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=3.681e^-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_3R_K	0.01168

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.6702	0.0968

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

295 significant hits at p-value < 0.001.

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
2L	14894979	2L_14894979_SNP [dm3] 2L_14894979_SNP [dm6]	A	C	7.553e^-9	2.466e^-4	INTERGENIC
2L	19799133	2L_19799133_SNP [dm3] 2L_19799133_SNP [dm6]	A	T	7.553e^-9	2.466e^-4	INTRON sick
2L	19799137	2L_19799137_SNP [dm3] 2L_19799137_SNP [dm6]	G	A	7.553e^-9	2.466e^-4	INTRON sick
2L	21914402	2L_21914402_SNP [dm3] 2L_21914402_SNP [dm6]	A	T	7.553e^-9	2.466e^-4	UTR_3_PRIME CG31600
2L	3720614	2L_3720614_SNP [dm3] 2L_3720614_SNP [dm6]	G	A	7.553e^-9	2.466e^-4	UPSTREAM Shaw INTRON Shaw
2L	8589492	2L_8589492_SNP [dm3] 2L_8589492_SNP [dm6]	T	C	7.553e^-9	2.466e^-4	DOWNSTREAM CR43855 INTRON Sema-1a	TF binding site mE1_TFBS_kn
2L	9052119	2L_9052119_SNP [dm3] 2L_9052119_SNP [dm6]	T	G	7.553e^-9	2.466e^-4	UTR_3_PRIME CG31708
2R	12854179	2R_12854179_SNP [dm3] 2R_16966674_SNP [dm6]	A	T	7.553e^-9	2.466e^-4	INTERGENIC
2R	15263539	2R_15263539_SNP [dm3] 2R_19376034_SNP [dm6]	C	A	7.553e^-9	2.466e^-4	UPSTREAM CG10062 INTRON CG10062
2R	20973870	2R_20973870_SNP [dm3] 2R_25086347_SNP [dm6]	G	T	7.553e^-9	2.466e^-4	UTR_3_PRIME lov DOWNSTREAM lov	TF binding site mE1_TFBS_bab1
2R	6442487	2R_6442487_SNP [dm3] 2R_10554982_SNP [dm6]	A	G	7.553e^-9	2.466e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_Trl
2R	8409806	2R_8409806_INS [dm3] 2R_12522301_INS [dm6]	G	GAATACA	7.553e^-9	2.466e^-4	DOWNSTREAM CG8569 INTRON CG33632
3L	16163764	3L_16163764_SNP [dm3] 3L_16170664_SNP [dm6]	A	C	7.553e^-9	2.466e^-4	UPSTREAM CG33796 DOWNSTREAM CG33795 INTERGENIC
3L	16935319	3L_16935319_INS [dm3] 3L_16942219_INS [dm6]	T	TT	7.553e^-9	2.466e^-4	INTRON Cpr73D
3R	11522883	3R_11522883_SNP [dm3] 3R_15697161_SNP [dm6]	A	C	7.553e^-9	2.466e^-4	UPSTREAM CR45635 DOWNSTREAM CG5399 INTERGENIC
X	12262426	X_12262426_SNP [dm3] X_12368393_SNP [dm6]	T	A	7.553e^-9	2.466e^-4	INTERGENIC
X	12331877	X_12331877_SNP [dm3] X_12437844_SNP [dm6]	C	T	7.553e^-9	2.466e^-4	INTRON Pkcdelta
X	14810618	X_14810618_SNP [dm3] X_14916585_SNP [dm6]	T	A	7.553e^-9	2.466e^-4	DOWNSTREAM Eo INTRON Flo2
X	17116780	X_17116780_SNP [dm3] X_17222747_SNP [dm6]	G	T	7.553e^-9	2.466e^-4	DOWNSTREAM CG34327 & 1 other INTERGENIC
X	17116787	X_17116787_SNP [dm3] X_17222754_SNP [dm6]	T	A	7.553e^-9	2.466e^-4	DOWNSTREAM CG34327 & 1 other INTERGENIC
X	18941054	X_18941054_SNP [dm3] X_19047021_SNP [dm6]	T	C	7.553e^-9	2.466e^-4	INTERGENIC
X	18941059	X_18941059_SNP [dm3] X_19047026_SNP [dm6]	C	T	7.553e^-9	2.466e^-4	INTERGENIC
X	3424027	X_3424027_SNP [dm3] X_3529994_SNP [dm6]	T	C	7.553e^-9	2.466e^-4	INTRON CG32791
X	3424034	X_3424034_SNP [dm3] X_3530001_SNP [dm6]	G	A	7.553e^-9	2.466e^-4	INTRON CG32791
X	3424041	X_3424041_SNP [dm3] X_3530008_SNP [dm6]	T	C	7.553e^-9	2.466e^-4	INTRON CG32791
2L	16497873	2L_16497873_SNP [dm3] 2L_16497873_SNP [dm6]	C	T	1.068e^-8	2.466e^-4	INTRON Tpr2
2L	1700871	2L_1700871_SNP [dm3] 2L_1700871_SNP [dm6]	C	A	1.068e^-8	2.466e^-4	UTR_3_PRIME chinmo
2L	3769159	2L_3769159_INS [dm3] 2L_3769159_INS [dm6]	A	ATGACAT	1.068e^-8	2.466e^-4	UTR_3_PRIME CG43707 DOWNSTREAM CR43704	TF binding site mE1_TFBS_HSA
2R	17592981	2R_17592981_SNP [dm3] 2R_21705476_SNP [dm6]	C	A	1.068e^-8	2.466e^-4	UPSTREAM HmgZ INTRON HmgZ & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	17592985	2R_17592985_SNP [dm3] 2R_21705480_SNP [dm6]	A	T	1.068e^-8	2.466e^-4	UPSTREAM HmgZ INTRON HmgZ & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
3L	14043159	3L_14043159_SNP [dm3] 3L_14050059_SNP [dm6]	C	T	1.068e^-8	2.466e^-4	UPSTREAM blue INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	15836309	3L_15836309_SNP [dm3] 3L_15843209_SNP [dm6]	C	A	1.068e^-8	2.466e^-4	DOWNSTREAM mir-263b INTRON CG32150	TF binding site mE1_TFBS_HSA
3L	15836322	3L_15836322_SNP [dm3] 3L_15843222_SNP [dm6]	T	G	1.068e^-8	2.466e^-4	DOWNSTREAM mir-263b INTRON CG32150	TF binding site mE1_TFBS_HSA
3L	18237416	3L_18237416_SNP [dm3] 3L_18244316_SNP [dm6]	C	A	1.068e^-8	2.466e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18237417	3L_18237417_INS [dm3] 3L_18244317_INS [dm6]	A	ATATATA	1.068e^-8	2.466e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18806425	3L_18806425_SNP [dm3] 3L_18813325_SNP [dm6]	A	T	1.068e^-8	2.466e^-4	INTRON CG14073
3L	18806435	3L_18806435_SNP [dm3] 3L_18813335_SNP [dm6]	G	T	1.068e^-8	2.466e^-4	INTRON CG14073
3L	2685097	3L_2685097_SNP [dm3] 3L_2685097_SNP [dm6]	A	G	1.068e^-8	2.466e^-4	INTRON Fife
3L	8813418	3L_8813418_SNP [dm3] 3L_8820318_SNP [dm6]	A	G	1.068e^-8	2.466e^-4	INTERGENIC
X	14722329	X_14722329_SNP [dm3] X_14828296_SNP [dm6]	C	T	1.068e^-8	2.466e^-4	INTRON CG14408	TF binding site BDTNP1_TFBS_dl
X	14722341	X_14722341_DEL [dm3] X_14828308_DEL [dm6]	TATGATCCAT	T	1.068e^-8	2.466e^-4	INTRON CG14408	TF binding site BDTNP1_TFBS_dl
X	19656721	X_19656721_SNP [dm3] X_19762688_SNP [dm6]	G	A	1.068e^-8	2.466e^-4	UTR_5_PRIME CG12702 UPSTREAM CG12702	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	20024572	X_20024572_SNP [dm3] X_20130539_SNP [dm6]	C	G	1.068e^-8	2.466e^-4	DOWNSTREAM CG42582 INTERGENIC
X	9036199	X_9036199_SNP [dm3] X_9142166_SNP [dm6]	G	T	1.068e^-8	2.466e^-4	UPSTREAM CG7065 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	13437669	2L_13437669_SNP [dm3] 2L_13437669_SNP [dm6]	G	A	1.308e^-8	2.466e^-4	DOWNSTREAM CR45683 INTRON CG42784 & 1 other
2L	13437672	2L_13437672_SNP [dm3] 2L_13437672_SNP [dm6]	T	A	1.308e^-8	2.466e^-4	DOWNSTREAM CR45683 INTRON CG42784 & 1 other
2L	13437673	2L_13437673_SNP [dm3] 2L_13437673_SNP [dm6]	C	T	1.308e^-8	2.466e^-4	DOWNSTREAM CR45683 INTRON CG42784 & 1 other
2L	13437684	2L_13437684_SNP [dm3] 2L_13437684_SNP [dm6]	A	G	1.308e^-8	2.466e^-4	DOWNSTREAM CR45683 INTRON CG42784 & 1 other
2L	14689887	2L_14689887_SNP [dm3] 2L_14689887_SNP [dm6]	A	C	1.308e^-8	2.466e^-4	UPSTREAM osp INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	14689901	2L_14689901_SNP [dm3] 2L_14689901_SNP [dm6]	T	A	1.308e^-8	2.466e^-4	UPSTREAM osp INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	5844077	2L_5844077_SNP [dm3] 2L_5844077_SNP [dm6]	T	C	1.308e^-8	2.466e^-4	INTRON TrissinR
2L	5844078	2L_5844078_SNP [dm3] 2L_5844078_SNP [dm6]	G	T	1.308e^-8	2.466e^-4	INTRON TrissinR
2L	6940259	2L_6940259_SNP [dm3] 2L_6940259_SNP [dm6]	T	C	1.308e^-8	2.466e^-4	INTRON CG18304	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_Trl
2R	11167941	2R_11167941_SNP [dm3] 2R_15280436_SNP [dm6]	G	A	1.308e^-8	2.466e^-4	INTRON Trpm
2R	5756777	2R_5756777_DEL [dm3] 2R_9869272_DEL [dm6]	TAA	T	1.308e^-8	2.466e^-4	DOWNSTREAM CR45138 INTRON cbx	transposable element FlyBase
3L	12623211	3L_12623211_SNP [dm3] 3L_12630111_SNP [dm6]	A	T	1.308e^-8	2.466e^-4	INTRON CR32111
3L	21945366	3L_21945366_SNP [dm3] 3L_21952266_SNP [dm6]	A	T	1.308e^-8	2.466e^-4	DOWNSTREAM CG7448 INTERGENIC
2R	21127947	2R_21127947_SNP [dm3] 2R_25240424_SNP [dm6]	C	T	1.488e^-8	2.466e^-4	INTRON CG9380
2R	9509784	2R_9509784_SNP [dm3] 2R_13622279_SNP [dm6]	A	G	1.488e^-8	2.466e^-4	UPSTREAM fas INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3L	2124809	3L_2124809_DEL [dm3] 3L_2124809_DEL [dm6]	AGTAAA	A	1.488e^-8	2.466e^-4	INTRON zormin
3R	13638795	3R_13638795_SNP [dm3] 3R_17813073_SNP [dm6]	T	C	1.488e^-8	2.466e^-4	INTRON tinc	TF binding site BDTNP1_TFBS_dl
X	13575010	X_13575010_SNP [dm3] X_13680977_SNP [dm6]	A	T	1.488e^-8	2.466e^-4	UPSTREAM CG12177 INTERGENIC
X	4244196	X_4244196_SNP [dm3] X_4350163_SNP [dm6]	A	T	1.488e^-8	2.466e^-4	INTRON norpA
2L	14169341	2L_14169341_SNP [dm3] 2L_14169341_SNP [dm6]	G	T	1.511e^-8	2.466e^-4	INTRON CG43333
2R	6382882	2R_6382882_SNP [dm3] 2R_10495377_SNP [dm6]	T	G	1.511e^-8	2.466e^-4	DOWNSTREAM lola INTRON lola
2R	7594514	2R_7594514_SNP [dm3] 2R_11707009_SNP [dm6]	A	T	1.511e^-8	2.466e^-4	UPSTREAM CR45377 INTERGENIC
2L	12055372	2L_12055372_SNP [dm3] 2L_12055372_SNP [dm6]	G	A	1.634e^-8	2.466e^-4	UPSTREAM RpL7-like & 1 other INTRON JhI-21	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Trl
2L	12670113	2L_12670113_SNP [dm3] 2L_12670113_SNP [dm6]	G	T	1.634e^-8	2.466e^-4	UPSTREAM CG15485 INTRON pdm2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14759284	2L_14759284_SNP [dm3] 2L_14759284_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	INTERGENIC
2L	16234725	2L_16234725_SNP [dm3] 2L_16234725_SNP [dm6]	G	C	1.634e^-8	2.466e^-4	INTRON CG42817	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	16234729	2L_16234729_SNP [dm3] 2L_16234729_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	INTRON CG42817	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	4157343	2L_4157343_SNP [dm3] 2L_4157343_SNP [dm6]	C	A	1.634e^-8	2.466e^-4	INTERGENIC
2L	8693963	2L_8693963_SNP [dm3] 2L_8693963_SNP [dm6]	A	T	1.634e^-8	2.466e^-4	INTRON Hnf4
2L	9121515	2L_9121515_SNP [dm3] 2L_9121515_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	DOWNSTREAM CR44616 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	10401226	2R_10401226_SNP [dm3] 2R_14513721_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	UPSTREAM CG30197 INTRON Cpr51A
2R	1664570	2R_1664570_SNP [dm3] 2R_5777065_SNP [dm6]	T	C	1.634e^-8	2.466e^-4	INTRON ZnT41F
2R	6076534	2R_6076534_INS [dm3] 2R_10189029_INS [dm6]	A	AAAA	1.634e^-8	2.466e^-4	INTRON KCNQ
3L	18372048	3L_18372048_SNP [dm3] 3L_18378948_SNP [dm6]	A	T	1.634e^-8	2.466e^-4	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	2947025	3L_2947025_SNP [dm3] 3L_2947025_SNP [dm6]	C	A	1.634e^-8	2.466e^-4	DOWNSTREAM Shab INTRON Shab
3R	14182115	3R_14182115_SNP [dm3] 3R_18356393_SNP [dm6]	A	T	1.634e^-8	2.466e^-4	INTRON CG15803	TF binding site mE1_TFBS_chinmo
3R	14182118	3R_14182118_DEL [dm3] 3R_18356396_DEL [dm6]	ATGTAGATATT...	A	1.634e^-8	2.466e^-4	INTRON CG15803	TF binding site mE1_TFBS_chinmo
3R	14182134	3R_14182134_DEL [dm3] 3R_18356412_DEL [dm6]	TTAAAATT	T	1.634e^-8	2.466e^-4	INTRON CG15803	TF binding site mE1_TFBS_chinmo
3R	14376709	3R_14376709_SNP [dm3] 3R_18550987_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	INTERGENIC
3R	17525623	3R_17525623_SNP [dm3] 3R_21699901_SNP [dm6]	G	A	1.634e^-8	2.466e^-4	INTRON CG31176
3R	17525633	3R_17525633_SNP [dm3] 3R_21699911_SNP [dm6]	C	T	1.634e^-8	2.466e^-4	INTRON CG31176
3R	19627351	3R_19627351_SNP [dm3] 3R_23801629_SNP [dm6]	G	C	1.634e^-8	2.466e^-4	UTR_3_PRIME mbc DOWNSTREAM CG33111
3R	20919936	3R_20919936_SNP [dm3] 3R_25094214_SNP [dm6]	T	C	1.634e^-8	2.466e^-4	UPSTREAM fd96Cb INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	24645762	3R_24645762_SNP [dm3] 3R_28820040_SNP [dm6]	T	G	1.634e^-8	2.466e^-4	UPSTREAM CG1647 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25750734	3R_25750734_SNP [dm3] 3R_29925012_SNP [dm6]	T	A	1.634e^-8	2.466e^-4	UPSTREAM Jon99Cii DOWNSTREAM Jon99Ci INTERGENIC
3R	7081277	3R_7081277_SNP [dm3] 3R_11255555_SNP [dm6]	A	C	1.634e^-8	2.466e^-4	EXON CR43283
X	10377910	X_10377910_DEL [dm3] X_10483877_DEL [dm6]	CT	A	1.634e^-8	2.466e^-4	INTRON CG32687
X	11801173	X_11801173_MNP [dm3] X_11907140_MNP [dm6]	GGT	AAG	1.634e^-8	2.466e^-4	UPSTREAM CG43156 DOWNSTREAM pot INTERGENIC
X	11801177	X_11801177_SNP [dm3] X_11907144_SNP [dm6]	A	G	1.634e^-8	2.466e^-4	UPSTREAM CG43156 DOWNSTREAM pot INTERGENIC
X	11801179	X_11801179_SNP [dm3] X_11907146_SNP [dm6]	G	A	1.634e^-8	2.466e^-4	UPSTREAM CG43156 DOWNSTREAM pot INTERGENIC
X	14872612	X_14872612_SNP [dm3] X_14978579_SNP [dm6]	G	T	1.634e^-8	2.466e^-4	INTRON eag
X	14872616	X_14872616_SNP [dm3] X_14978583_SNP [dm6]	G	A	1.634e^-8	2.466e^-4	INTRON eag
X	15555266	X_15555266_INS [dm3] X_15661233_INS [dm6]	A	ATAA	1.634e^-8	2.466e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	15794593	X_15794593_SNP [dm3] X_15900560_SNP [dm6]	C	G	1.634e^-8	2.466e^-4	INTRON shi
2L	17425565	2L_17425565_SNP [dm3] 2L_17425565_SNP [dm6]	C	T	1.689e^-8	2.466e^-4	INTRON Dif
2R	15014311	2R_15014311_SNP [dm3] 2R_19126806_SNP [dm6]	A	G	1.689e^-8	2.466e^-4	UPSTREAM CG15117 INTRON CG15117

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By genomic position
Variant impact
Gene name

cg42404P phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results