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=4.311e^-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

Covariate	p-value	Significance
In_2L_t	0.008465

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.9997	0.0498

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1709 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	12282638	3L_12282638_SNP [dm3] 3L_12289538_SNP [dm6]	A	T	1.765e^-7	0.093	EXON CR45658
3L	12282646	3L_12282646_SNP [dm3] 3L_12289546_SNP [dm6]	G	T	1.765e^-7	0.093	EXON CR45658
3L	12282655	3L_12282655_SNP [dm3] 3L_12289555_SNP [dm6]	G	T	1.765e^-7	0.093	EXON CR45658
3L	2335765	3L_2335765_SNP [dm3] 3L_2335765_SNP [dm6]	C	A	2.052e^-7	0.093	INTRON MsR1
3L	12282654	3L_12282654_SNP [dm3] 3L_12289554_SNP [dm6]	C	G	3.107e^-7	0.113	EXON CR45658
3L	10396532	3L_10396532_SNP [dm3] 3L_10403432_SNP [dm6]	C	A	5.092e^-7	0.154	INTERGENIC
3L	21968433	3L_21968433_SNP [dm3] 3L_21975333_SNP [dm6]	A	G	1.246e^-6	0.273	INTRON CG7470
3L	2335729	3L_2335729_SNP [dm3] 3L_2335729_SNP [dm6]	T	G	1.288e^-6	0.273	INTRON MsR1
3L	12282614	3L_12282614_SNP [dm3] 3L_12289514_SNP [dm6]	C	T	1.351e^-6	0.273	EXON CR45658
3L	7411553	3L_7411553_SNP [dm3] 3L_7418453_SNP [dm6]	A	G	2.107e^-6	0.377	INTERGENIC
3L	7411563	3L_7411563_SNP [dm3] 3L_7418463_SNP [dm6]	G	A	2.284e^-6	0.377	INTERGENIC
3L	10396510	3L_10396510_SNP [dm3] 3L_10403410_SNP [dm6]	T	A	3.590e^-6	0.543	INTERGENIC
2R	11900270	2R_11900270_SNP [dm3] 2R_16012765_SNP [dm6]	A	G	4.889e^-6	0.626	SYNONYMOUS_CODING CG8389	TF binding site BDTNP1_TFBS_sna
X	12388124	X_12388124_SNP [dm3] X_12494091_SNP [dm6]	C	G	5.168e^-6	0.626	DOWNSTREAM Mks1 INTERGENIC
X	12388126	X_12388126_SNP [dm3] X_12494093_SNP [dm6]	A	T	5.168e^-6	0.626	DOWNSTREAM Mks1 INTERGENIC
3R	22527085	3R_22527085_SNP [dm3] 3R_26701363_SNP [dm6]	A	T	6.524e^-6	0.673	INTRON amon
2R	18600700	2R_18600700_SNP [dm3] 2R_22713195_SNP [dm6]	T	C	6.692e^-6	0.673	SYNONYMOUS_CODING CG30268 DOWNSTREAM CG30275
3R	6492186	3R_6492186_SNP [dm3] 3R_10666464_SNP [dm6]	G	A	7.558e^-6	0.673	INTERGENIC
3L	11208724	3L_11208724_SNP [dm3] 3L_11215624_SNP [dm6]	A	T	7.932e^-6	0.673	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_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
X	12387047	X_12387047_SNP [dm3] X_12493014_SNP [dm6]	A	C	8.857e^-6	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
2L	10194988	2L_10194988_DEL [dm3] 2L_10194988_DEL [dm6]	GTT	AA	8.901e^-6	0.673	SPLICE_SITE_REGION Sur INTRON Sur
2L	4343818	2L_4343818_SNP [dm3] 2L_4343818_SNP [dm6]	C	G	8.947e^-6	0.673	SYNONYMOUS_CODING Atet DOWNSTREAM mir-1005	TF binding site mE1_TFBS_inv
3L	3720208	3L_3720208_SNP [dm3] 3L_3720208_SNP [dm6]	G	C	9.456e^-6	0.673	INTRON CG32264
3R	26394899	3R_26394899_SNP [dm3] 3R_30569177_SNP [dm6]	G	C	9.564e^-6	0.673	INTRON tmod	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	26394906	3R_26394906_SNP [dm3] 3R_30569184_SNP [dm6]	T	C	9.564e^-6	0.673	INTRON tmod	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	11900267	2R_11900267_SNP [dm3] 2R_16012762_SNP [dm6]	G	C	1.025e^-5	0.673	SYNONYMOUS_CODING CG8389	TF binding site BDTNP1_TFBS_sna
3L	11208027	3L_11208027_SNP [dm3] 3L_11214927_SNP [dm6]	A	G	1.184e^-5	0.673	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	1.206e^-5	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387064	X_12387064_SNP [dm3] X_12493031_SNP [dm6]	G	T	1.206e^-5	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387065	X_12387065_SNP [dm3] X_12493032_SNP [dm6]	C	T	1.206e^-5	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387069	X_12387069_SNP [dm3] X_12493036_SNP [dm6]	T	G	1.206e^-5	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387073	X_12387073_SNP [dm3] X_12493040_SNP [dm6]	A	T	1.206e^-5	0.673	DOWNSTREAM Lsp1alpha INTERGENIC
3L	11715659	3L_11715659_SNP [dm3] 3L_11722559_SNP [dm6]	G	A	1.305e^-5	0.673	INTRON Bmcp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	11208359	3L_11208359_SNP [dm3] 3L_11215259_SNP [dm6]	C	G	1.323e^-5	0.673	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
3L	21968126	3L_21968126_SNP [dm3] 3L_21975026_SNP [dm6]	T	A	1.383e^-5	0.673	INTRON CG7470
3L	21968129	3L_21968129_SNP [dm3] 3L_21975029_SNP [dm6]	T	C	1.383e^-5	0.673	INTRON CG7470
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	1.383e^-5	0.673	INTRON CG7470
3L	11208193	3L_11208193_SNP [dm3] 3L_11215093_SNP [dm6]	C	G	1.467e^-5	0.673	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
3L	16052921	3L_16052921_SNP [dm3] 3L_16059821_SNP [dm6]	T	A	1.476e^-5	0.673	INTRON Mbs
3L	13277467	3L_13277467_SNP [dm3] 3L_13284367_SNP [dm6]	C	T	1.514e^-5	0.673	DOWNSTREAM CR43146 & 1 other EXON CR43913
3L	9309606	3L_9309606_SNP [dm3] 3L_9316506_SNP [dm6]	C	G	1.520e^-5	0.673	INTERGENIC
3L	11192359	3L_11192359_SNP [dm3] 3L_11199259_SNP [dm6]	C	T	1.556e^-5	0.673	SPLICE_SITE_REGION Plod UPSTREAM CG7607 INTRON Plod	TF binding site mE1_TFBS_sens
3L	3720223	3L_3720223_SNP [dm3] 3L_3720223_SNP [dm6]	T	C	1.604e^-5	0.677	INTRON CG32264
3L	2559800	3L_2559800_SNP [dm3] 3L_2559800_SNP [dm6]	G	A	1.724e^-5	0.699	INTRON msn
X	12388723	X_12388723_SNP [dm3] X_12494690_SNP [dm6]	A	G	1.731e^-5	0.699	SYNONYMOUS_CODING Mks1
3L	8127098	3L_8127098_SNP [dm3] 3L_8133998_SNP [dm6]	A	T	1.830e^-5	0.723	INTRON CG7504
3L	8958470	3L_8958470_SNP [dm3] 3L_8965370_SNP [dm6]	G	A	1.882e^-5	0.728	SYNONYMOUS_CODING CG5653 UPSTREAM CG5660	TF binding site mE1_TFBS_chinmo
3L	18270020	3L_18270020_INS [dm3] 3L_18276920_INS [dm6]	T	TT	2.053e^-5	0.762	INTERGENIC
3R	27612051	3R_27612051_SNP [dm3] 3R_31786329_SNP [dm6]	A	T	2.084e^-5	0.762	INTRON faf	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	10022362	3L_10022362_SNP [dm3] 3L_10029262_SNP [dm6]	C	A	2.096e^-5	0.762	DOWNSTREAM CR45155 INTRON dpr6
2L	3659330	2L_3659330_SNP [dm3] 2L_3659330_SNP [dm6]	A	G	2.161e^-5	0.77	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	13063145	3R_13063145_SNP [dm3] 3R_17237423_SNP [dm6]	T	C	2.242e^-5	0.783	INTRON beat-IIb
X	12388116	X_12388116_SNP [dm3] X_12494083_SNP [dm6]	G	A	2.364e^-5	0.81	DOWNSTREAM Mks1 INTERGENIC
X	12387048	X_12387048_SNP [dm3] X_12493015_SNP [dm6]	A	T	2.480e^-5	0.818	DOWNSTREAM Lsp1alpha INTERGENIC
X	12765438	X_12765438_SNP [dm3] X_12871405_SNP [dm6]	T	G	2.501e^-5	0.818	INTRON Pde9	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	18245214	3L_18245214_SNP [dm3] 3L_18252114_SNP [dm6]	C	T	2.522e^-5	0.818	SYNONYMOUS_CODING CheA75a
2R	11900136	2R_11900136_SNP [dm3] 2R_16012631_SNP [dm6]	A	C	2.654e^-5	0.833	INTRON CG8389	TF binding site BDTNP1_TFBS_sna
X	18732115	X_18732115_SNP [dm3] X_18838082_SNP [dm6]	A	G	2.744e^-5	0.833	NON_SYNONYMOUS_CODING Pvf1 SPLICE_SITE_REGION Pvf1 INTRON Pvf1
2L	7559183	2L_7559183_SNP [dm3] 2L_7559183_SNP [dm6]	C	A	2.745e^-5	0.833	INTRON RapGAP1
2R	16059546	2R_16059546_SNP [dm3] 2R_20172041_SNP [dm6]	G	A	2.752e^-5	0.833	INTERGENIC	TF binding site mE1_TFBS_Kr
3R	22527082	3R_22527082_SNP [dm3] 3R_26701360_SNP [dm6]	G	A	2.823e^-5	0.841	INTRON amon
3R	5726399	3R_5726399_SNP [dm3] 3R_9900677_SNP [dm6]	C	T	2.955e^-5	0.85	INTRON Glut4EF
3L	3720162	3L_3720162_INS [dm3] 3L_3720162_INS [dm6]	T	TCC	3.000e^-5	0.85	INTRON CG32264
X	10343184	X_10343184_SNP [dm3] X_10449151_SNP [dm6]	C	T	3.059e^-5	0.85	INTRON CG32683
X	4839708	X_4839708_SNP [dm3] X_4945675_SNP [dm6]	C	G	3.200e^-5	0.85	INTRON Ptp4E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	19994325	X_19994325_SNP [dm3] X_20100292_SNP [dm6]	G	A	3.223e^-5	0.85	INTERGENIC	transposable element FlyBase
X	12388447	X_12388447_DEL [dm3] X_12494414_DEL [dm6]	TA	T	3.296e^-5	0.85	UTR_3_PRIME Mks1
2L	10072746	2L_10072746_SNP [dm3] 2L_10072746_SNP [dm6]	T	G	3.324e^-5	0.85	INTRON CG44153	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	8127065	3L_8127065_SNP [dm3] 3L_8133965_SNP [dm6]	T	C	3.333e^-5	0.85	SYNONYMOUS_CODING CG7504
2R	12572245	2R_12572245_DEL [dm3] 2R_16684740_DEL [dm6]	AGTAGTTTCCAA...	A	3.400e^-5	0.85	UPSTREAM CG30463 INTRON CG30463
3L	16052983	3L_16052983_SNP [dm3] 3L_16059883_SNP [dm6]	T	C	3.445e^-5	0.85	INTRON Mbs
3L	12282492	3L_12282492_SNP [dm3] 3L_12289392_SNP [dm6]	C	G	3.465e^-5	0.85	EXON CR45658
3L	12282496	3L_12282496_SNP [dm3] 3L_12289396_SNP [dm6]	C	T	3.465e^-5	0.85	EXON CR45658
3L	13277124	3L_13277124_SNP [dm3] 3L_13284024_SNP [dm6]	A	G	3.510e^-5	0.85	DOWNSTREAM CR43146 INTRON CR43913
X	4690315	X_4690315_SNP [dm3] X_4796282_SNP [dm6]	G	A	3.510e^-5	0.85	DOWNSTREAM CG2861 INTERGENIC
3L	1002042	3L_1002042_SNP [dm3] 3L_1002042_SNP [dm6]	C	A	3.560e^-5	0.851	INTRON trio
X	13349755	X_13349755_SNP [dm3] X_13455722_SNP [dm6]	A	G	3.812e^-5	0.885	DOWNSTREAM CG34324 INTRON Neto
2L	3659304	2L_3659304_SNP [dm3] 2L_3659304_SNP [dm6]	T	A	3.849e^-5	0.885	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	2712404	X_2712404_SNP [dm3] X_2818371_SNP [dm6]	C	G	3.850e^-5	0.885	INTRON kirre
2R	17315450	2R_17315450_SNP [dm3] 2R_21427945_SNP [dm6]	A	G	3.898e^-5	0.885	INTRON Sdc
3L	2335692	3L_2335692_SNP [dm3] 3L_2335692_SNP [dm6]	T	C	4.103e^-5	0.888	INTRON MsR1
2L	7558758	2L_7558758_SNP [dm3] 2L_7558758_SNP [dm6]	C	T	4.120e^-5	0.888	INTRON RapGAP1
3R	5720560	3R_5720560_DEL [dm3] 3R_9894838_DEL [dm6]	CCCAGTTTTGAAATCGC...	C	4.160e^-5	0.888	INTRON Glut4EF	TF binding site mE1_TFBS_inv
2L	3659359	2L_3659359_SNP [dm3] 2L_3659359_SNP [dm6]	A	T	4.260e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	3659371	2L_3659371_SNP [dm3] 2L_3659371_SNP [dm6]	C	A	4.260e^-5	0.888	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	22527071	3R_22527071_INS [dm3] 3R_26701349_INS [dm6]	A	ACATACATA	4.290e^-5	0.888	INTRON amon
2R	13508698	2R_13508698_SNP [dm3] 2R_17621193_SNP [dm6]	C	T	4.422e^-5	0.888	INTRON CG10936
3R	23479462	3R_23479462_SNP [dm3] 3R_27653740_SNP [dm6]	G	A	4.446e^-5	0.888	DOWNSTREAM RpS10a INTRON tau
X	6758820	X_6758820_DEL [dm3] X_6864787_DEL [dm6]	TGAGTTTTAACTG...	T	4.499e^-5	0.888	INTRON CG14434 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	16337711	3R_16337711_SNP [dm3] 3R_20511989_SNP [dm6]	T	G	4.549e^-5	0.888	INTRON CG4288	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	16337724	3R_16337724_SNP [dm3] 3R_20512002_SNP [dm6]	C	T	4.549e^-5	0.888	INTRON CG4288	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	17299361	X_17299361_SNP [dm3] X_17405328_SNP [dm6]	T	C	4.564e^-5	0.888	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11715678	3L_11715678_SNP [dm3] 3L_11722578_SNP [dm6]	T	C	4.645e^-5	0.888	INTRON Bmcp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	4614305	2R_4614305_INS [dm3] 2R_8726800_INS [dm6]	T	CCCA	4.692e^-5	0.888	INTRON gcl
2L	15795162	2L_15795162_SNP [dm3] 2L_15795162_SNP [dm6]	G	T	4.734e^-5	0.888	INTERGENIC
2L	7559398	2L_7559398_SNP [dm3] 2L_7559398_SNP [dm6]	A	T	4.864e^-5	0.888	INTRON RapGAP1
2L	7559404	2L_7559404_SNP [dm3] 2L_7559404_SNP [dm6]	T	A	4.864e^-5	0.888	INTRON RapGAP1
2L	7559419	2L_7559419_SNP [dm3] 2L_7559419_SNP [dm6]	T	A	4.864e^-5	0.888	INTRON RapGAP1
2R	16621768	2R_16621768_SNP [dm3] 2R_20734263_SNP [dm6]	T	C	4.864e^-5	0.888	INTRON dpr
2R	3022198	2R_3022198_SNP [dm3] 2R_7134693_SNP [dm6]	G	A	4.894e^-5	0.888	EXON CR44443

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_PElem_GC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results