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=1.226e^-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	0.08468
In_2R_NS	0.07825

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.516	0.0634
In_2R_NS	5.6273	0.06

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2547 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	12680355	2R_12680355_SNP [dm3] 2R_16792850_SNP [dm6]	T	A	6.365e^-7	0.717	DOWNSTREAM CG15615 & 1 other INTRON CG15919
2R	12680354	2R_12680354_SNP [dm3] 2R_16792849_SNP [dm6]	C	T	1.007e^-6	0.717	DOWNSTREAM CG15615 & 1 other INTRON CG15919
3L	1909764	3L_1909764_SNP [dm3] 3L_1909764_SNP [dm6]	T	C	1.236e^-6	0.717	INTRON CG1887
2R	17685083	2R_17685083_DEL [dm3] 2R_21797578_DEL [dm6]	GTC	G	2.580e^-6	0.717	DOWNSTREAM CG34204 & 1 other INTERGENIC
2L	19129166	2L_19129166_INS [dm3] 2L_19129166_INS [dm6]	T	TGATTT	2.811e^-6	0.717	UTR_3_PRIME l_2_37Cd DOWNSTREAM Aats-asn	TF binding site mE1_TFBS_cad
2L	15175615	2L_15175615_SNP [dm3] 2L_15175615_SNP [dm6]	A	C	2.818e^-6	0.717	INTRON CG4168
X	16700589	X_16700589_SNP [dm3] X_16806556_SNP [dm6]	A	G	4.025e^-6	0.717	DOWNSTREAM CG13005 INTRON ppk28 & 1 other
2R	16304273	2R_16304273_SNP [dm3] 2R_20416768_SNP [dm6]	C	A	4.155e^-6	0.717	INTERGENIC
2R	786462	2R_786462_SNP [dm3] 2R_4898957_SNP [dm6]	A	C	4.758e^-6	0.717	INTRON CG44102	transposable element FlyBase
2R	15248610	2R_15248610_SNP [dm3] 2R_19361105_SNP [dm6]	A	C	4.906e^-6	0.717	SYNONYMOUS_CODING CG11961
2R	15248616	2R_15248616_SNP [dm3] 2R_19361111_SNP [dm6]	T	C	4.906e^-6	0.717	SYNONYMOUS_CODING CG11961
2R	16176361	2R_16176361_SNP [dm3] 2R_20288856_SNP [dm6]	T	C	5.207e^-6	0.717	UTR_3_PRIME Cpr56F UPSTREAM CkIIbeta2 DOWNSTREAM CG34199	TF binding site mE1_TFBS_chinmo
X	9733635	X_9733635_SNP [dm3] X_9839602_SNP [dm6]	T	G	5.405e^-6	0.717	INTRON CG32698
3L	1673072	3L_1673072_SNP [dm3] 3L_1673072_SNP [dm6]	G	C	5.525e^-6	0.717	UPSTREAM CG13930 INTERGENIC	TF binding site mE1_TFBS_cad
2L	19101233	2L_19101233_INS [dm3] 2L_19101233_INS [dm6]	A	AA	7.617e^-6	0.717	UPSTREAM CG17344 & 1 other INTRON Lim3
3R	11018344	3R_11018344_SNP [dm3] 3R_15192622_SNP [dm6]	T	G	8.185e^-6	0.717	SYNONYMOUS_CODING CG6752 UPSTREAM mir-3644
2L	10686264	2L_10686264_SNP [dm3] 2L_10686264_SNP [dm6]	T	C	8.422e^-6	0.717	UTR_3_PRIME CG7296 DOWNSTREAM CG7296	TF binding site mE1_TFBS_zfh1
2R	9505716	2R_9505716_SNP [dm3] 2R_13618211_SNP [dm6]	C	T	8.589e^-6	0.717	INTERGENIC
3L	9919556	3L_9919556_SNP [dm3] 3L_9926456_SNP [dm6]	T	C	8.977e^-6	0.717	INTRON CG34356
3R	19070239	3R_19070239_SNP [dm3] 3R_23244517_SNP [dm6]	A	G	9.627e^-6	0.717	INTRON CG4467
3R	20405065	3R_20405065_SNP [dm3] 3R_24579343_SNP [dm6]	G	A	1.019e^-5	0.717	INTRON CG13624	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9405390	2L_9405390_SNP [dm3] 2L_9405390_SNP [dm6]	G	A	1.039e^-5	0.717	INTRON Shawl
X	20784905	X_20784905_SNP [dm3] X_20913878_SNP [dm6]	T	C	1.050e^-5	0.717	INTRON shakB
3L	17443844	3L_17443844_SNP [dm3] 3L_17450744_SNP [dm6]	C	G	1.071e^-5	0.717	NON_SYNONYMOUS_CODING CG18265	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	988963	2L_988963_SNP [dm3] 2L_988963_SNP [dm6]	G	T	1.099e^-5	0.717	EXON CR44801	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3246304	2L_3246304_SNP [dm3] 2L_3246304_SNP [dm6]	G	A	1.248e^-5	0.717	INTERGENIC
2L	3246291	2L_3246291_SNP [dm3] 2L_3246291_SNP [dm6]	T	A	1.299e^-5	0.717	INTERGENIC
2L	3246301	2L_3246301_SNP [dm3] 2L_3246301_SNP [dm6]	G	T	1.321e^-5	0.717	INTERGENIC
2R	16177451	2R_16177451_SNP [dm3] 2R_20289946_SNP [dm6]	A	C	1.337e^-5	0.717	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
2L	11302153	2L_11302153_SNP [dm3] 2L_11302153_SNP [dm6]	T	A	1.339e^-5	0.717	INTERGENIC
2R	12670723	2R_12670723_SNP [dm3] 2R_16783218_SNP [dm6]	T	C	1.407e^-5	0.717	UPSTREAM CG5522 DOWNSTREAM resilin INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	1589711	3L_1589711_SNP [dm3] 3L_1589711_SNP [dm6]	T	C	1.513e^-5	0.717	INTRON CG13917
X	8578764	X_8578764_INS [dm3] X_8684731_INS [dm6]	T	TC	1.520e^-5	0.717	UPSTREAM CG11284 INTRON CG11284
3R	19070234	3R_19070234_SNP [dm3] 3R_23244512_SNP [dm6]	A	G	1.582e^-5	0.717	INTRON CG4467
2L	11302671	2L_11302671_SNP [dm3] 2L_11302671_SNP [dm6]	G	A	1.672e^-5	0.717	INTERGENIC
2R	9505718	2R_9505718_SNP [dm3] 2R_13618213_SNP [dm6]	G	T	1.692e^-5	0.717	INTERGENIC
X	13200743	X_13200743_SNP [dm3] X_13306710_SNP [dm6]	T	G	1.781e^-5	0.717	SYNONYMOUS_CODING IP3K2 INTRON IP3K2 EXON CR45018	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	16177429	2R_16177429_SNP [dm3] 2R_20289924_SNP [dm6]	T	C	1.806e^-5	0.717	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
X	15738163	X_15738163_SNP [dm3] X_15844130_SNP [dm6]	C	A	1.825e^-5	0.717	START_GAINED Aats-arg UTR_5_PRIME Aats-arg UPSTREAM CG8578	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Ubx
3L	15935943	3L_15935943_SNP [dm3] 3L_15942843_SNP [dm6]	G	A	1.975e^-5	0.717	INTRON Pka-C3
3R	24418101	3R_24418101_SNP [dm3] 3R_28592379_SNP [dm6]	G	A	1.983e^-5	0.717	DOWNSTREAM MRE23 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cnc
2L	8321657	2L_8321657_SNP [dm3] 2L_8321657_SNP [dm6]	A	T	2.015e^-5	0.717	UTR_3_PRIME CG7781 DOWNSTREAM CG7787
3L	8999109	3L_8999109_SNP [dm3] 3L_9006009_SNP [dm6]	A	G	2.058e^-5	0.717	SYNONYMOUS_CODING Doc3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	6810284	X_6810284_INS [dm3] X_6916251_INS [dm6]	T	TAT	2.092e^-5	0.717	INTRON CG14431
X	6810287	X_6810287_SNP [dm3] X_6916254_SNP [dm6]	A	G	2.092e^-5	0.717	INTRON CG14431
3L	15886227	3L_15886227_SNP [dm3] 3L_15893127_SNP [dm6]	G	A	2.113e^-5	0.717	INTRON pHCl
2L	12725164	2L_12725164_SNP [dm3] 2L_12725164_SNP [dm6]	T	A	2.130e^-5	0.717	INTRON MRP
2L	12725341	2L_12725341_SNP [dm3] 2L_12725341_SNP [dm6]	T	C	2.130e^-5	0.717	INTRON MRP
2L	12726295	2L_12726295_SNP [dm3] 2L_12726295_SNP [dm6]	G	C	2.130e^-5	0.717	SYNONYMOUS_CODING MRP	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	8449097	2L_8449097_SNP [dm3] 2L_8449097_SNP [dm6]	C	T	2.226e^-5	0.717	SPLICE_SITE_REGION U26 SYNONYMOUS_CODING U26 DOWNSTREAM fu12
2L	11305847	2L_11305847_SNP [dm3] 2L_11305847_SNP [dm6]	C	A	2.268e^-5	0.717	INTERGENIC	TF binding site mE1_TFBS_cad
X	9118394	X_9118394_SNP [dm3] X_9224361_SNP [dm6]	A	G	2.300e^-5	0.717	INTERGENIC
3L	8891584	3L_8891584_SNP [dm3] 3L_8898484_SNP [dm6]	C	T	2.477e^-5	0.717	INTRON TrpA1
2L	13792113	2L_13792113_SNP [dm3] 2L_13792113_SNP [dm6]	T	A	2.634e^-5	0.717	NON_SYNONYMOUS_CODING CG16863	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	19100085	2L_19100085_SNP [dm3] 2L_19100085_SNP [dm6]	G	A	2.649e^-5	0.717	INTRON Lim3
X	9803183	X_9803183_SNP [dm3] X_9909150_SNP [dm6]	A	G	2.659e^-5	0.717	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
2R	12681104	2R_12681104_SNP [dm3] 2R_16793599_SNP [dm6]	C	A	2.689e^-5	0.717	SYNONYMOUS_CODING CG15615 DOWNSTREAM CG15919
3L	2351752	3L_2351752_SNP [dm3] 3L_2351752_SNP [dm6]	A	G	2.818e^-5	0.717	INTERGENIC
3L	8891777	3L_8891777_SNP [dm3] 3L_8898677_SNP [dm6]	C	T	2.981e^-5	0.717	INTRON TrpA1
2L	12725735	2L_12725735_SNP [dm3] 2L_12725735_SNP [dm6]	C	T	3.046e^-5	0.717	SYNONYMOUS_CODING MRP
3R	13026585	3R_13026585_SNP [dm3] 3R_17200863_SNP [dm6]	T	A	3.101e^-5	0.717	INTRON Mur89F
3L	8891550	3L_8891550_SNP [dm3] 3L_8898450_SNP [dm6]	A	T	3.102e^-5	0.717	INTRON TrpA1
3L	8892095	3L_8892095_SNP [dm3] 3L_8898995_SNP [dm6]	C	G	3.102e^-5	0.717	INTRON TrpA1
3L	8892127	3L_8892127_SNP [dm3] 3L_8899027_SNP [dm6]	C	T	3.102e^-5	0.717	INTRON TrpA1
3L	15469589	3L_15469589_SNP [dm3] 3L_15476489_SNP [dm6]	C	G	3.176e^-5	0.717	INTERGENIC
2L	7715589	2L_7715589_SNP [dm3] 2L_7715589_SNP [dm6]	A	T	3.200e^-5	0.717	NON_SYNONYMOUS_CODING CG33296
2R	16177498	2R_16177498_SNP [dm3] 2R_20289993_SNP [dm6]	C	G	3.250e^-5	0.717	SYNONYMOUS_CODING CkIIbeta2 INTRON Cpr56F
2L	12151606	2L_12151606_SNP [dm3] 2L_12151606_SNP [dm6]	G	A	3.263e^-5	0.717	INTRON CG31760
2L	4790558	2L_4790558_SNP [dm3] 2L_4790558_SNP [dm6]	A	T	3.304e^-5	0.717	INTRON CG15630
2R	6975347	2R_6975347_INS [dm3] 2R_11087842_INS [dm6]	T	TCGTCTAGGTT...	3.365e^-5	0.717	UPSTREAM CG43189 INTRON luna & 1 other	TF binding site mE1_TFBS_Kr
3L	5474372	3L_5474372_SNP [dm3] 3L_5481272_SNP [dm6]	G	C	3.384e^-5	0.717	SYNONYMOUS_CODING CG4835
3L	5374564	3L_5374564_SNP [dm3] 3L_5381464_SNP [dm6]	C	G	3.416e^-5	0.717	INTRON Ir64a
X	7903827	X_7903827_INS [dm3] X_8009794_INS [dm6]	A	AAAACCA	3.540e^-5	0.717	INTRON Tbh
3L	16532066	3L_16532066_DEL [dm3] 3L_16538966_DEL [dm6]	CA	C	3.615e^-5	0.717	INTRON CG43373
3L	1847857	3L_1847857_SNP [dm3] 3L_1847857_SNP [dm6]	G	A	3.653e^-5	0.717	INTERGENIC
X	12088603	X_12088603_SNP [dm3] X_12194570_SNP [dm6]	G	A	3.667e^-5	0.717	INTRON Ten-a
3L	12565167	3L_12565167_SNP [dm3] 3L_12572067_SNP [dm6]	C	A	3.681e^-5	0.717	SYNONYMOUS_CODING sowah	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	12883585	3L_12883585_SNP [dm3] 3L_12890485_SNP [dm6]	T	A	3.692e^-5	0.717	UPSTREAM CR45748 INTRON CG43894
2R	13669741	2R_13669741_SNP [dm3] 2R_17782236_SNP [dm6]	T	A	3.741e^-5	0.717	UPSTREAM fab1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3L	11539460	3L_11539460_SNP [dm3] 3L_11546360_SNP [dm6]	C	T	3.819e^-5	0.717	INTRON Mob2
3R	17358439	3R_17358439_SNP [dm3] 3R_21532717_SNP [dm6]	T	C	3.887e^-5	0.717	EXON CR43372
X	19954196	X_19954196_SNP [dm3] X_20060163_SNP [dm6]	A	G	3.892e^-5	0.717	INTRON Dop2R
2L	10723776	2L_10723776_SNP [dm3] 2L_10723776_SNP [dm6]	A	T	3.975e^-5	0.717	UPSTREAM CG6431 INTERGENIC
X	9803438	X_9803438_SNP [dm3] X_9909405_SNP [dm6]	G	A	4.001e^-5	0.717	UTR_3_PRIME CG1986
2L	11301493	2L_11301493_SNP [dm3] 2L_11301493_SNP [dm6]	T	A	4.213e^-5	0.717	INTERGENIC
2R	6942081	2R_6942081_SNP [dm3] 2R_11054576_SNP [dm6]	A	C	4.243e^-5	0.717	INTRON luna
3L	10032780	3L_10032780_SNP [dm3] 3L_10039680_SNP [dm6]	C	A	4.250e^-5	0.717	INTRON dpr6	TF binding site BDTNP1_TFBS_dl
3R	24257966	3R_24257966_SNP [dm3] 3R_28432244_SNP [dm6]	G	A	4.253e^-5	0.717	INTRON beat-VI
3L	19285729	3L_19285729_SNP [dm3] 3L_19292629_SNP [dm6]	G	A	4.283e^-5	0.717	UTR_5_PRIME Gbs-76A UPSTREAM Gbs-76A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
2R	17669278	2R_17669278_SNP [dm3] 2R_21781773_SNP [dm6]	T	C	4.314e^-5	0.717	INTERGENIC
2L	11306890	2L_11306890_SNP [dm3] 2L_11306890_SNP [dm6]	A	G	4.514e^-5	0.717	UPSTREAM CR43721 INTERGENIC	TF binding site mE1_TFBS_cad
3L	12127147	3L_12127147_SNP [dm3] 3L_12134047_SNP [dm6]	C	T	4.529e^-5	0.717	SYNONYMOUS_CODING CG5645 DOWNSTREAM CG11534
3L	1715681	3L_1715681_MNP [dm3] 3L_1715681_MNP [dm6]	GTTA	TAAC	4.547e^-5	0.717	UTR_3_PRIME drpr DOWNSTREAM drpr & 1 other
3L	1715686	3L_1715686_INS [dm3] 3L_1715686_INS [dm6]	A	AT	4.547e^-5	0.717	UTR_3_PRIME drpr DOWNSTREAM drpr & 1 other
2L	16395828	2L_16395828_SNP [dm3] 2L_16395828_SNP [dm6]	G	A	4.556e^-5	0.717	INTERGENIC
3L	12883596	3L_12883596_SNP [dm3] 3L_12890496_SNP [dm6]	C	T	4.582e^-5	0.717	UPSTREAM CR45748 INTRON CG43894
3L	12883597	3L_12883597_SNP [dm3] 3L_12890497_SNP [dm6]	G	A	4.582e^-5	0.717	UPSTREAM CR45748 INTRON CG43894
2R	6942078	2R_6942078_SNP [dm3] 2R_11054573_SNP [dm6]	G	C	4.615e^-5	0.717	INTRON luna
3L	12391055	3L_12391055_SNP [dm3] 3L_12397955_SNP [dm6]	A	T	4.620e^-5	0.717	DOWNSTREAM Obp69a INTRON CG32104	TF binding site mE1_TFBS_HSA
2R	9505695	2R_9505695_SNP [dm3] 2R_13618190_SNP [dm6]	A	T	4.670e^-5	0.717	INTERGENIC

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By genomic position
Variant impact
Gene name

BacterialLoad_PR_ADJ phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results