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=6.332e^-7)
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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	5.0038	0.0819

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2074 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
3R	21765101	3R_21765101_SNP [dm3] 3R_25939379_SNP [dm6]	T	C	8.594e^-8	0.147	INTRON CCAP-R
3R	21765117	3R_21765117_SNP [dm3] 3R_25939395_SNP [dm6]	C	A	1.573e^-7	0.147	INTRON CCAP-R
3L	12090492	3L_12090492_SNP [dm3] 3L_12097392_SNP [dm6]	C	T	3.809e^-7	0.195	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	21765153	3R_21765153_SNP [dm3] 3R_25939431_SNP [dm6]	C	T	4.155e^-7	0.195	INTRON CCAP-R
3R	7405095	3R_7405095_SNP [dm3] 3R_11579373_SNP [dm6]	G	A	6.206e^-7	0.233	SYNONYMOUS_CODING CG5342 UPSTREAM CG6790
3L	10428014	3L_10428014_SNP [dm3] 3L_10434914_SNP [dm6]	A	G	1.589e^-6	0.433	UPSTREAM Ir67c INTERGENIC
X	11753161	X_11753161_SNP [dm3] X_11859128_SNP [dm6]	T	A	1.867e^-6	0.433	INTRON ATP7	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
3L	13856445	3L_13856445_SNP [dm3] 3L_13863345_SNP [dm6]	G	T	2.221e^-6	0.433	INTRON CG8745	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2L	3319372	2L_3319372_SNP [dm3] 2L_3319372_SNP [dm6]	T	G	2.281e^-6	0.433	NON_SYNONYMOUS_CODING CG3326 UPSTREAM CG8837	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	7405598	3R_7405598_SNP [dm3] 3R_11579876_SNP [dm6]	C	T	2.307e^-6	0.433	SYNONYMOUS_CODING CG5342
2L	4925780	2L_4925780_SNP [dm3] 2L_4925780_SNP [dm6]	C	T	2.787e^-6	0.455	INTRON hoe1
2R	12469126	2R_12469126_SNP [dm3] 2R_16581621_SNP [dm6]	T	A	2.958e^-6	0.455	DOWNSTREAM CR44375 INTRON Cdk4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_Trl
3L	4781227	3L_4781227_SNP [dm3] 3L_4781227_SNP [dm6]	G	T	3.158e^-6	0.455	INTRON RhoGEF64C
X	14937788	X_14937788_SNP [dm3] X_15043755_SNP [dm6]	A	C	3.779e^-6	0.502	UPSTREAM CG5541 INTRON hiw	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	6027243	3L_6027243_SNP [dm3] 3L_6034143_SNP [dm6]	G	C	4.727e^-6	0.502	SYNONYMOUS_CODING CG10477
3L	20823783	3L_20823783_SNP [dm3] 3L_20830683_SNP [dm6]	T	C	4.816e^-6	0.502	INTRON Pka-R1
3L	12090477	3L_12090477_SNP [dm3] 3L_12097377_SNP [dm6]	G	A	5.280e^-6	0.502	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	12725446	3R_12725446_SNP [dm3] 3R_16899724_SNP [dm6]	T	C	5.292e^-6	0.502	EXON iab-8	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	1526854	2R_1526854_SNP [dm3] 2R_5639349_SNP [dm6]	T	C	5.720e^-6	0.502	INTERGENIC	transposable element FlyBase
2L	3319211	2L_3319211_SNP [dm3] 2L_3319211_SNP [dm6]	C	T	6.174e^-6	0.502	INTRON CG3326
3L	6444416	3L_6444416_SNP [dm3] 3L_6451316_SNP [dm6]	G	C	6.221e^-6	0.502	INTRON CG42747
2R	1526912	2R_1526912_SNP [dm3] 2R_5639407_SNP [dm6]	C	G	6.576e^-6	0.502	INTERGENIC	transposable element FlyBase
2R	1526842	2R_1526842_SNP [dm3] 2R_5639337_SNP [dm6]	T	G	6.895e^-6	0.502	INTERGENIC	transposable element FlyBase
2L	3319196	2L_3319196_SNP [dm3] 2L_3319196_SNP [dm6]	T	C	6.984e^-6	0.502	INTRON CG3326
2R	1527456	2R_1527456_SNP [dm3] 2R_5639951_SNP [dm6]	C	A	7.495e^-6	0.502	DOWNSTREAM CG11665 INTERGENIC	TF binding site mE1_TFBS_sens
2L	21942650	2L_21942650_SNP [dm3] 2L_21942650_SNP [dm6]	G	A	7.559e^-6	0.502	INTERGENIC
3L	1879981	3L_1879981_SNP [dm3] 3L_1879981_SNP [dm6]	T	G	7.701e^-6	0.502	INTRON CG13937
3L	15535565	3L_15535565_SNP [dm3] 3L_15542465_SNP [dm6]	G	A	7.762e^-6	0.502	INTRON CrebA
2R	1527352	2R_1527352_SNP [dm3] 2R_5639847_SNP [dm6]	G	T	8.067e^-6	0.502	INTERGENIC	TF binding site mE1_TFBS_sens
X	5929427	X_5929427_INS [dm3] X_6035394_INS [dm6]	T	TGTGCA	8.254e^-6	0.502	DOWNSTREAM rux INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	7405258	3R_7405258_SNP [dm3] 3R_11579536_SNP [dm6]	G	C	8.294e^-6	0.502	NON_SYNONYMOUS_CODING CG5342 UPSTREAM CG6790
2R	12225410	2R_12225410_SNP [dm3] 2R_16337905_SNP [dm6]	A	T	9.594e^-6	0.562	UPSTREAM Hmgs INTRON Hmgs
X	15140053	X_15140053_DEL [dm3] X_15246020_DEL [dm6]	TA	T	1.097e^-5	0.605	INTERGENIC
2R	18024993	2R_18024993_SNP [dm3] 2R_22137488_SNP [dm6]	C	T	1.108e^-5	0.605	UTR_5_PRIME a INTRON a	TF binding site mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Trl
3L	1880245	3L_1880245_SNP [dm3] 3L_1880245_SNP [dm6]	A	G	1.170e^-5	0.605	INTRON CG13937
X	15140070	X_15140070_SNP [dm3] X_15246037_SNP [dm6]	C	A	1.203e^-5	0.605	INTERGENIC
2R	10530718	2R_10530718_SNP [dm3] 2R_14643213_SNP [dm6]	A	G	1.216e^-5	0.605	INTERGENIC
2L	7602294	2L_7602294_SNP [dm3] 2L_7602294_SNP [dm6]	T	C	1.238e^-5	0.605	INTERGENIC
2R	13715758	2R_13715758_DEL [dm3] 2R_17828253_DEL [dm6]	TT	T	1.305e^-5	0.605	INTRON grh
3L	2701891	3L_2701891_INS [dm3] 3L_2701891_INS [dm6]	T	TTGCCATGTCGAAAT...	1.326e^-5	0.605	INTRON Fife
2L	13679639	2L_13679639_SNP [dm3] 2L_13679639_SNP [dm6]	C	T	1.348e^-5	0.605	INTRON CG31814
3L	4814409	3L_4814409_SNP [dm3] 3L_4814409_SNP [dm6]	C	A	1.374e^-5	0.605	SYNONYMOUS_CODING Dhc64C	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	11252739	2L_11252739_SNP [dm3] 2L_11252739_SNP [dm6]	A	G	1.388e^-5	0.605	INTRON ab
3L	10427978	3L_10427978_SNP [dm3] 3L_10434878_SNP [dm6]	A	C	1.423e^-5	0.606	UPSTREAM Ir67c INTERGENIC
2L	18221155	2L_18221155_SNP [dm3] 2L_18221155_SNP [dm6]	A	G	1.489e^-5	0.621	INTRON CG42750
2L	7465289	2L_7465289_SNP [dm3] 2L_7465289_SNP [dm6]	G	A	1.526e^-5	0.622	INTERGENIC
2L	9816396	2L_9816396_SNP [dm3] 2L_9816396_SNP [dm6]	G	A	1.566e^-5	0.625	INTRON nAChRalpha6
3L	15535891	3L_15535891_SNP [dm3] 3L_15542791_SNP [dm6]	G	T	1.655e^-5	0.637	INTRON CrebA
3R	23399255	3R_23399255_SNP [dm3] 3R_27573533_SNP [dm6]	G	A	1.705e^-5	0.637	INTRON wdb
3L	5002002	3L_5002002_SNP [dm3] 3L_5002002_SNP [dm6]	G	A	1.714e^-5	0.637	INTRON Con	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	1526909	2R_1526909_INS [dm3] 2R_5639404_INS [dm6]	T	TT	1.734e^-5	0.637	INTERGENIC	transposable element FlyBase
2L	9837384	2L_9837384_SNP [dm3] 2L_9837384_SNP [dm6]	C	T	1.777e^-5	0.637	INTRON nAChRalpha6
3R	17909495	3R_17909495_SNP [dm3] 3R_22083773_SNP [dm6]	C	T	1.801e^-5	0.637	DOWNSTREAM CG13408 INTERGENIC
X	5030428	X_5030428_SNP [dm3] X_5136395_SNP [dm6]	C	A	1.868e^-5	0.637	INTRON rg & 1 other
2R	1526911	2R_1526911_SNP [dm3] 2R_5639406_SNP [dm6]	A	G	1.868e^-5	0.637	INTERGENIC	transposable element FlyBase
3L	17706810	3L_17706810_SNP [dm3] 3L_17713710_SNP [dm6]	C	A	1.911e^-5	0.637	INTRON Ccn	TF binding site BDTNP1_TFBS_twi
2R	13715573	2R_13715573_SNP [dm3] 2R_17828068_SNP [dm6]	T	A	1.936e^-5	0.637	INTRON grh
2R	13715820	2R_13715820_SNP [dm3] 2R_17828315_SNP [dm6]	T	C	1.993e^-5	0.644	INTRON grh
2L	3309778	2L_3309778_SNP [dm3] 2L_3309778_SNP [dm6]	G	C	2.144e^-5	0.66	SYNONYMOUS_CODING CG15406 INTRON CG3277
X	15140057	X_15140057_SNP [dm3] X_15246024_SNP [dm6]	C	T	2.181e^-5	0.66	INTERGENIC
X	12445482	X_12445482_SNP [dm3] X_12551449_SNP [dm6]	G	A	2.199e^-5	0.66	INTRON CG43921
3L	12090482	3L_12090482_SNP [dm3] 3L_12097382_SNP [dm6]	T	C	2.233e^-5	0.66	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	17909507	3R_17909507_SNP [dm3] 3R_22083785_SNP [dm6]	G	T	2.238e^-5	0.66	DOWNSTREAM CG13408 INTERGENIC
3L	16682919	3L_16682919_SNP [dm3] 3L_16689819_SNP [dm6]	C	T	2.253e^-5	0.66	INTRON Lasp & 2 others EXON CR45179
2L	15795648	2L_15795648_SNP [dm3] 2L_15795648_SNP [dm6]	A	G	2.349e^-5	0.678	INTERGENIC
X	14947930	X_14947930_SNP [dm3] X_15053897_SNP [dm6]	G	A	2.398e^-5	0.681	SYNONYMOUS_CODING hiw	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	1879909	3L_1879909_SNP [dm3] 3L_1879909_SNP [dm6]	C	T	2.512e^-5	0.7	INTRON CG13937
3R	17308414	3R_17308414_SNP [dm3] 3R_21482692_SNP [dm6]	A	G	2.539e^-5	0.7	SYNONYMOUS_CODING CG7922	TF binding site mE1_TFBS_sens
X	5929438	X_5929438_SNP [dm3] X_6035405_SNP [dm6]	C	T	2.624e^-5	0.708	DOWNSTREAM rux INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3L	10684999	3L_10684999_SNP [dm3] 3L_10691899_SNP [dm6]	A	T	2.641e^-5	0.708	UTR_3_PRIME CG11811 DOWNSTREAM CG33493
3L	3457966	3L_3457966_SNP [dm3] 3L_3457966_SNP [dm6]	A	C	2.741e^-5	0.724	SYNONYMOUS_CODING eIF5B	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	1442721	2R_1442721_SNP [dm3] 2R_5555216_SNP [dm6]	C	T	2.804e^-5	0.729	INTERGENIC	transposable element FlyBase
3L	15535784	3L_15535784_SNP [dm3] 3L_15542684_SNP [dm6]	G	A	2.839e^-5	0.729	INTRON CrebA
3R	14380596	3R_14380596_SNP [dm3] 3R_18554874_SNP [dm6]	T	G	2.920e^-5	0.733	INTERGENIC
3L	1879982	3L_1879982_INS [dm3] 3L_1879982_INS [dm6]	C	CT	2.932e^-5	0.733	INTRON CG13937
3L	18326323	3L_18326323_SNP [dm3] 3L_18333223_SNP [dm6]	G	A	3.017e^-5	0.744	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	1529403	2R_1529403_SNP [dm3] 2R_5641898_SNP [dm6]	A	T	3.127e^-5	0.754	UTR_3_PRIME CG11665
2L	3885087	2L_3885087_SNP [dm3] 2L_3885087_SNP [dm6]	T	C	3.135e^-5	0.754	INTRON capu
3L	20805578	3L_20805578_INS [dm3] 3L_20812478_INS [dm6]	A	ATA	3.284e^-5	0.777	DOWNSTREAM CG3618 INTRON CG3680	TF binding site mE1_TFBS_sens
2R	9494640	2R_9494640_SNP [dm3] 2R_13607135_SNP [dm6]	A	T	3.331e^-5	0.777	INTERGENIC
2L	20749865	2L_20749865_SNP [dm3] 2L_20749865_SNP [dm6]	A	T	3.386e^-5	0.777	UTR_3_PRIME Fs_2_Ket
2L	1558647	2L_1558647_SNP [dm3] 2L_1558647_SNP [dm6]	A	C	3.401e^-5	0.777	INTRON haf
2R	3258089	2R_3258089_SNP [dm3] 2R_7370584_SNP [dm6]	A	G	3.441e^-5	0.777	INTRON Dscam1	regulatory region REDfly_CRMs
3L	1870055	3L_1870055_SNP [dm3] 3L_1870055_SNP [dm6]	C	A	3.512e^-5	0.778	NON_SYNONYMOUS_CODING CG13924 UPSTREAM CG13924 DOWNSTREAM CG12025	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	9069821	X_9069821_DEL [dm3] X_9175788_DEL [dm6]	CG	C	3.582e^-5	0.778	UTR_3_PRIME mei-P26 DOWNSTREAM mei-P26
3L	14762054	3L_14762054_SNP [dm3] 3L_14768954_SNP [dm6]	A	T	3.664e^-5	0.778	NON_SYNONYMOUS_CODING CG17173 DOWNSTREAM mop
2R	1526843	2R_1526843_SNP [dm3] 2R_5639338_SNP [dm6]	T	G	3.707e^-5	0.778	INTERGENIC	transposable element FlyBase
3R	22997258	3R_22997258_SNP [dm3] 3R_27171536_SNP [dm6]	C	T	3.711e^-5	0.778	DOWNSTREAM Ser INTERGENIC	regulatory region REDfly_CRMs
X	5798293	X_5798293_INS [dm3] X_5904260_INS [dm6]	A	ACA	3.715e^-5	0.778	UTR_3_PRIME Act5C DOWNSTREAM Act5C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	15401156	X_15401156_SNP [dm3] X_15507123_SNP [dm6]	T	C	3.733e^-5	0.778	UPSTREAM mir-283 INTRON Gmap	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14031381	2R_14031381_SNP [dm3] 2R_18143876_SNP [dm6]	C	T	3.924e^-5	0.79	SYNONYMOUS_CODING pAbp DOWNSTREAM snoRNA:Psi18S-1347a & 2 others	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	21768184	3R_21768184_SNP [dm3] 3R_25942462_SNP [dm6]	A	C	3.929e^-5	0.79	INTRON CCAP-R
3L	9655465	3L_9655465_SNP [dm3] 3L_9662365_SNP [dm6]	T	C	3.955e^-5	0.79	INTRON fry	TF binding site BDTNP1_TFBS_twi
3R	22750326	3R_22750326_SNP [dm3] 3R_26924604_SNP [dm6]	A	T	3.971e^-5	0.79	INTRON sda
2L	16372991	2L_16372991_SNP [dm3] 2L_16372991_SNP [dm6]	A	G	4.003e^-5	0.79	INTERGENIC
3L	10652324	3L_10652324_SNP [dm3] 3L_10659224_SNP [dm6]	G	T	4.050e^-5	0.791	INTRON CG32066	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2L	20300823	2L_20300823_SNP [dm3] 2L_20300823_SNP [dm6]	C	T	4.104e^-5	0.793	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	12102515	3L_12102515_SNP [dm3] 3L_12109415_SNP [dm6]	C	G	4.155e^-5	0.795	INTERGENIC
3L	5277429	3L_5277429_INS [dm3] 3L_5284329_INS [dm6]	A	AG	4.404e^-5	0.828	INTERGENIC
3R	15551825	3R_15551825_SNP [dm3] 3R_19726103_SNP [dm6]	A	G	4.413e^-5	0.828	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

midgut_mitosis_PA phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results