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=5.060e^-6)
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_3R_K	0.07606

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1381 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	11625068	2R_11625068_SNP [dm3] 2R_15737563_SNP [dm6]	C	A	5.115e^-6	1	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	4435945	2R_4435945_SNP [dm3] 2R_8548440_SNP [dm6]	C	G	6.672e^-6	1	INTERGENIC
3L	1190565	3L_1190565_SNP [dm3] 3L_1190565_SNP [dm6]	G	T	7.682e^-6	1	UTR_3_PRIME Trh DOWNSTREAM CG13912
3L	1906229	3L_1906229_SNP [dm3] 3L_1906229_SNP [dm6]	T	G	7.976e^-6	1	INTRON CG1887
2R	10883757	2R_10883757_SNP [dm3] 2R_14996252_SNP [dm6]	T	C	8.780e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11499936	2L_11499936_SNP [dm3] 2L_11499936_SNP [dm6]	T	C	9.865e^-6	1	UPSTREAM CG6488 INTERGENIC
X	12599988	X_12599988_SNP [dm3] X_12705955_SNP [dm6]	T	C	1.033e^-5	1	UTR_5_PRIME CG15725 INTRON Smr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7518609	2R_7518609_SNP [dm3] 2R_11631104_SNP [dm6]	G	A	1.142e^-5	1	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	4299050	2R_4299050_SNP [dm3] 2R_8411545_SNP [dm6]	C	T	1.376e^-5	1	UPSTREAM CG2121 INTRON CG2121
3R	3718365	3R_3718365_SNP [dm3] 3R_7892643_SNP [dm6]	C	A	1.447e^-5	1	INTRON mRpS9 & 1 other	TF binding site mE1_TFBS_cad
2L	1191383	2L_1191383_SNP [dm3] 2L_1191383_SNP [dm6]	A	T	1.687e^-5	1	INTRON CG5001
2R	8665720	2R_8665720_SNP [dm3] 2R_12778215_SNP [dm6]	C	T	1.698e^-5	1	EXON CR45266	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	3515866	X_3515866_SNP [dm3] X_3621833_SNP [dm6]	C	G	1.849e^-5	1	INTRON AstA-R1
2R	4017312	2R_4017312_SNP [dm3] 2R_8129807_SNP [dm6]	A	G	1.885e^-5	1	SYNONYMOUS_CODING Pbp49 UTR_3_PRIME CG42516 DOWNSTREAM Socs44A	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	13319402	2L_13319402_SNP [dm3] 2L_13319402_SNP [dm6]	T	A	1.951e^-5	1	INTRON CG43778	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
2L	1261603	2L_1261603_INS [dm3] 2L_1261603_INS [dm6]	T	TTCAT	1.971e^-5	1	INTRON robo3
X	8647270	X_8647270_SNP [dm3] X_8753237_SNP [dm6]	C	T	2.094e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	4335697	2R_4335697_SNP [dm3] 2R_8448192_SNP [dm6]	T	C	2.176e^-5	1	SYNONYMOUS_CODING Cyp4e1
X	16892077	X_16892077_SNP [dm3] X_16998044_SNP [dm6]	T	C	2.195e^-5	1	INTRON CG45002
2R	12039256	2R_12039256_DEL [dm3] 2R_16151751_DEL [dm6]	GTG	G	2.251e^-5	1	INTRON lbk
2L	13319388	2L_13319388_INS [dm3] 2L_13319388_INS [dm6]	T	TGAAT	2.304e^-5	1	INTRON CG43778	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	19060178	2R_19060178_SNP [dm3] 2R_23172655_SNP [dm6]	T	C	2.341e^-5	1	SYNONYMOUS_CODING CG34371	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
2R	19881125	2R_19881125_DEL [dm3] 2R_23993602_DEL [dm6]	TT	T	2.423e^-5	1	UPSTREAM mir-1009 INTRON CG3860
3L	18266224	3L_18266224_SNP [dm3] 3L_18273124_SNP [dm6]	T	C	2.437e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	19060226	2R_19060226_SNP [dm3] 2R_23172703_SNP [dm6]	A	G	2.444e^-5	1	SYNONYMOUS_CODING CG34371	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
2L	7583975	2L_7583975_SNP [dm3] 2L_7583975_SNP [dm6]	T	A	2.517e^-5	1	DOWNSTREAM Spn28B INTERGENIC
2L	13319399	2L_13319399_SNP [dm3] 2L_13319399_SNP [dm6]	T	C	2.528e^-5	1	INTRON CG43778	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	4626449	2R_4626449_SNP [dm3] 2R_8738944_SNP [dm6]	C	G	2.638e^-5	1	INTRON CG8740
3L	2854049	3L_2854049_SNP [dm3] 3L_2854049_SNP [dm6]	T	C	2.696e^-5	1	INTRON CG43444
3L	12228960	3L_12228960_SNP [dm3] 3L_12235860_SNP [dm6]	T	A	2.809e^-5	1	INTRON app
2L	7090261	2L_7090261_SNP [dm3] 2L_7090261_SNP [dm6]	G	A	3.009e^-5	1	INTERGENIC
3L	2854029	3L_2854029_SNP [dm3] 3L_2854029_SNP [dm6]	G	C	3.010e^-5	1	INTRON CG43444
3L	2854020	3L_2854020_SNP [dm3] 3L_2854020_SNP [dm6]	C	G	3.057e^-5	1	INTRON CG43444
2L	11499855	2L_11499855_SNP [dm3] 2L_11499855_SNP [dm6]	G	C	3.087e^-5	1	UPSTREAM CG6488 INTERGENIC
3L	2921203	3L_2921203_SNP [dm3] 3L_2921203_SNP [dm6]	G	T	3.102e^-5	1	INTRON Shab
3R	3635786	3R_3635786_SNP [dm3] 3R_7810064_SNP [dm6]	T	A	3.334e^-5	1	UPSTREAM CG31472 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
2L	8578182	2L_8578182_SNP [dm3] 2L_8578182_SNP [dm6]	G	A	3.355e^-5	1	INTRON Sema-1a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	18266238	3L_18266238_DEL [dm3] 3L_18273138_DEL [dm6]	AA	A	3.480e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2L	4711791	2L_4711791_SNP [dm3] 2L_4711791_SNP [dm6]	A	G	3.570e^-5	1	INTRON CG34351	TF binding site mE1_TFBS_chinmo
2L	4711793	2L_4711793_SNP [dm3] 2L_4711793_SNP [dm6]	A	G	3.570e^-5	1	INTRON CG34351	TF binding site mE1_TFBS_chinmo
2R	13118523	2R_13118523_SNP [dm3] 2R_17231018_SNP [dm6]	G	A	3.601e^-5	1	INTRON mbl
2R	19881218	2R_19881218_SNP [dm3] 2R_23993695_SNP [dm6]	G	A	3.609e^-5	1	SYNONYMOUS_CODING CG3860 UPSTREAM mir-1009
2L	11499744	2L_11499744_SNP [dm3] 2L_11499744_SNP [dm6]	T	C	3.731e^-5	1	UPSTREAM CG6488 INTERGENIC
2R	5238727	2R_5238727_INS [dm3] 2R_9351222_INS [dm6]	T	TA	3.824e^-5	1	INTRON CG13954 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	9740097	X_9740097_SNP [dm3] X_9846064_SNP [dm6]	C	T	3.843e^-5	1	SYNONYMOUS_CODING CG32698
2L	7583967	2L_7583967_SNP [dm3] 2L_7583967_SNP [dm6]	A	G	3.894e^-5	1	DOWNSTREAM Spn28B INTERGENIC
X	4535918	X_4535918_SNP [dm3] X_4641885_SNP [dm6]	C	T	3.995e^-5	1	NON_SYNONYMOUS_CODING CG3062 UTR_5_PRIME CG3081 UPSTREAM CG3081	TF binding site mE1_TFBS_chinmo
3L	20347240	3L_20347240_SNP [dm3] 3L_20354140_SNP [dm6]	G	A	4.295e^-5	1	UTR_5_PRIME CG5618 DOWNSTREAM eRF1
2R	18865056	2R_18865056_SNP [dm3] 2R_22977533_SNP [dm6]	C	G	4.397e^-5	1	INTERGENIC
2L	19886315	2L_19886315_SNP [dm3] 2L_19886315_SNP [dm6]	A	T	4.504e^-5	1	INTRON sick
X	22056225	X_22056225_SNP [dm3] X_22654389_SNP [dm6]	A	T	4.543e^-5	1	INTERGENIC
2R	16647594	2R_16647594_SNP [dm3] 2R_20760089_SNP [dm6]	G	T	4.654e^-5	1	INTERGENIC
2L	10376696	2L_10376696_INS [dm3] 2L_10376696_INS [dm6]	G	GG	4.685e^-5	1	UTR_5_PRIME dpr19 UPSTREAM CG33303 INTRON dpr19	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_ttk
2L	8578206	2L_8578206_SNP [dm3] 2L_8578206_SNP [dm6]	G	A	4.917e^-5	1	INTRON Sema-1a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	3682061	3R_3682061_SNP [dm3] 3R_7856339_SNP [dm6]	T	G	5.340e^-5	1	UTR_3_PRIME CG17816 DOWNSTREAM CG34384
2R	20011212	2R_20011212_SNP [dm3] 2R_24123689_SNP [dm6]	A	C	5.363e^-5	1	SPLICE_SITE_REGION CG43775 & 2 others DOWNSTREAM CG3257 INTRON CG43775 & 2 others	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	1903555	3L_1903555_SNP [dm3] 3L_1903555_SNP [dm6]	G	T	5.427e^-5	1	INTRON CG1887
2L	1261584	2L_1261584_INS [dm3] 2L_1261584_INS [dm6]	C	CTCATC	5.456e^-5	1	INTRON robo3
2L	15251787	2L_15251787_SNP [dm3] 2L_15251787_SNP [dm6]	G	A	5.476e^-5	1	SYNONYMOUS_CODING dao	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11502636	2L_11502636_SNP [dm3] 2L_11502636_SNP [dm6]	C	A	5.490e^-5	1	INTRON spz4	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	2151186	3L_2151186_SNP [dm3] 3L_2151186_SNP [dm6]	G	T	5.630e^-5	1	INTRON zormin	TF binding site mE1_TFBS_Trl
3R	16050138	3R_16050138_SNP [dm3] 3R_20224416_SNP [dm6]	G	A	5.652e^-5	1	INTRON Nlg4
3R	21970106	3R_21970106_SNP [dm3] 3R_26144384_SNP [dm6]	C	T	5.714e^-5	1	INTERGENIC
2L	8506999	2L_8506999_SNP [dm3] 2L_8506999_SNP [dm6]	A	G	5.937e^-5	1	UPSTREAM Dh31 INTERGENIC
3L	11358604	3L_11358604_SNP [dm3] 3L_11365504_SNP [dm6]	A	G	6.016e^-5	1	UPSTREAM CG6163 EXON CR45036	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	18266324	3L_18266324_SNP [dm3] 3L_18273224_SNP [dm6]	A	T	6.261e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	12645013	3R_12645013_SNP [dm3] 3R_16819291_SNP [dm6]	C	T	6.418e^-5	1	INTRON abd-A	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_Kr
2R	9658161	2R_9658161_SNP [dm3] 2R_13770656_SNP [dm6]	G	T	6.586e^-5	1	INTRON Cpr50Ca	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	13838014	3R_13838014_SNP [dm3] 3R_18012292_SNP [dm6]	T	C	6.586e^-5	1	INTRON cpo
2R	10734508	2R_10734508_SNP [dm3] 2R_14847003_SNP [dm6]	G	C	6.614e^-5	1	SYNONYMOUS_CODING CG10209	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	19758194	3R_19758194_SNP [dm3] 3R_23932472_SNP [dm6]	G	A	6.673e^-5	1	SYNONYMOUS_CODING CG13599 UPSTREAM Rpt2 DOWNSTREAM RpS19b
3L	18266225	3L_18266225_SNP [dm3] 3L_18273125_SNP [dm6]	T	C	6.676e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
3L	1907513	3L_1907513_SNP [dm3] 3L_1907513_SNP [dm6]	C	A	6.770e^-5	1	INTRON CG1887
2L	1191388	2L_1191388_DEL [dm3] 2L_1191388_DEL [dm6]	CTC	C	7.027e^-5	1	INTRON CG5001
3L	1907491	3L_1907491_SNP [dm3] 3L_1907491_SNP [dm6]	A	G	7.047e^-5	1	INTRON CG1887
3L	1908256	3L_1908256_SNP [dm3] 3L_1908256_SNP [dm6]	A	T	7.047e^-5	1	INTRON CG1887
2L	9643399	2L_9643399_SNP [dm3] 2L_9643399_SNP [dm6]	C	T	7.122e^-5	1	SYNONYMOUS_CODING Apoltp	TF binding site mE1_TFBS_cad
2L	14017522	2L_14017522_SNP [dm3] 2L_14017522_SNP [dm6]	G	A	7.225e^-5	1	INTRON bgm
2R	17019353	2R_17019353_SNP [dm3] 2R_21131848_SNP [dm6]	T	C	7.548e^-5	1	NON_SYNONYMOUS_CODING Magi	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11502567	2L_11502567_SNP [dm3] 2L_11502567_SNP [dm6]	C	T	7.607e^-5	1	INTRON spz4	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	3645837	3R_3645837_SNP [dm3] 3R_7820115_SNP [dm6]	C	T	7.694e^-5	1	INTRON CG34384
3L	19159293	3L_19159293_SNP [dm3] 3L_19166193_SNP [dm6]	T	A	7.755e^-5	1	INTRON fz2	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
2L	2494361	2L_2494361_SNP [dm3] 2L_2494361_SNP [dm6]	G	T	7.783e^-5	1	INTRON oaf	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	14015782	2L_14015782_SNP [dm3] 2L_14015782_SNP [dm6]	A	T	7.785e^-5	1	SPLICE_SITE_REGION bgm INTRON bgm	TF binding site mE1_TFBS_cad
3R	14886268	3R_14886268_DEL [dm3] 3R_19060546_DEL [dm6]	TCAAGT	T	7.802e^-5	1	INTRON cdi
X	19484422	X_19484422_SNP [dm3] X_19590389_SNP [dm6]	T	G	7.914e^-5	1	UPSTREAM CG14219 INTERGENIC
3R	23303513	3R_23303513_SNP [dm3] 3R_27477791_SNP [dm6]	G	A	7.927e^-5	1	UPSTREAM Cyp6a18 INTERGENIC
2R	11625044	2R_11625044_SNP [dm3] 2R_15737539_SNP [dm6]	T	A	7.980e^-5	1	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	16805177	2R_16805177_SNP [dm3] 2R_20917672_SNP [dm6]	G	A	8.030e^-5	1	INTRON Rx
2L	2358491	2L_2358491_SNP [dm3] 2L_2358491_SNP [dm6]	A	G	8.092e^-5	1	UTR_3_PRIME eys DOWNSTREAM Rab5 & 1 other
X	3249525	X_3249525_SNP [dm3] X_3355492_SNP [dm6]	C	T	8.260e^-5	1	INTERGENIC
2L	8969162	2L_8969162_SNP [dm3] 2L_8969162_SNP [dm6]	A	C	8.362e^-5	1	SYNONYMOUS_CODING CG18088
3L	18266229	3L_18266229_SNP [dm3] 3L_18273129_SNP [dm6]	G	A	8.478e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
3L	19457034	3L_19457034_SNP [dm3] 3L_19463934_SNP [dm6]	A	G	8.724e^-5	1	DOWNSTREAM CG14095 INTERGENIC
3L	18266360	3L_18266360_SNP [dm3] 3L_18273260_SNP [dm6]	A	T	8.765e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	2252376	3R_2252376_SNP [dm3] 3R_6426654_SNP [dm6]	A	C	8.943e^-5	1	INTRON gpp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_z mE1_TFBS_HSA
X	6503416	X_6503416_SNP [dm3] X_6609383_SNP [dm6]	C	T	9.001e^-5	1	INTRON pigs
3L	18266323	3L_18266323_SNP [dm3] 3L_18273223_SNP [dm6]	G	T	9.256e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	3473617	3R_3473617_SNP [dm3] 3R_7647895_SNP [dm6]	A	T	9.364e^-5	1	INTERGENIC
3L	10940015	3L_10940015_SNP [dm3] 3L_10946915_SNP [dm6]	G	C	9.407e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv

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Missing results

By genomic position
Variant impact
Gene name

Survival_Paeruginosa phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results