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=5.993e^-12)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

17021 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
2L	14624481	2L_14624481_SNP [dm3] 2L_14624481_SNP [dm6]	C	A	1.520e^-229	1.870e^-224	INTRON osp
2L	5501535	2L_5501535_SNP [dm3] 2L_5501535_SNP [dm6]	C	T	1.520e^-229	1.870e^-224	INTERGENIC	TF binding site mE1_TFBS_cad
3L	15320369	3L_15320369_SNP [dm3] 3L_15327269_SNP [dm6]	G	A	1.520e^-229	1.870e^-224	INTERGENIC
3L	6799080	3L_6799080_SNP [dm3] 3L_6805980_SNP [dm6]	C	T	1.520e^-229	1.870e^-224	INTERGENIC	regulatory region REDfly_CRMs
3L	7617312	3L_7617312_SNP [dm3] 3L_7624212_SNP [dm6]	A	G	1.520e^-229	1.870e^-224	INTRON CG33275
3L	9704881	3L_9704881_SNP [dm3] 3L_9711781_SNP [dm6]	G	A	1.520e^-229	1.870e^-224	SYNONYMOUS_CODING SH3PX1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	10284789	3R_10284789_SNP [dm3] 3R_14459067_SNP [dm6]	T	C	1.520e^-229	1.870e^-224	INTRON cv-c
3R	10306475	3R_10306475_SNP [dm3] 3R_14480753_SNP [dm6]	G	T	1.520e^-229	1.870e^-224	UTR_5_PRIME cv-c	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	14120070	3R_14120070_SNP [dm3] 3R_18294348_SNP [dm6]	G	A	1.520e^-229	1.870e^-224	INTRON l_3_05822
3R	4948144	3R_4948144_SNP [dm3] 3R_9122422_SNP [dm6]	T	A	1.520e^-229	1.870e^-224	INTRON pum
3R	8023893	3R_8023893_SNP [dm3] 3R_12198171_SNP [dm6]	T	A	1.520e^-229	1.870e^-224	NON_SYNONYMOUS_CODING CG3809
3R	9260976	3R_9260976_DEL [dm3] 3R_13435254_DEL [dm6]	TT	T	1.520e^-229	1.870e^-224	UPSTREAM yrt INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_jumu
3R	9295369	3R_9295369_SNP [dm3] 3R_13469647_SNP [dm6]	G	A	1.520e^-229	1.870e^-224	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	17183395	X_17183395_SNP [dm3] X_17289362_SNP [dm6]	A	T	1.520e^-229	1.870e^-224	INTRON CG5445 & 1 other
X	17390493	X_17390493_SNP [dm3] X_17496460_SNP [dm6]	C	G	1.520e^-229	1.870e^-224	UPSTREAM CR44692 INTRON CG43658	TF binding site mE1_TFBS_Kr
2L	3012467	2L_3012467_SNP [dm3] 2L_3012467_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	INTRON CG17265	TF binding site mE1_TFBS_inv
2L	6990941	2L_6990941_SNP [dm3] 2L_6990941_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	INTRON uif
2L	7603981	2L_7603981_DEL [dm3] 2L_7603981_DEL [dm6]	TA	C	1.031e^-226	5.141e^-222	UPSTREAM CR45370 INTERGENIC
3L	10523616	3L_10523616_SNP [dm3] 3L_10530516_SNP [dm6]	C	A	1.031e^-226	5.141e^-222	INTRON A2bp1
3L	17998418	3L_17998418_SNP [dm3] 3L_18005318_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	INTRON Eip75B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Trl
3L	4533670	3L_4533670_SNP [dm3] 3L_4533670_SNP [dm6]	G	A	1.031e^-226	5.141e^-222	INTRON CG11353
3L	5914024	3L_5914024_SNP [dm3] 3L_5920924_SNP [dm6]	C	A	1.031e^-226	5.141e^-222	INTRON CG10483
3L	6969243	3L_6969243_SNP [dm3] 3L_6976143_SNP [dm6]	C	A	1.031e^-226	5.141e^-222	UPSTREAM CR32385 INTRON Galphai	TF binding site BDTNP1_TFBS_dl
3L	9705181	3L_9705181_SNP [dm3] 3L_9712081_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	SYNONYMOUS_CODING SH3PX1	TF binding site mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
3R	15387030	3R_15387030_SNP [dm3] 3R_19561308_SNP [dm6]	G	C	1.031e^-226	5.141e^-222	INTRON Dys
3R	15387057	3R_15387057_SNP [dm3] 3R_19561335_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	INTRON Dys
3R	7887333	3R_7887333_SNP [dm3] 3R_12061611_SNP [dm6]	A	G	1.031e^-226	5.141e^-222	SPLICE_SITE_REGION CG14740 INTRON CG14740
3R	9251019	3R_9251019_SNP [dm3] 3R_13425297_SNP [dm6]	G	T	1.031e^-226	5.141e^-222	UPSTREAM Act87E DOWNSTREAM CR45591 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9259592	3R_9259592_SNP [dm3] 3R_13433870_SNP [dm6]	C	T	1.031e^-226	5.141e^-222	INTRON yrt	TF binding site BDTNP1_TFBS_dl
3R	9285003	3R_9285003_SNP [dm3] 3R_13459281_SNP [dm6]	T	G	1.031e^-226	5.141e^-222	INTRON CR17025 & 1 other
3R	9297101	3R_9297101_SNP [dm3] 3R_13471379_SNP [dm6]	T	A	1.031e^-226	5.141e^-222	INTERGENIC
X	16081350	X_16081350_SNP [dm3] X_16187317_SNP [dm6]	A	G	1.031e^-226	5.141e^-222	INTERGENIC
X	16423220	X_16423220_SNP [dm3] X_16529187_SNP [dm6]	A	C	1.031e^-226	5.141e^-222	INTRON para
X	17135251	X_17135251_SNP [dm3] X_17241218_SNP [dm6]	G	A	1.031e^-226	5.141e^-222	UTR_3_PRIME CG8915 DOWNSTREAM CG8915 INTRON f
X	18117476	X_18117476_SNP [dm3] X_18223443_SNP [dm6]	G	A	1.031e^-226	5.141e^-222	INTRON CG33639
X	7359185	X_7359185_SNP [dm3] X_7465152_SNP [dm6]	G	A	1.031e^-226	5.141e^-222	INTERGENIC
X	8735695	X_8735695_SNP [dm3] X_8841662_SNP [dm6]	A	T	1.031e^-226	5.141e^-222	INTRON CG12075
2R	14978508	2R_14978508_SNP [dm3] 2R_19091003_SNP [dm6]	C	A	9.499e^-224	3.925e^-219	NON_SYNONYMOUS_CODING 5-HT1A
3R	14059688	3R_14059688_SNP [dm3] 3R_18233966_SNP [dm6]	G	A	9.499e^-224	3.925e^-219	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_sens
3R	23085806	3R_23085806_SNP [dm3] 3R_27260084_SNP [dm6]	G	C	9.499e^-224	3.925e^-219	SPLICE_SITE_REGION woc UPSTREAM woc INTRON woc EXON CR44049	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	8721821	3R_8721821_SNP [dm3] 3R_12896099_SNP [dm6]	G	C	9.499e^-224	3.925e^-219	INTERGENIC
X	10106652	X_10106652_SNP [dm3] X_10212619_SNP [dm6]	C	A	9.499e^-224	3.925e^-219	UPSTREAM l_1_G0230 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Ubx
3R	16843319	3R_16843319_SNP [dm3] 3R_21017597_SNP [dm6]	C	A	9.629e^-224	3.925e^-219	UPSTREAM Rlip DOWNSTREAM CG5697 INTERGENIC	TF binding site mE1_TFBS_cad transposable element FlyBase
3L	6969060	3L_6969060_SNP [dm3] 3L_6975960_SNP [dm6]	A	T	9.632e^-224	3.925e^-219	UPSTREAM CR32385 INTRON Galphai	TF binding site BDTNP1_TFBS_dl
3L	5682891	3L_5682891_SNP [dm3] 3L_5689791_SNP [dm6]	C	T	9.786e^-224	3.925e^-219	INTRON sif
3R	26691331	3R_26691331_SNP [dm3] 3R_30865609_SNP [dm6]	A	G	9.786e^-224	3.925e^-219	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3R	10289962	3R_10289962_SNP [dm3] 3R_14464240_SNP [dm6]	T	G	1.064e^-223	4.006e^-219	INTRON cv-c
3R	3771429	3R_3771429_SNP [dm3] 3R_7945707_SNP [dm6]	C	T	1.064e^-223	4.006e^-219	INTRON dsx
X	17390487	X_17390487_SNP [dm3] X_17496454_SNP [dm6]	T	C	1.064e^-223	4.006e^-219	UPSTREAM CR44692 INTRON CG43658	TF binding site mE1_TFBS_Kr
3L	24124183	3L_24124183_SNP [dm3] 3L_24131083_SNP [dm6]	T	G	3.968e^-222	1.331e^-217	INTRON Snap25
3L	9138509	3L_9138509_DEL [dm3] 3L_9145409_DEL [dm6]	TAT	T	3.968e^-222	1.331e^-217	UTR_3_PRIME nwk DOWNSTREAM mir-4940 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
3R	14094838	3R_14094838_SNP [dm3] 3R_18269116_SNP [dm6]	A	T	3.968e^-222	1.331e^-217	INTRON CG18599	TF binding site mE1_TFBS_inv
X	12366491	X_12366491_INS [dm3] X_12472458_INS [dm6]	T	TAGATC	3.968e^-222	1.331e^-217	INTRON CG42258	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	12369054	X_12369054_SNP [dm3] X_12475021_SNP [dm6]	G	C	3.968e^-222	1.331e^-217	UPSTREAM CG42258 INTRON CG42258
X	18591176	X_18591176_SNP [dm3] X_18697143_SNP [dm6]	G	T	3.968e^-222	1.331e^-217	INTERGENIC
3R	9339324	3R_9339324_DEL [dm3] 3R_13513602_DEL [dm6]	AACACTACACAATACAGGA...	A	5.184e^-221	1.514e^-216	INTERGENIC
2L	4314167	2L_4314167_SNP [dm3] 2L_4314167_SNP [dm6]	A	G	5.233e^-221	1.514e^-216	INTRON tutl
2L	4314192	2L_4314192_DEL [dm3] 2L_4314192_DEL [dm6]	AA	A	5.233e^-221	1.514e^-216	INTRON tutl
3L	1040899	3L_1040899_SNP [dm3] 3L_1040899_SNP [dm6]	C	T	5.279e^-221	1.514e^-216	INTRON bab1
3R	10354959	3R_10354959_SNP [dm3] 3R_14529237_SNP [dm6]	T	A	5.279e^-221	1.514e^-216	SYNONYMOUS_CODING Pde6	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	9306119	3R_9306119_SNP [dm3] 3R_13480397_SNP [dm6]	C	T	5.279e^-221	1.514e^-216	INTERGENIC
3L	1678548	3L_1678548_DEL [dm3] 3L_1678548_DEL [dm6]	TTG	T	5.312e^-221	1.514e^-216	INTRON CG7991	TF binding site mE1_TFBS_chinmo
2L	12187929	2L_12187929_SNP [dm3] 2L_12187929_SNP [dm6]	C	T	5.581e^-221	1.514e^-216	INTRON aret
2L	7418680	2L_7418680_SNP [dm3] 2L_7418680_SNP [dm6]	T	G	5.581e^-221	1.514e^-216	DOWNSTREAM chm INTRON chm	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2L	9227429	2L_9227429_SNP [dm3] 2L_9227429_SNP [dm6]	T	C	5.581e^-221	1.514e^-216	INTRON tai
2R	12026562	2R_12026562_SNP [dm3] 2R_16139057_SNP [dm6]	C	T	5.581e^-221	1.514e^-216	DOWNSTREAM spin INTRON Got1	TF binding site BDTNP1_TFBS_dl
3L	10524828	3L_10524828_SNP [dm3] 3L_10531728_SNP [dm6]	A	G	5.581e^-221	1.514e^-216	INTRON A2bp1	TF binding site BDTNP1_TFBS_dl
3L	4755038	3L_4755038_SNP [dm3] 3L_4755038_SNP [dm6]	C	T	5.581e^-221	1.514e^-216	UPSTREAM CR43881 INTRON RhoGEF64C
3R	14264044	3R_14264044_SNP [dm3] 3R_18438322_SNP [dm6]	T	C	4.846e^-220	1.230e^-215	INTRON fru
3R	16112783	3R_16112783_SNP [dm3] 3R_20287061_SNP [dm6]	A	G	4.846e^-220	1.230e^-215	INTRON cic	TF binding site BDTNP1_TFBS_dl
2L	2834264	2L_2834264_SNP [dm3] 2L_2834264_SNP [dm6]	T	C	4.869e^-220	1.230e^-215	DOWNSTREAM CG3119 INTERGENIC
2R	7455567	2R_7455567_SNP [dm3] 2R_11568062_SNP [dm6]	C	G	4.869e^-220	1.230e^-215	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
3L	16435941	3L_16435941_SNP [dm3] 3L_16442841_SNP [dm6]	G	A	4.869e^-220	1.230e^-215	INTRON CG33158 & 1 other
2R	8295737	2R_8295737_SNP [dm3] 2R_12408232_SNP [dm6]	C	T	4.445e^-216	1.079e^-211	SYNONYMOUS_CODING Cpr49Ag UPSTREAM CG30050
3L	14621503	3L_14621503_SNP [dm3] 3L_14628403_SNP [dm6]	T	A	4.445e^-216	1.079e^-211	SPLICE_SITE_REGION RecQ5 SYNONYMOUS_CODING RecQ5 UTR_3_PRIME RecQ5 DOWNSTREAM CG9628
3R	14092269	3R_14092269_SNP [dm3] 3R_18266547_SNP [dm6]	A	C	4.445e^-216	1.079e^-211	INTERGENIC
X	17007384	X_17007384_SNP [dm3] X_17113351_SNP [dm6]	T	G	4.548e^-216	1.079e^-211	INTRON CG5004
3L	1044627	3L_1044627_SNP [dm3] 3L_1044627_SNP [dm6]	G	A	4.572e^-216	1.079e^-211	INTRON bab1
2L	14802321	2L_14802321_SNP [dm3] 2L_14802321_SNP [dm6]	T	C	4.622e^-216	1.079e^-211	UPSTREAM CG33308 INTERGENIC
2L	18161911	2L_18161911_SNP [dm3] 2L_18161911_SNP [dm6]	G	A	5.075e^-216	1.156e^-211	INTRON CG42750
3R	24778165	3R_24778165_SNP [dm3] 3R_28952443_SNP [dm6]	G	C	5.075e^-216	1.156e^-211	INTRON CG14521
3R	17843666	3R_17843666_SNP [dm3] 3R_22017944_SNP [dm6]	A	G	1.522e^-214	3.425e^-210	INTRON CG6439
2L	15442394	2L_15442394_SNP [dm3] 2L_15442394_SNP [dm6]	T	G	1.636e^-214	3.593e^-210	DOWNSTREAM CR44862 INTERGENIC	TF binding site mE1_TFBS_cad
3R	9248790	3R_9248790_SNP [dm3] 3R_13423068_SNP [dm6]	C	A	1.636e^-214	3.593e^-210	SYNONYMOUS_CODING Ir87a
2R	18006260	2R_18006260_SNP [dm3] 2R_22118755_SNP [dm6]	C	T	1.666e^-214	3.616e^-210	INTRON Vrp1
3R	9283518	3R_9283518_SNP [dm3] 3R_13457796_SNP [dm6]	T	C	1.773e^-214	3.804e^-210	SYNONYMOUS_CODING CG14372 EXON CR17025
X	17277115	X_17277115_SNP [dm3] X_17383082_SNP [dm6]	T	G	1.994e^-213	4.228e^-209	INTERGENIC
2R	17688679	2R_17688679_SNP [dm3] 2R_21801174_SNP [dm6]	A	C	2.096e^-213	4.345e^-209	UPSTREAM CG4386 INTERGENIC
X	4296533	X_4296533_SNP [dm3] X_4402500_SNP [dm6]	A	T	2.096e^-213	4.345e^-209	INTRON CR32773	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	7487142	2R_7487142_INS [dm3] 2R_11599637_INS [dm6]	T	TT	2.154e^-213	4.415e^-209	SPLICE_SITE_REGION tou UTR_5_PRIME tou INTRON tou	TF binding site BDTNP1_TFBS_dl
2R	7044513	2R_7044513_SNP [dm3] 2R_11157008_SNP [dm6]	C	T	2.277e^-213	4.566e^-209	INTRON CG13229
2R	8296274	2R_8296274_SNP [dm3] 2R_12408769_SNP [dm6]	G	C	2.277e^-213	4.566e^-209	UPSTREAM CG30050 DOWNSTREAM Cpr49Ag INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	21103935	X_21103935_SNP [dm3] X_21232908_SNP [dm6]	T	G	1.696e^-212	3.364e^-208	DOWNSTREAM tRNA:R:19F INTRON CG32521	TF binding site mE1_TFBS_chinmo
2L	14015190	2L_14015190_SNP [dm3] 2L_14015190_SNP [dm6]	C	G	1.864e^-212	3.658e^-208	INTRON bgm
2L	4452991	2L_4452991_SNP [dm3] 2L_4452991_SNP [dm6]	T	C	2.120e^-208	4.077e^-204	UTR_5_PRIME CG15439 DOWNSTREAM CG15440	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23542569	3R_23542569_SNP [dm3] 3R_27716847_SNP [dm6]	C	T	2.122e^-208	4.077e^-204	INTERGENIC
X	720503	X_720503_SNP [dm3] X_826470_SNP [dm6]	C	T	2.197e^-208	4.179e^-204	INTRON CG43867	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	14268085	3R_14268085_SNP [dm3] 3R_18442363_SNP [dm6]	T	G	2.348e^-208	4.377e^-204	INTRON fru
2L	16487107	2L_16487107_SNP [dm3] 2L_16487107_SNP [dm6]	C	T	2.349e^-208	4.377e^-204	INTERGENIC	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	22977050	3R_22977050_SNP [dm3] 3R_27151328_SNP [dm6]	A	T	2.736e^-208	4.961e^-204	UPSTREAM Men-b & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_MB_Alpha_Thin phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results