [dm3] X_12494091_SNP [dm6]	C	G	5.152e^-6	0.711	DOWNSTREAM Mks1 INTERGENIC
X	12388126	X_12388126_SNP [dm3] X_12494093_SNP [dm6]	A	T	5.152e^-6	0.711	DOWNSTREAM Mks1 INTERGENIC
3R	13063145	3R_13063145_SNP [dm3] 3R_17237423_SNP [dm6]	T	C	5.496e^-6	0.711	INTRON beat-IIb
3L	7423041	3L_7423041_SNP [dm3] 3L_7429941_SNP [dm6]	G	A	5.725e^-6	0.711	INTRON CG42458	TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
X	12388116	X_12388116_SNP [dm3] X_12494083_SNP [dm6]	G	A	6.222e^-6	0.711	DOWNSTREAM Mks1 INTERGENIC
2L	22099807	2L_22099807_SNP [dm3] 2L_22099807_SNP [dm6]	T	C	6.651e^-6	0.711	INTERGENIC
2L	22099816	2L_22099816_SNP [dm3] 2L_22099816_SNP [dm6]	C	A	6.651e^-6	0.711	INTERGENIC
2L	22099817	2L_22099817_SNP [dm3] 2L_22099817_SNP [dm6]	A	T	6.651e^-6	0.711	INTERGENIC
3L	18620796	3L_18620796_SNP [dm3] 3L_18627696_SNP [dm6]	T	A	6.754e^-6	0.711	INTRON MYPT-75D	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	2210081	3L_2210081_SNP [dm3] 3L_2210081_SNP [dm6]	T	C	6.850e^-6	0.711	DOWNSTREAM CG15878 INTERGENIC
3R	22527085	3R_22527085_SNP [dm3] 3R_26701363_SNP [dm6]	A	T	8.375e^-6	0.711	INTRON amon
3R	13780986	3R_13780986_DEL [dm3] 3R_17955264_DEL [dm6]	TT	T	8.607e^-6	0.711	INTRON cpo	TF binding site mE1_TFBS_cad
3L	11208027	3L_11208027_SNP [dm3] 3L_11214927_SNP [dm6]	A	G	9.384e^-6	0.711	UPSTREAM CG42671 DOWNSTREAM CG7600 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl
X	12387044	X_12387044_SNP [dm3] X_12493011_SNP [dm6]	G	T	9.424e^-6	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387064	X_12387064_SNP [dm3] X_12493031_SNP [dm6]	G	T	9.424e^-6	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387065	X_12387065_SNP [dm3] X_12493032_SNP [dm6]	C	T	9.424e^-6	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387069	X_12387069_SNP [dm3] X_12493036_SNP [dm6]	T	G	9.424e^-6	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387073	X_12387073_SNP [dm3] X_12493040_SNP [dm6]	A	T	9.424e^-6	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387047	X_12387047_SNP [dm3] X_12493014_SNP [dm6]	A	C	1.105e^-5	0.711	DOWNSTREAM Lsp1alpha INTERGENIC
3L	17909708	3L_17909708_SNP [dm3] 3L_17916608_SNP [dm6]	A	G	1.185e^-5	0.711	INTERGENIC
3L	17908064	3L_17908064_SNP [dm3] 3L_17914964_SNP [dm6]	A	G	1.207e^-5	0.711	INTERGENIC
3L	17908077	3L_17908077_SNP [dm3] 3L_17914977_SNP [dm6]	C	A	1.207e^-5	0.711	INTERGENIC
3L	12282638	3L_12282638_SNP [dm3] 3L_12289538_SNP [dm6]	A	T	1.243e^-5	0.711	EXON CR45658
3L	12282646	3L_12282646_SNP [dm3] 3L_12289546_SNP [dm6]	G	T	1.243e^-5	0.711	EXON CR45658
3L	12282655	3L_12282655_SNP [dm3] 3L_12289555_SNP [dm6]	G	T	1.243e^-5	0.711	EXON CR45658
3L	8206920	3L_8206920_SNP [dm3] 3L_8213820_SNP [dm6]	T	A	1.277e^-5	0.711	DOWNSTREAM CG8006 INTERGENIC
3L	12179891	3L_12179891_SNP [dm3] 3L_12186791_SNP [dm6]	C	A	1.286e^-5	0.711	SYNONYMOUS_CODING CG6910	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	3753167	X_3753167_SNP [dm3] X_3859134_SNP [dm6]	A	G	1.324e^-5	0.711	EXON roX1
3L	11208193	3L_11208193_SNP [dm3] 3L_11215093_SNP [dm6]	C	G	1.342e^-5	0.711	UPSTREAM CG42671 DOWNSTREAM CG7600 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl
3R	26011106	3R_26011106_SNP [dm3] 3R_30185384_SNP [dm6]	G	A	1.386e^-5	0.711	UPSTREAM CR44262 DOWNSTREAM CG9747 INTERGENIC
3L	21968136	3L_21968136_DEL [dm3] 3L_21975036_DEL [dm6]	AA	A	1.408e^-5	0.711	INTRON CG7470
2L	7558758	2L_7558758_SNP [dm3] 2L_7558758_SNP [dm6]	C	T	1.524e^-5	0.711	INTRON RapGAP1
3R	13063674	3R_13063674_SNP [dm3] 3R_17237952_SNP [dm6]	C	A	1.552e^-5	0.711	INTRON beat-IIb
2L	13710150	2L_13710150_SNP [dm3] 2L_13710150_SNP [dm6]	G	C	1.555e^-5	0.711	NON_SYNONYMOUS_CODING CG7311 UTR_3_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	5866010	2L_5866010_SNP [dm3] 2L_5866010_SNP [dm6]	T	C	1.566e^-5	0.711	INTRON rau
3R	25134623	3R_25134623_SNP [dm3] 3R_29308901_SNP [dm6]	C	T	1.604e^-5	0.711	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens
2R	10998820	2R_10998820_SNP [dm3] 2R_15111315_SNP [dm6]	A	G	1.722e^-5	0.729	INTERGENIC
2L	8010395	2L_8010395_SNP [dm3] 2L_8010395_SNP [dm6]	A	C	1.786e^-5	0.729	UPSTREAM CG12560 INTRON CG34010	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	17904485	3L_17904485_SNP [dm3] 3L_17911385_SNP [dm6]	T	G	1.800e^-5	0.729	SYNONYMOUS_CODING CG5290	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	659647	3L_659647_SNP [dm3] 3L_659647_SNP [dm6]	T	C	1.809e^-5	0.729	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	9314780	2R_9314780_SNP [dm3] 2R_13427275_SNP [dm6]	G	A	1.845e^-5	0.729	INTRON CG42321	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
X	12387048	X_12387048_SNP [dm3] X_12493015_SNP [dm6]	A	T	1.931e^-5	0.741	DOWNSTREAM Lsp1alpha INTERGENIC
2R	5285409	2R_5285409_SNP [dm3] 2R_9397904_SNP [dm6]	G	A	2.012e^-5	0.741	SYNONYMOUS_CODING CG8801	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	12388723	X_12388723_SNP [dm3] X_12494690_SNP [dm6]	A	G	2.024e^-5	0.741	SYNONYMOUS_CODING Mks1
3L	10396223	3L_10396223_INS [dm3] 3L_10403123_INS [dm6]	G	GA	2.040e^-5	0.741	INTERGENIC
3L	17886042	3L_17886042_SNP [dm3] 3L_17892942_SNP [dm6]	G	A	2.141e^-5	0.749	INTRON Tsp74F	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	4774003	X_4774003_SNP [dm3] X_4879970_SNP [dm6]	T	C	2.255e^-5	0.749	INTRON CG42594
3R	23749545	3R_23749545_SNP [dm3] 3R_27923823_SNP [dm6]	A	T	2.279e^-5	0.749	UPSTREAM snoRNA:Or-aca3 INTRON RpL4	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	505775	3L_505775_SNP [dm3] 3L_505775_SNP [dm6]	C	A	2.509e^-5	0.749	INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
3L	12282654	3L_12282654_SNP [dm3] 3L_12289554_SNP [dm6]	C	G	2.520e^-5	0.749	EXON CR45658
3L	17905541	3L_17905541_SNP [dm3] 3L_17912441_SNP [dm6]	G	T	2.564e^-5	0.749	UTR_5_PRIME CG5290	TF binding site mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
3L	17905773	3L_17905773_SNP [dm3] 3L_17912673_SNP [dm6]	A	T	2.564e^-5	0.749	UPSTREAM CG5290 INTERGENIC	TF binding site mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2R	8129061	2R_8129061_SNP [dm3] 2R_12241556_SNP [dm6]	A	G	2.598e^-5	0.749	UPSTREAM CG43316 DOWNSTREAM CG13170 INTRON CG43315
2R	8129062	2R_8129062_SNP [dm3] 2R_12241557_SNP [dm6]	T	A	2.598e^-5	0.749	UPSTREAM CG43316 DOWNSTREAM CG13170 INTRON CG43315
X	20431728	X_20431728_SNP [dm3] X_20560701_SNP [dm6]	G	A	2.610e^-5	0.749	INTRON RunxB
3L	8012180	3L_8012180_SNP [dm3] 3L_8019080_SNP [dm6]	A	G	2.703e^-5	0.749	INTRON nmo
3R	13063983	3R_13063983_SNP [dm3] 3R_17238261_SNP [dm6]	A	G	2.711e^-5	0.749	INTRON beat-IIb
3L	11237468	3L_11237468_SNP [dm3] 3L_11244368_SNP [dm6]	T	C	2.749e^-5	0.749	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_sens mE1_TFBS_Trl
X	3753160	X_3753160_SNP [dm3] X_3859127_SNP [dm6]	C	A	2.765e^-5	0.749	EXON roX1
2L	7559398	2L_7559398_SNP [dm3] 2L_7559398_SNP [dm6]	A	T	2.781e^-5	0.749	INTRON RapGAP1
2L	7559404	2L_7559404_SNP [dm3] 2L_7559404_SNP [dm6]	T	A	2.781e^-5	0.749	INTRON RapGAP1
2L	7559419	2L_7559419_SNP [dm3] 2L_7559419_SNP [dm6]	T	A	2.781e^-5	0.749	INTRON RapGAP1
2L	10111671	2L_10111671_SNP [dm3] 2L_10111671_SNP [dm6]	T	C	2.803e^-5	0.749	INTRON CG44153 & 1 other
3L	17909904	3L_17909904_SNP [dm3] 3L_17916804_SNP [dm6]	A	G	2.850e^-5	0.749	INTERGENIC
2L	5866536	2L_5866536_SNP [dm3] 2L_5866536_SNP [dm6]	A	G	2.887e^-5	0.749	INTRON rau	TF binding site BDTNP1_TFBS_da
3R	5720560	3R_5720560_DEL [dm3] 3R_9894838_DEL [dm6]	CCCAGTTTTGAAATCGC...	C	3.014e^-5	0.769	INTRON Glut4EF	TF binding site mE1_TFBS_inv
2L	3018605	2L_3018605_SNP [dm3] 2L_3018605_SNP [dm6]	A	T	3.131e^-5	0.769	START_GAINED CG17264 UTR_5_PRIME CG17264 UPSTREAM CG17264 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	3018613	2L_3018613_SNP [dm3] 2L_3018613_SNP [dm6]	T	A	3.131e^-5	0.769	UTR_5_PRIME CG17264 UPSTREAM CG17264 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	3018621	2L_3018621_SNP [dm3] 2L_3018621_SNP [dm6]	A	G	3.131e^-5	0.769	UTR_5_PRIME CG17264 UPSTREAM CG17264 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12388447	X_12388447_DEL [dm3] X_12494414_DEL [dm6]	TA	T	3.306e^-5	0.801	UTR_3_PRIME Mks1
2R	13856870	2R_13856870_SNP [dm3] 2R_17969365_SNP [dm6]	C	T	3.396e^-5	0.811	INTERGENIC
2R	6114693	2R_6114693_SNP [dm3] 2R_10227188_SNP [dm6]	G	A	3.440e^-5	0.811	INTRON Hr46 & 1 other	TF binding site mE1_TFBS_Trl
2R	7359258	2R_7359258_INS [dm3] 2R_11471753_INS [dm6]	A	TATAT	3.510e^-5	0.811	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	12282614	3L_12282614_SNP [dm3] 3L_12289514_SNP [dm6]	C	T	3.525e^-5	0.811	EXON CR45658
2R	4662137	2R_4662137_SNP [dm3] 2R_8774632_SNP [dm6]	A	C	3.970e^-5	0.882	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4368139	3L_4368139_SNP [dm3] 3L_4368139_SNP [dm6]	T	A	3.981e^-5	0.882	UTR_3_PRIME DopEcR UPSTREAM CG11342 DOWNSTREAM DopEcR	TF binding site mE1_TFBS_sens
3L	4368154	3L_4368154_SNP [dm3] 3L_4368154_SNP [dm6]	T	A	3.981e^-5	0.882	UTR_3_PRIME DopEcR UPSTREAM CG11342 DOWNSTREAM DopEcR	TF binding site mE1_TFBS_sens
3R	13789861	3R_13789861_SNP [dm3] 3R_17964139_SNP [dm6]	C	A	4.087e^-5	0.893	INTRON cpo
2R	6139671	2R_6139671_SNP [dm3] 2R_10252166_SNP [dm6]	A	T	4.130e^-5	0.893	UTR_5_PRIME Syb INTRON CG12913 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
2R	14498690	2R_14498690_DEL [dm3] 2R_18611185_DEL [dm6]	TACGGA	T	4.260e^-5	0.911	UTR_5_PRIME GEFmeso DOWNSTREAM CG42697	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens mE1_TFBS_Trl
X	4839708	X_4839708_SNP [dm3] X_4945675_SNP [dm6]	C	G	4.360e^-5	0.921	INTRON Ptp4E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	3440719	3R_3440719_SNP [dm3] 3R_7614997_SNP [dm6]	C	T	4.432e^-5	0.925	INTRON CG34127
3L	761571	3L_761571_SNP [dm3] 3L_761571_SNP [dm6]	A	G	4.686e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med
2L	8010057	2L_8010057_SNP [dm3] 2L_8010057_SNP [dm6]	C	A	4.768e^-5	0.946	SYNONYMOUS_CODING CG34010 UPSTREAM CG12560	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
3R	19572363	3R_19572363_SNP [dm3] 3R_23746641_SNP [dm6]	G	A	4.782e^-5	0.946	INTRON Hmgcr	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10086031	2R_10086031_SNP [dm3] 2R_14198526_SNP [dm6]	T	C	4.790e^-5	0.946	UTR_3_PRIME VGAT DOWNSTREAM CG30069
2R	18292034	2R_18292034_SNP [dm3] 2R_22404529_SNP [dm6]	C	T	4.800e^-5	0.946	INTRON CG6044	TF binding site BDTNP1_TFBS_dl
2L	8010187	2L_8010187_SNP [dm3] 2L_8010187_SNP [dm6]	C	A	4.841e^-5	0.946	NON_SYNONYMOUS_CODING CG34010 UPSTREAM CG12560	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	5214920	X_5214920_SNP [dm3] X_5320887_SNP [dm6]	G	A	5.075e^-5	0.974	SYNONYMOUS_CODING Rnp4F	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	9314848	2R_9314848_SNP [dm3] 2R_13427343_SNP [dm6]	C	G	5.159e^-5	0.974	INTRON CG42321	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3L	17902944	3L_17902944_SNP [dm3] 3L_17909844_SNP [dm6]	A	G	5.422e^-5	0.974	NON_SYNONYMOUS_CODING CG5290 DOWNSTREAM CG14353
2L	5121453	2L_5121453_SNP [dm3] 2L_5121453_SNP [dm6]	A	T	5.692e^-5	0.974	INTRON Msp300
3R	13062827	3R_13062827_SNP [dm3] 3R_17237105_SNP [dm6]	T	A	5.737e^-5	0.974	INTRON beat-IIb
3R	17844184	3R_17844184_SNP [dm3] 3R_22018462_SNP [dm6]	A	C	5.745e^-5	0.974	INTRON CG6439	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11208359	3L_11208359_SNP [dm3] 3L_11215259_SNP [dm6]	C	G	5.822e^-5	0.974	UPSTREAM CG42671 INTRON CG42671	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_Dll mE1_TFBS_Kr mE1_TFBS_Trl

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_PElem_HC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results