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=5.031e^-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
wolba	0.06143
In_2L_t	0.02847
In_3R_Mo	0.04763

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.6182	0.0603
In_3R_Mo	6.5813	0.0372

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2337 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	17685083	2R_17685083_DEL [dm3] 2R_21797578_DEL [dm6]	GTC	G	5.564e^-7	0.789	DOWNSTREAM CG34204 & 1 other INTERGENIC
3L	1909764	3L_1909764_SNP [dm3] 3L_1909764_SNP [dm6]	T	C	1.144e^-6	0.789	INTRON CG1887
X	9733635	X_9733635_SNP [dm3] X_9839602_SNP [dm6]	T	G	1.540e^-6	0.789	INTRON CG32698
2R	16176361	2R_16176361_SNP [dm3] 2R_20288856_SNP [dm6]	T	C	4.332e^-6	0.789	UTR_3_PRIME Cpr56F UPSTREAM CkIIbeta2 DOWNSTREAM CG34199	TF binding site mE1_TFBS_chinmo
2L	19129166	2L_19129166_INS [dm3] 2L_19129166_INS [dm6]	T	TGATTT	5.476e^-6	0.789	UTR_3_PRIME l_2_37Cd DOWNSTREAM Aats-asn	TF binding site mE1_TFBS_cad
2L	19101233	2L_19101233_INS [dm3] 2L_19101233_INS [dm6]	A	AA	6.446e^-6	0.789	UPSTREAM CG17344 & 1 other INTRON Lim3
2R	16177451	2R_16177451_SNP [dm3] 2R_20289946_SNP [dm6]	A	C	6.603e^-6	0.789	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
3L	10755458	3L_10755458_SNP [dm3] 3L_10762358_SNP [dm6]	C	A	8.406e^-6	0.789	INTERGENIC
2R	786462	2R_786462_SNP [dm3] 2R_4898957_SNP [dm6]	A	C	9.364e^-6	0.789	INTRON CG44102	transposable element FlyBase
2R	16177429	2R_16177429_SNP [dm3] 2R_20289924_SNP [dm6]	T	C	1.025e^-5	0.789	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
2R	12680355	2R_12680355_SNP [dm3] 2R_16792850_SNP [dm6]	T	A	1.077e^-5	0.789	DOWNSTREAM CG15615 & 1 other INTRON CG15919
2R	15213498	2R_15213498_SNP [dm3] 2R_19325993_SNP [dm6]	C	G	1.086e^-5	0.789	SYNONYMOUS_CODING Rgk1 UPSTREAM Rgk1	TF binding site mE1_TFBS_chinmo mE1_TFBS_Trl
2R	670107	2R_670107_SNP [dm3] 2R_4782602_SNP [dm6]	C	A	1.198e^-5	0.789	INTRON CR43281
3L	1589711	3L_1589711_SNP [dm3] 3L_1589711_SNP [dm6]	T	C	1.210e^-5	0.789	INTRON CG13917
3L	5374564	3L_5374564_SNP [dm3] 3L_5381464_SNP [dm6]	C	G	1.269e^-5	0.789	INTRON Ir64a
3L	12523392	3L_12523392_SNP [dm3] 3L_12530292_SNP [dm6]	A	C	1.275e^-5	0.789	UPSTREAM nst DOWNSTREAM Tsf2 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20405065	3R_20405065_SNP [dm3] 3R_24579343_SNP [dm6]	G	A	1.303e^-5	0.789	INTRON CG13624	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15175615	2L_15175615_SNP [dm3] 2L_15175615_SNP [dm6]	A	C	1.346e^-5	0.789	INTRON CG4168
3R	24418101	3R_24418101_SNP [dm3] 3R_28592379_SNP [dm6]	G	A	1.347e^-5	0.789	DOWNSTREAM MRE23 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cnc
3L	10032780	3L_10032780_SNP [dm3] 3L_10039680_SNP [dm6]	C	A	1.355e^-5	0.789	INTRON dpr6	TF binding site BDTNP1_TFBS_dl
X	9803438	X_9803438_SNP [dm3] X_9909405_SNP [dm6]	G	A	1.471e^-5	0.789	UTR_3_PRIME CG1986
3L	12391055	3L_12391055_SNP [dm3] 3L_12397955_SNP [dm6]	A	T	1.678e^-5	0.789	DOWNSTREAM Obp69a INTRON CG32104	TF binding site mE1_TFBS_HSA
X	16700589	X_16700589_SNP [dm3] X_16806556_SNP [dm6]	A	G	1.691e^-5	0.789	DOWNSTREAM CG13005 INTRON ppk28 & 1 other
2R	12680354	2R_12680354_SNP [dm3] 2R_16792849_SNP [dm6]	C	T	1.743e^-5	0.789	DOWNSTREAM CG15615 & 1 other INTRON CG15919
X	9803377	X_9803377_SNP [dm3] X_9909344_SNP [dm6]	T	A	1.746e^-5	0.789	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
3L	12883585	3L_12883585_SNP [dm3] 3L_12890485_SNP [dm6]	T	A	1.783e^-5	0.789	UPSTREAM CR45748 INTRON CG43894
2L	4078242	2L_4078242_SNP [dm3] 2L_4078242_SNP [dm6]	T	G	1.864e^-5	0.789	INTRON ed
X	8578764	X_8578764_INS [dm3] X_8684731_INS [dm6]	T	TC	1.910e^-5	0.789	UPSTREAM CG11284 INTRON CG11284
X	9118394	X_9118394_SNP [dm3] X_9224361_SNP [dm6]	A	G	2.084e^-5	0.789	INTERGENIC
3L	5212528	3L_5212528_SNP [dm3] 3L_5219428_SNP [dm6]	C	T	2.162e^-5	0.789	INTRON shep
2R	785933	2R_785933_SNP [dm3] 2R_4898428_SNP [dm6]	G	A	2.271e^-5	0.789	INTRON CG44102	TF binding site mE1_TFBS_HSA mE1_TFBS_sens transposable element FlyBase
2L	8321657	2L_8321657_SNP [dm3] 2L_8321657_SNP [dm6]	A	T	2.309e^-5	0.789	UTR_3_PRIME CG7781 DOWNSTREAM CG7787
2L	9981354	2L_9981354_INS [dm3] 2L_9981354_INS [dm6]	G	CGGTT	2.329e^-5	0.789	INTERGENIC	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3L	12883596	3L_12883596_SNP [dm3] 3L_12890496_SNP [dm6]	C	T	2.345e^-5	0.789	UPSTREAM CR45748 INTRON CG43894
3L	12883597	3L_12883597_SNP [dm3] 3L_12890497_SNP [dm6]	G	A	2.345e^-5	0.789	UPSTREAM CR45748 INTRON CG43894
3L	8605037	3L_8605037_INS [dm3] 3L_8611937_INS [dm6]	T	TTTT	2.492e^-5	0.789	INTRON CG6282
2R	17475405	2R_17475405_DEL [dm3] 2R_21587900_DEL [dm6]	GG	A	2.508e^-5	0.789	INTERGENIC
3L	1673072	3L_1673072_SNP [dm3] 3L_1673072_SNP [dm6]	G	C	2.558e^-5	0.789	UPSTREAM CG13930 INTERGENIC	TF binding site mE1_TFBS_cad
X	6100552	X_6100552_SNP [dm3] X_6206519_SNP [dm6]	T	C	2.566e^-5	0.789	INTERGENIC
2R	668322	2R_668322_SNP [dm3] 2R_4780817_SNP [dm6]	G	A	2.668e^-5	0.789	EXON CR43281
3L	1715681	3L_1715681_MNP [dm3] 3L_1715681_MNP [dm6]	GTTA	TAAC	2.669e^-5	0.789	UTR_3_PRIME drpr DOWNSTREAM drpr & 1 other
3L	1715686	3L_1715686_INS [dm3] 3L_1715686_INS [dm6]	A	AT	2.669e^-5	0.789	UTR_3_PRIME drpr DOWNSTREAM drpr & 1 other
3R	22993931	3R_22993931_SNP [dm3] 3R_27168209_SNP [dm6]	C	A	2.674e^-5	0.789	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_chinmo
2L	12151606	2L_12151606_SNP [dm3] 2L_12151606_SNP [dm6]	G	A	2.727e^-5	0.789	INTRON CG31760
X	6100641	X_6100641_SNP [dm3] X_6206608_SNP [dm6]	T	A	2.753e^-5	0.789	INTERGENIC
X	6810284	X_6810284_INS [dm3] X_6916251_INS [dm6]	T	TAT	2.762e^-5	0.789	INTRON CG14431
X	6810287	X_6810287_SNP [dm3] X_6916254_SNP [dm6]	A	G	2.762e^-5	0.789	INTRON CG14431
2R	17475403	2R_17475403_SNP [dm3] 2R_21587898_SNP [dm6]	G	A	2.854e^-5	0.789	INTERGENIC
3R	10504827	3R_10504827_SNP [dm3] 3R_14679105_SNP [dm6]	C	T	2.897e^-5	0.789	INTRON Meltrin	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
3R	14969810	3R_14969810_SNP [dm3] 3R_19144088_SNP [dm6]	G	C	3.135e^-5	0.789	INTRON Ppcs
2R	14752050	2R_14752050_SNP [dm3] 2R_18864545_SNP [dm6]	T	A	3.236e^-5	0.789	UTR_3_PRIME CG43070 DOWNSTREAM CG43071
2R	6308590	2R_6308590_SNP [dm3] 2R_10421085_SNP [dm6]	C	G	3.310e^-5	0.789	UPSTREAM CG33474 & 1 other INTRON CG11825	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	20405199	3R_20405199_SNP [dm3] 3R_24579477_SNP [dm6]	C	A	3.315e^-5	0.789	INTRON CG13624	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	9803183	X_9803183_SNP [dm3] X_9909150_SNP [dm6]	A	G	3.382e^-5	0.789	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
2L	11302671	2L_11302671_SNP [dm3] 2L_11302671_SNP [dm6]	G	A	3.470e^-5	0.789	INTERGENIC
3L	13434402	3L_13434402_SNP [dm3] 3L_13441302_SNP [dm6]	T	C	3.525e^-5	0.789	UPSTREAM CG10140 INTRON CG14109
3L	11628460	3L_11628460_SNP [dm3] 3L_11635360_SNP [dm6]	T	A	3.555e^-5	0.789	INTRON CG32091
2R	14754449	2R_14754449_SNP [dm3] 2R_18866944_SNP [dm6]	G	T	3.612e^-5	0.789	UPSTREAM DptB DOWNSTREAM Dpt & 1 other INTERGENIC
2R	16177498	2R_16177498_SNP [dm3] 2R_20289993_SNP [dm6]	C	G	3.683e^-5	0.789	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
2L	11302153	2L_11302153_SNP [dm3] 2L_11302153_SNP [dm6]	T	A	3.749e^-5	0.789	INTERGENIC
3R	11018344	3R_11018344_SNP [dm3] 3R_15192622_SNP [dm6]	T	G	3.855e^-5	0.789	SYNONYMOUS_CODING CG6752 UPSTREAM mir-3644
3L	3207810	3L_3207810_SNP [dm3] 3L_3207810_SNP [dm6]	T	C	3.987e^-5	0.789	NON_SYNONYMOUS_CODING CG32269 UTR_3_PRIME CG32270 INTRON gry	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	16395828	2L_16395828_SNP [dm3] 2L_16395828_SNP [dm6]	G	A	3.993e^-5	0.789	INTERGENIC
2R	7494186	2R_7494186_SNP [dm3] 2R_11606681_SNP [dm6]	C	A	3.999e^-5	0.789	INTRON tou	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	9774047	2L_9774047_SNP [dm3] 2L_9774047_SNP [dm6]	G	A	4.002e^-5	0.789	SYNONYMOUS_CODING ppk11
2L	4185886	2L_4185886_SNP [dm3] 2L_4185886_SNP [dm6]	T	C	4.121e^-5	0.789	DOWNSTREAM CG31961 INTRON CR44057	TF binding site BDTNP1_TFBS_twi
2R	14641561	2R_14641561_INS [dm3] 2R_18754056_INS [dm6]	A	ATA	4.130e^-5	0.789	UTR_3_PRIME Hs3st-A UPSTREAM Cyp12b2
3R	22813578	3R_22813578_SNP [dm3] 3R_26987856_SNP [dm6]	A	C	4.154e^-5	0.789	UPSTREAM CG31075 INTRON CG31075
2L	9773943	2L_9773943_SNP [dm3] 2L_9773943_SNP [dm6]	A	G	4.161e^-5	0.789	NON_SYNONYMOUS_CODING ppk11 UPSTREAM ppk16
2R	17397098	2R_17397098_SNP [dm3] 2R_21509593_SNP [dm6]	G	T	4.236e^-5	0.789	INTRON MESK2
2R	14091188	2R_14091188_SNP [dm3] 2R_18203683_SNP [dm6]	T	A	4.302e^-5	0.789	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6571470	3L_6571470_SNP [dm3] 3L_6578370_SNP [dm6]	G	T	4.308e^-5	0.789	INTRON CG18769 & 1 other
X	8501008	X_8501008_DEL [dm3] X_8606975_DEL [dm6]	TCTTCCCAAGTTT...	T	4.308e^-5	0.789	UPSTREAM Caf1-180 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl mE1_TFBS_bab1
2L	7715589	2L_7715589_SNP [dm3] 2L_7715589_SNP [dm6]	A	T	4.322e^-5	0.789	NON_SYNONYMOUS_CODING CG33296
X	9803405	X_9803405_SNP [dm3] X_9909372_SNP [dm6]	C	T	4.326e^-5	0.789	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
2R	10819815	2R_10819815_SNP [dm3] 2R_14932310_SNP [dm6]	A	G	4.417e^-5	0.789	SYNONYMOUS_CODING CG10253
2R	766632	2R_766632_SNP [dm3] 2R_4879127_SNP [dm6]	G	T	4.425e^-5	0.789	INTERGENIC
2R	784188	2R_784188_SNP [dm3] 2R_4896683_SNP [dm6]	A	C	4.446e^-5	0.789	INTRON CG44102	transposable element FlyBase
3L	19285729	3L_19285729_SNP [dm3] 3L_19292629_SNP [dm6]	G	A	4.448e^-5	0.789	UTR_5_PRIME Gbs-76A UPSTREAM Gbs-76A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
3L	1909694	3L_1909694_SNP [dm3] 3L_1909694_SNP [dm6]	G	T	4.455e^-5	0.789	INTRON CG1887
X	5071240	X_5071240_SNP [dm3] X_5177207_SNP [dm6]	T	C	4.464e^-5	0.789	INTRON rg & 1 other
2L	14664874	2L_14664874_SNP [dm3] 2L_14664874_SNP [dm6]	A	T	4.475e^-5	0.789	INTRON osp
X	20784905	X_20784905_SNP [dm3] X_20913878_SNP [dm6]	T	C	4.514e^-5	0.789	INTRON shakB
2R	14753586	2R_14753586_SNP [dm3] 2R_18866081_SNP [dm6]	G	A	4.535e^-5	0.789	SYNONYMOUS_CODING Dpt UPSTREAM CG43071
2R	678603	2R_678603_SNP [dm3] 2R_4791098_SNP [dm6]	G	C	4.617e^-5	0.789	INTERGENIC	transposable element FlyBase
3L	9919556	3L_9919556_SNP [dm3] 3L_9926456_SNP [dm6]	T	C	4.643e^-5	0.789	INTRON CG34356
3R	14969796	3R_14969796_SNP [dm3] 3R_19144074_SNP [dm6]	G	C	4.710e^-5	0.789	INTRON Ppcs
2R	14754408	2R_14754408_SNP [dm3] 2R_18866903_SNP [dm6]	A	G	4.856e^-5	0.789	UPSTREAM DptB DOWNSTREAM Dpt & 1 other INTERGENIC
2R	16545394	2R_16545394_SNP [dm3] 2R_20657889_SNP [dm6]	T	A	4.878e^-5	0.789	UPSTREAM tRNA:CR30155 DOWNSTREAM tRNA:CR30211 INTRON Lrt
3L	1589984	3L_1589984_SNP [dm3] 3L_1589984_SNP [dm6]	A	T	4.882e^-5	0.789	INTRON CG13917
3L	16532066	3L_16532066_DEL [dm3] 3L_16538966_DEL [dm6]	CA	C	4.894e^-5	0.789	INTRON CG43373
X	12848994	X_12848994_SNP [dm3] X_12954961_SNP [dm6]	T	A	4.914e^-5	0.789	INTRON hec
2R	780675	2R_780675_SNP [dm3] 2R_4893170_SNP [dm6]	C	T	4.916e^-5	0.789	INTERGENIC	transposable element FlyBase
2L	11376410	2L_11376410_SNP [dm3] 2L_11376410_SNP [dm6]	T	C	4.918e^-5	0.789	INTERGENIC	regulatory region REDfly_CRMs
X	20056736	X_20056736_SNP [dm3] X_20162703_SNP [dm6]	C	G	4.944e^-5	0.789	UTR_5_PRIME Phf7	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	3443251	2R_3443251_SNP [dm3] 2R_7555746_SNP [dm6]	T	G	4.995e^-5	0.789	INTRON Corin
2L	9104303	2L_9104303_SNP [dm3] 2L_9104303_SNP [dm6]	G	A	5.069e^-5	0.789	INTERGENIC
3L	12127147	3L_12127147_SNP [dm3] 3L_12134047_SNP [dm6]	C	T	5.086e^-5	0.789	SYNONYMOUS_CODING CG5645 DOWNSTREAM CG11534
2R	787845	2R_787845_SNP [dm3] 2R_4900340_SNP [dm6]	C	T	5.107e^-5	0.789	INTRON CG44102	transposable element FlyBase
3L	6375402	3L_6375402_SNP [dm3] 3L_6382302_SNP [dm6]	C	T	5.123e^-5	0.789	INTERGENIC

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By genomic position
Variant impact
Gene name

BacterialLoad_PR phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results