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=1.994e^-2)
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

Covariate	p-value	Significance
In_2L_t	0.09852

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	7.1513	0.028

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1232 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
X	13575989	X_13575989_SNP [dm3] X_13681956_SNP [dm6]	C	T	3.885e^-6	0.996	UPSTREAM CG11158 INTERGENIC
3R	14974297	3R_14974297_SNP [dm3] 3R_19148575_SNP [dm6]	A	G	4.489e^-6	0.996	UPSTREAM Ppcs & 1 other DOWNSTREAM CG5835 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
3R	14974342	3R_14974342_SNP [dm3] 3R_19148620_SNP [dm6]	A	T	4.489e^-6	0.996	UPSTREAM Ppcs & 1 other DOWNSTREAM CG5835 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2L	7558758	2L_7558758_SNP [dm3] 2L_7558758_SNP [dm6]	C	T	4.634e^-6	0.996	INTRON RapGAP1
2L	7559398	2L_7559398_SNP [dm3] 2L_7559398_SNP [dm6]	A	T	4.791e^-6	0.996	INTRON RapGAP1
2L	7559404	2L_7559404_SNP [dm3] 2L_7559404_SNP [dm6]	T	A	4.791e^-6	0.996	INTRON RapGAP1
2L	7559419	2L_7559419_SNP [dm3] 2L_7559419_SNP [dm6]	T	A	4.791e^-6	0.996	INTRON RapGAP1
2L	13274158	2L_13274158_SNP [dm3] 2L_13274158_SNP [dm6]	G	T	5.930e^-6	0.996	INTRON CG44085
3R	25277606	3R_25277606_SNP [dm3] 3R_29451884_SNP [dm6]	T	A	5.988e^-6	0.996	INTRON Ptp99A
2L	7559183	2L_7559183_SNP [dm3] 2L_7559183_SNP [dm6]	C	A	9.874e^-6	0.996	INTRON RapGAP1
2L	16558473	2L_16558473_SNP [dm3] 2L_16558473_SNP [dm6]	G	T	1.165e^-5	0.996	SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad
3L	10396546	3L_10396546_SNP [dm3] 3L_10403446_SNP [dm6]	G	C	1.250e^-5	0.996	INTERGENIC
3R	15126021	3R_15126021_SNP [dm3] 3R_19300299_SNP [dm6]	A	T	1.507e^-5	0.996	INTERGENIC
2L	16558413	2L_16558413_SNP [dm3] 2L_16558413_SNP [dm6]	T	A	1.638e^-5	0.996	SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad
3R	25304834	3R_25304834_SNP [dm3] 3R_29479112_SNP [dm6]	A	T	1.850e^-5	0.996	UPSTREAM Ptp99A INTRON Ptp99A	TF binding site mE1_TFBS_cad
3L	14070495	3L_14070495_SNP [dm3] 3L_14077395_SNP [dm6]	G	A	1.940e^-5	0.996	INTRON btl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14070496	3L_14070496_SNP [dm3] 3L_14077396_SNP [dm6]	T	C	1.940e^-5	0.996	INTRON btl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15262087	3R_15262087_SNP [dm3] 3R_19436365_SNP [dm6]	T	C	1.975e^-5	0.996	INTRON CG31221
3R	13969673	3R_13969673_SNP [dm3] 3R_18143951_SNP [dm6]	G	C	2.144e^-5	0.996	INTERGENIC
3R	16824633	3R_16824633_SNP [dm3] 3R_20998911_SNP [dm6]	T	G	2.171e^-5	0.996	INTRON Calx
3L	21968126	3L_21968126_SNP [dm3] 3L_21975026_SNP [dm6]	T	A	2.208e^-5	0.996	INTRON CG7470
3L	21968129	3L_21968129_SNP [dm3] 3L_21975029_SNP [dm6]	T	C	2.208e^-5	0.996	INTRON CG7470
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	2.208e^-5	0.996	INTRON CG7470
3L	9309606	3L_9309606_SNP [dm3] 3L_9316506_SNP [dm6]	C	G	2.250e^-5	0.996	INTERGENIC
3L	11208027	3L_11208027_SNP [dm3] 3L_11214927_SNP [dm6]	A	G	2.397e^-5	0.996	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	18391760	X_18391760_SNP [dm3] X_18497727_SNP [dm6]	T	A	2.628e^-5	0.996	INTRON GalNAc-T2
2R	10710564	2R_10710564_SNP [dm3] 2R_14823059_SNP [dm6]	C	T	2.741e^-5	0.996	DOWNSTREAM CR45329 INTERGENIC
3L	11208193	3L_11208193_SNP [dm3] 3L_11215093_SNP [dm6]	C	G	2.874e^-5	0.996	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
2R	10715629	2R_10715629_SNP [dm3] 2R_14828124_SNP [dm6]	A	G	3.195e^-5	0.996	INTERGENIC
2L	9571456	2L_9571456_SNP [dm3] 2L_9571456_SNP [dm6]	A	T	3.233e^-5	0.996	INTRON CG3838
2R	19833852	2R_19833852_SNP [dm3] 2R_23946329_SNP [dm6]	T	G	3.264e^-5	0.996	DOWNSTREAM CG13565 INTRON Galphas
X	6679124	X_6679124_SNP [dm3] X_6785091_SNP [dm6]	A	G	3.424e^-5	0.996	INTRON C3G	TF binding site mE1_TFBS_HSA
3L	761241	3L_761241_SNP [dm3] 3L_761241_SNP [dm6]	G	A	3.468e^-5	0.996	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb mE1_TFBS_HSA
3L	9608146	3L_9608146_SNP [dm3] 3L_9615046_SNP [dm6]	T	C	3.514e^-5	0.996	UPSTREAM LanB2 INTRON LanB2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	18601161	3L_18601161_SNP [dm3] 3L_18608061_SNP [dm6]	C	A	3.661e^-5	0.996	NON_SYNONYMOUS_CODING CG18231 DOWNSTREAM CG18233 INTRON CG4174 & 1 other
3L	9675977	3L_9675977_SNP [dm3] 3L_9682877_SNP [dm6]	T	C	3.734e^-5	0.996	SYNONYMOUS_CODING alphaTub67C DOWNSTREAM CG6767	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	13413265	3R_13413265_SNP [dm3] 3R_17587543_SNP [dm6]	T	G	3.916e^-5	0.996	INTERGENIC
X	13155905	X_13155905_SNP [dm3] X_13261872_SNP [dm6]	T	A	3.930e^-5	0.996	UTR_3_PRIME comt DOWNSTREAM HDAC4
X	13155912	X_13155912_SNP [dm3] X_13261879_SNP [dm6]	C	T	3.930e^-5	0.996	UTR_3_PRIME comt DOWNSTREAM HDAC4
3R	14374772	3R_14374772_SNP [dm3] 3R_18549050_SNP [dm6]	A	G	3.973e^-5	0.996	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14973232	3R_14973232_SNP [dm3] 3R_19147510_SNP [dm6]	G	C	3.976e^-5	0.996	UTR_5_PRIME Ppcs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	13576002	X_13576002_SNP [dm3] X_13681969_SNP [dm6]	A	G	4.071e^-5	0.996	UPSTREAM CG11158 INTERGENIC
3L	2853983	3L_2853983_SNP [dm3] 3L_2853983_SNP [dm6]	T	C	4.126e^-5	0.996	INTRON CG43444
3L	16470855	3L_16470855_SNP [dm3] 3L_16477755_SNP [dm6]	A	T	4.210e^-5	0.996	INTRON CG33158 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16470867	3L_16470867_INS [dm3] 3L_16477767_INS [dm6]	A	AC	4.210e^-5	0.996	INTRON CG33158 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16470884	3L_16470884_SNP [dm3] 3L_16477784_SNP [dm6]	T	C	4.210e^-5	0.996	INTRON CG33158 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	12387047	X_12387047_SNP [dm3] X_12493014_SNP [dm6]	A	C	4.423e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
3R	15970826	3R_15970826_SNP [dm3] 3R_20145104_SNP [dm6]	C	T	4.487e^-5	0.996	INTERGENIC
3R	15970838	3R_15970838_DEL [dm3] 3R_20145116_DEL [dm6]	TCCATTT	T	4.512e^-5	0.996	INTERGENIC
2R	18036696	2R_18036696_SNP [dm3] 2R_22149191_SNP [dm6]	C	A	4.687e^-5	0.996	INTRON a
2L	10482154	2L_10482154_SNP [dm3] 2L_10482154_SNP [dm6]	G	A	4.693e^-5	0.996	SYNONYMOUS_CODING RluA-2 UTR_3_PRIME RluA-2	TF binding site mE1_TFBS_sens
2L	3659304	2L_3659304_SNP [dm3] 2L_3659304_SNP [dm6]	T	A	4.751e^-5	0.996	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	10396510	3L_10396510_SNP [dm3] 3L_10403410_SNP [dm6]	T	A	4.781e^-5	0.996	INTERGENIC
X	13575984	X_13575984_SNP [dm3] X_13681951_SNP [dm6]	T	A	4.798e^-5	0.996	INTERGENIC
2L	16558500	2L_16558500_SNP [dm3] 2L_16558500_SNP [dm6]	A	C	5.053e^-5	0.996	SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad
X	12387044	X_12387044_SNP [dm3] X_12493011_SNP [dm6]	G	T	5.133e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387064	X_12387064_SNP [dm3] X_12493031_SNP [dm6]	G	T	5.133e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387065	X_12387065_SNP [dm3] X_12493032_SNP [dm6]	C	T	5.133e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387069	X_12387069_SNP [dm3] X_12493036_SNP [dm6]	T	G	5.133e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
X	12387073	X_12387073_SNP [dm3] X_12493040_SNP [dm6]	A	T	5.133e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
3R	17543897	3R_17543897_SNP [dm3] 3R_21718175_SNP [dm6]	A	T	5.152e^-5	0.996	INTRON CG31176	TF binding site BDTNP1_TFBS_twi
3R	17543959	3R_17543959_SNP [dm3] 3R_21718237_SNP [dm6]	T	A	5.152e^-5	0.996	INTRON CG31176	TF binding site BDTNP1_TFBS_twi
3R	17543984	3R_17543984_SNP [dm3] 3R_21718262_SNP [dm6]	A	T	5.152e^-5	0.996	INTRON CG31176	TF binding site BDTNP1_TFBS_twi
X	16528000	X_16528000_SNP [dm3] X_16633967_SNP [dm6]	G	C	5.166e^-5	0.996	INTRON Rok
3R	20960323	3R_20960323_SNP [dm3] 3R_25134601_SNP [dm6]	C	T	5.188e^-5	0.996	SYNONYMOUS_CODING Bili
2L	7559420	2L_7559420_SNP [dm3] 2L_7559420_SNP [dm6]	G	A	5.328e^-5	0.996	INTRON RapGAP1
3L	8215472	3L_8215472_SNP [dm3] 3L_8222372_SNP [dm6]	T	G	5.334e^-5	0.996	INTRON CG13678
2L	3659359	2L_3659359_SNP [dm3] 2L_3659359_SNP [dm6]	A	T	5.451e^-5	0.996	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	3659371	2L_3659371_SNP [dm3] 2L_3659371_SNP [dm6]	C	A	5.451e^-5	0.996	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	19009750	3R_19009750_SNP [dm3] 3R_23184028_SNP [dm6]	A	T	5.471e^-5	0.996	SYNONYMOUS_CODING Irk1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	3272655	3L_3272655_SNP [dm3] 3L_3272655_SNP [dm6]	T	C	5.707e^-5	0.996	INTRON CG14960
3L	2869275	3L_2869275_SNP [dm3] 3L_2869275_SNP [dm6]	G	T	5.709e^-5	0.996	INTRON CG43444	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4043937	3L_4043937_SNP [dm3] 3L_4043937_SNP [dm6]	C	G	5.724e^-5	0.996	INTERGENIC
3L	768328	3L_768328_DEL [dm3] 3L_768328_DEL [dm6]	TT	T	5.896e^-5	0.996	INTERGENIC
2L	5806335	2L_5806335_SNP [dm3] 2L_5806335_SNP [dm6]	T	C	6.845e^-5	0.996	INTRON CG11034
3R	23672880	3R_23672880_INS [dm3] 3R_27847158_INS [dm6]	A	ACATAGATATA...	6.877e^-5	0.996	INTRON CG34353 & 1 other
3R	16991750	3R_16991750_DEL [dm3] 3R_21166028_DEL [dm6]	AA	A	6.908e^-5	0.996	DOWNSTREAM CG5810 INTRON SNF4Agamma & 1 other
3R	16991762	3R_16991762_SNP [dm3] 3R_21166040_SNP [dm6]	A	C	6.908e^-5	0.996	DOWNSTREAM CG5810 INTRON SNF4Agamma & 1 other
3R	26410498	3R_26410498_SNP [dm3] 3R_30584776_SNP [dm6]	T	C	6.967e^-5	0.996	SYNONYMOUS_CODING CG9717	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	13349755	X_13349755_SNP [dm3] X_13455722_SNP [dm6]	A	G	6.985e^-5	0.996	DOWNSTREAM CG34324 INTRON Neto
3R	19927809	3R_19927809_SNP [dm3] 3R_24102087_SNP [dm6]	G	T	7.302e^-5	0.996	INTRON 4EHP & 1 other
3R	17211173	3R_17211173_SNP [dm3] 3R_21385451_SNP [dm6]	A	T	7.331e^-5	0.996	INTERGENIC	regulatory region REDfly_CRMs
3R	16824689	3R_16824689_SNP [dm3] 3R_20998967_SNP [dm6]	C	G	7.415e^-5	0.996	INTRON Calx
3R	16824780	3R_16824780_SNP [dm3] 3R_20999058_SNP [dm6]	C	T	7.617e^-5	0.996	INTRON Calx
3L	14381391	3L_14381391_SNP [dm3] 3L_14388291_SNP [dm6]	A	C	7.760e^-5	0.996	INTERGENIC
2L	16558338	2L_16558338_SNP [dm3] 2L_16558338_SNP [dm6]	G	T	7.814e^-5	0.996	NON_SYNONYMOUS_CODING CG42389	TF binding site mE1_TFBS_cad
3L	16461469	3L_16461469_SNP [dm3] 3L_16468369_SNP [dm6]	T	A	7.815e^-5	0.996	INTRON CG33158
2R	1363884	2R_1363884_SNP [dm3] 2R_5476379_SNP [dm6]	C	T	7.844e^-5	0.996	INTRON CG30440	transposable element FlyBase
3L	10396532	3L_10396532_SNP [dm3] 3L_10403432_SNP [dm6]	C	A	7.986e^-5	0.996	INTERGENIC
3L	9608244	3L_9608244_SNP [dm3] 3L_9615144_SNP [dm6]	G	A	8.353e^-5	0.996	UPSTREAM LanB2 INTRON LanB2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	14460526	X_14460526_SNP [dm3] X_14566493_SNP [dm6]	A	G	8.400e^-5	0.996	INTERGENIC
X	12388723	X_12388723_SNP [dm3] X_12494690_SNP [dm6]	A	G	8.411e^-5	0.996	SYNONYMOUS_CODING Mks1
3L	12565386	3L_12565386_SNP [dm3] 3L_12572286_SNP [dm6]	T	C	8.554e^-5	0.996	INTRON sowah	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	15257241	3R_15257241_INS [dm3] 3R_19431519_INS [dm6]	T	TT	8.747e^-5	0.996	INTRON CG31221
2R	17389268	2R_17389268_SNP [dm3] 2R_21501763_SNP [dm6]	C	G	8.825e^-5	0.996	UPSTREAM MESK2 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_Ubx
X	12387048	X_12387048_SNP [dm3] X_12493015_SNP [dm6]	A	T	8.913e^-5	0.996	DOWNSTREAM Lsp1alpha INTERGENIC
2R	11900270	2R_11900270_SNP [dm3] 2R_16012765_SNP [dm6]	A	G	8.927e^-5	0.996	SYNONYMOUS_CODING CG8389	TF binding site BDTNP1_TFBS_sna
3L	10860571	3L_10860571_SNP [dm3] 3L_10867471_SNP [dm6]	T	C	9.118e^-5	0.996	INTRON tna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	14066885	3L_14066885_SNP [dm3] 3L_14073785_SNP [dm6]	G	A	9.600e^-5	0.996	SYNONYMOUS_CODING Pex1	TF binding site mE1_TFBS_sens
2R	12012596	2R_12012596_SNP [dm3] 2R_16125091_SNP [dm6]	A	T	9.680e^-5	0.996	UTR_5_PRIME spin DOWNSTREAM CG30095	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx

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Missing results

By genomic position
Variant impact
Gene name

pc_FL_PElem_GS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results