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=9.416e^-13)
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

Covariate	χ²	p-value	Significance
In_2L_t	7.445	0.0242

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2373 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
3L	12641483	3L_12641483_SNP [dm3] 3L_12648383_SNP [dm6]	G	C	4.045e^-7	0.43	DOWNSTREAM CR43431 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	11822820	2R_11822820_SNP [dm3] 2R_15935315_SNP [dm6]	C	A	4.587e^-7	0.43	SYNONYMOUS_CODING CG8297 UPSTREAM Iap2 DOWNSTREAM Mlf	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	14015256	3R_14015256_SNP [dm3] 3R_18189534_SNP [dm6]	T	C	2.216e^-6	0.658	SYNONYMOUS_CODING MED17 UPSTREAM CG12321	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	18917480	2R_18917480_SNP [dm3] 2R_23029957_SNP [dm6]	G	A	2.902e^-6	0.658	INTRON twi & 1 other
3L	9180908	3L_9180908_SNP [dm3] 3L_9187808_SNP [dm6]	C	A	3.083e^-6	0.658	INTERGENIC
3R	19206622	3R_19206622_SNP [dm3] 3R_23380900_SNP [dm6]	G	A	3.284e^-6	0.658	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_chinmo
3R	27281690	3R_27281690_SNP [dm3] 3R_31455968_SNP [dm6]	C	A	3.742e^-6	0.658	INTRON Gprk2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11822829	2R_11822829_SNP [dm3] 2R_15935324_SNP [dm6]	C	T	4.525e^-6	0.658	SYNONYMOUS_CODING CG8297 UPSTREAM Iap2 DOWNSTREAM Mlf	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	12641484	3L_12641484_SNP [dm3] 3L_12648384_SNP [dm6]	T	G	4.696e^-6	0.658	DOWNSTREAM CR43431 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
X	12730510	X_12730510_SNP [dm3] X_12836477_SNP [dm6]	C	A	4.768e^-6	0.658	INTRON Pde9
3L	4701011	3L_4701011_SNP [dm3] 3L_4701011_SNP [dm6]	A	C	5.025e^-6	0.658	INTRON RhoGEF64C
3R	18423737	3R_18423737_SNP [dm3] 3R_22598015_SNP [dm6]	C	T	5.398e^-6	0.658	INTRON Efa6	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	4701369	3L_4701369_SNP [dm3] 3L_4701369_SNP [dm6]	C	T	6.308e^-6	0.658	INTRON RhoGEF64C
3L	4700971	3L_4700971_SNP [dm3] 3L_4700971_SNP [dm6]	C	A	6.370e^-6	0.658	INTRON RhoGEF64C
2L	10526475	2L_10526475_SNP [dm3] 2L_10526475_SNP [dm6]	C	G	6.564e^-6	0.658	INTERGENIC
2L	15953972	2L_15953972_SNP [dm3] 2L_15953972_SNP [dm6]	T	C	6.779e^-6	0.658	INTRON beat-Ib
2L	14056324	2L_14056324_SNP [dm3] 2L_14056324_SNP [dm6]	A	G	6.954e^-6	0.658	INTRON nAChRalpha5
2R	7007339	2R_7007339_SNP [dm3] 2R_11119834_SNP [dm6]	T	C	6.997e^-6	0.658	UTR_3_PRIME Cyp12d1-p DOWNSTREAM Cyp12d1-p
2L	10526465	2L_10526465_SNP [dm3] 2L_10526465_SNP [dm6]	T	A	7.470e^-6	0.658	INTERGENIC
2L	10526469	2L_10526469_SNP [dm3] 2L_10526469_SNP [dm6]	A	C	7.470e^-6	0.658	INTERGENIC
2L	10526455	2L_10526455_SNP [dm3] 2L_10526455_SNP [dm6]	G	A	7.749e^-6	0.658	INTERGENIC
3L	4701154	3L_4701154_SNP [dm3] 3L_4701154_SNP [dm6]	C	A	8.353e^-6	0.658	INTRON RhoGEF64C
3L	4701186	3L_4701186_SNP [dm3] 3L_4701186_SNP [dm6]	C	T	8.583e^-6	0.658	INTRON RhoGEF64C
2L	3262966	2L_3262966_SNP [dm3] 2L_3262966_SNP [dm6]	G	C	8.955e^-6	0.658	UPSTREAM CR45338 INTERGENIC
3L	12647311	3L_12647311_SNP [dm3] 3L_12654211_SNP [dm6]	A	G	9.097e^-6	0.658	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	12070583	3L_12070583_SNP [dm3] 3L_12077483_SNP [dm6]	G	A	1.085e^-5	0.658	INTRON Sema-5c	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13780395	3L_13780395_SNP [dm3] 3L_13787295_SNP [dm6]	C	T	1.090e^-5	0.658	INTRON bru-3
X	13399845	X_13399845_SNP [dm3] X_13505812_SNP [dm6]	A	T	1.144e^-5	0.658	INTRON Neto
X	3823569	X_3823569_SNP [dm3] X_3929536_SNP [dm6]	A	G	1.191e^-5	0.658	INTRON CG42541
2L	14056321	2L_14056321_SNP [dm3] 2L_14056321_SNP [dm6]	T	G	1.226e^-5	0.658	INTRON nAChRalpha5
3L	11115216	3L_11115216_SNP [dm3] 3L_11122116_SNP [dm6]	T	A	1.235e^-5	0.658	SYNONYMOUS_CODING Ufd1-like DOWNSTREAM mRpL2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5134713	2L_5134713_SNP [dm3] 2L_5134713_SNP [dm6]	C	T	1.274e^-5	0.658	SYNONYMOUS_CODING Msp300 INTRON Msp300
3L	4521149	3L_4521149_SNP [dm3] 3L_4521149_SNP [dm6]	C	T	1.394e^-5	0.658	INTRON Tie
3L	10648482	3L_10648482_SNP [dm3] 3L_10655382_SNP [dm6]	A	T	1.411e^-5	0.658	INTRON CG32066
3L	4521226	3L_4521226_SNP [dm3] 3L_4521226_SNP [dm6]	T	C	1.510e^-5	0.658	INTRON Tie
3L	14497724	3L_14497724_SNP [dm3] 3L_14504624_SNP [dm6]	C	A	1.547e^-5	0.658	INTRON bbg
2L	14056317	2L_14056317_SNP [dm3] 2L_14056317_SNP [dm6]	A	G	1.568e^-5	0.658	INTRON nAChRalpha5
2R	17087208	2R_17087208_SNP [dm3] 2R_21199703_SNP [dm6]	C	G	1.578e^-5	0.658	UPSTREAM Glycogenin & 1 other DOWNSTREAM Lapsyn INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3L	22557224	3L_22557224_SNP [dm3] 3L_22564124_SNP [dm6]	C	A	1.594e^-5	0.658	INTERGENIC
3L	10648717	3L_10648717_SNP [dm3] 3L_10655617_SNP [dm6]	T	A	1.595e^-5	0.658	INTRON CG32066
3R	21741221	3R_21741221_SNP [dm3] 3R_25915499_SNP [dm6]	T	G	1.606e^-5	0.658	SYNONYMOUS_CODING CG42235 DOWNSTREAM CG42235 INTRON CG42235
2R	7004530	2R_7004530_SNP [dm3] 2R_11117025_SNP [dm6]	T	A	1.655e^-5	0.658	UPSTREAM luna DOWNSTREAM Cyp12d1-p INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	13945259	3L_13945259_SNP [dm3] 3L_13952159_SNP [dm6]	T	A	1.719e^-5	0.658	INTRON CG32137
X	8291549	X_8291549_SNP [dm3] X_8397516_SNP [dm6]	A	C	1.769e^-5	0.658	NON_SYNONYMOUS_CODING CG15345
2R	7121593	2R_7121593_SNP [dm3] 2R_11234088_SNP [dm6]	A	G	1.808e^-5	0.658	NON_SYNONYMOUS_CODING CG13228 UPSTREAM CG13218
3R	20440372	3R_20440372_INS [dm3] 3R_24614650_INS [dm6]	T	TG	1.849e^-5	0.658	INTRON mld
2L	10531640	2L_10531640_SNP [dm3] 2L_10531640_SNP [dm6]	C	A	1.883e^-5	0.658	UTR_3_PRIME Lip4 UPSTREAM CG18301 DOWNSTREAM Lip4
2R	16529056	2R_16529056_SNP [dm3] 2R_20641551_SNP [dm6]	T	A	1.884e^-5	0.658	UTR_3_PRIME maf-S UPSTREAM rig & 1 other DOWNSTREAM CG33785 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	6994275	2R_6994275_SNP [dm3] 2R_11106770_SNP [dm6]	G	T	1.909e^-5	0.658	UTR_5_PRIME luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	10526473	2L_10526473_SNP [dm3] 2L_10526473_SNP [dm6]	A	G	1.936e^-5	0.658	INTERGENIC
2R	7121606	2R_7121606_SNP [dm3] 2R_11234101_SNP [dm6]	C	T	1.937e^-5	0.658	SYNONYMOUS_CODING CG13228 UPSTREAM CG13218
3L	13780404	3L_13780404_SNP [dm3] 3L_13787304_SNP [dm6]	A	C	1.953e^-5	0.658	INTRON bru-3
2R	19680144	2R_19680144_INS [dm3] 2R_23792621_INS [dm6]	C	GCATCCATCCA...	1.955e^-5	0.658	INTRON CG9850	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	11810792	2R_11810792_SNP [dm3] 2R_15923287_SNP [dm6]	G	A	1.959e^-5	0.658	SYNONYMOUS_CODING bdg	TF binding site mE1_TFBS_cad
3R	26014491	3R_26014491_SNP [dm3] 3R_30188769_SNP [dm6]	A	G	1.980e^-5	0.658	INTRON CG9747
2R	18388359	2R_18388359_SNP [dm3] 2R_22500854_SNP [dm6]	T	C	2.020e^-5	0.658	INTRON px
2L	8584498	2L_8584498_SNP [dm3] 2L_8584498_SNP [dm6]	C	T	2.075e^-5	0.658	INTRON Sema-1a
3R	27281756	3R_27281756_SNP [dm3] 3R_31456034_SNP [dm6]	G	T	2.117e^-5	0.658	INTRON Gprk2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10551758	2L_10551758_SNP [dm3] 2L_10551758_SNP [dm6]	C	T	2.124e^-5	0.658	INTRON Trim9	TF binding site mE1_TFBS_cad
2R	17088175	2R_17088175_SNP [dm3] 2R_21200670_SNP [dm6]	C	T	2.178e^-5	0.658	INTRON Glycogenin & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	16864876	2L_16864876_SNP [dm3] 2L_16864876_SNP [dm6]	G	A	2.235e^-5	0.658	INTERGENIC
2L	16864878	2L_16864878_SNP [dm3] 2L_16864878_SNP [dm6]	A	T	2.235e^-5	0.658	INTERGENIC
3R	23585129	3R_23585129_SNP [dm3] 3R_27759407_SNP [dm6]	A	G	2.313e^-5	0.658	INTERGENIC	TF binding site mE1_TFBS_cad
2R	16954085	2R_16954085_SNP [dm3] 2R_21066580_SNP [dm6]	T	G	2.327e^-5	0.658	SYNONYMOUS_CODING Cht4	TF binding site mE1_TFBS_cad
2L	10509425	2L_10509425_SNP [dm3] 2L_10509425_SNP [dm6]	T	C	2.355e^-5	0.658	INTRON CG7384	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	11808615	2R_11808615_INS [dm3] 2R_15921110_INS [dm6]	A	ATC	2.412e^-5	0.658	INTRON sli	TF binding site BDTNP1_TFBS_dl
2R	7121591	2R_7121591_SNP [dm3] 2R_11234086_SNP [dm6]	G	A	2.450e^-5	0.658	SYNONYMOUS_CODING CG13228 UPSTREAM CG13218
3R	23486869	3R_23486869_SNP [dm3] 3R_27661147_SNP [dm6]	A	T	2.473e^-5	0.658	UPSTREAM Mlc1 INTERGENIC
2L	8153321	2L_8153321_SNP [dm3] 2L_8153321_SNP [dm6]	A	T	2.486e^-5	0.658	SYNONYMOUS_CODING CG43394 INTRON CG8552	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	7004543	2R_7004543_SNP [dm3] 2R_11117038_SNP [dm6]	A	G	2.535e^-5	0.658	UPSTREAM luna DOWNSTREAM Cyp12d1-p INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	17086797	2R_17086797_SNP [dm3] 2R_21199292_SNP [dm6]	C	T	2.553e^-5	0.658	UTR_3_PRIME Lapsyn	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
2R	11808618	2R_11808618_INS [dm3] 2R_15921113_INS [dm6]	A	ATCA	2.606e^-5	0.658	INTRON sli	TF binding site BDTNP1_TFBS_dl
3R	23584837	3R_23584837_SNP [dm3] 3R_27759115_SNP [dm6]	G	T	2.650e^-5	0.658	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	11117578	3L_11117578_SNP [dm3] 3L_11124478_SNP [dm6]	T	G	2.663e^-5	0.658	INTRON CG42575	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
2R	6994584	2R_6994584_INS [dm3] 2R_11107079_INS [dm6]	A	ACATAC	2.673e^-5	0.658	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	4376251	X_4376251_SNP [dm3] X_4482218_SNP [dm6]	C	T	2.692e^-5	0.658	SYNONYMOUS_CODING bi INTRON CR32773
2L	13983851	2L_13983851_SNP [dm3] 2L_13983851_SNP [dm6]	G	A	2.700e^-5	0.658	SYNONYMOUS_CODING rk DOWNSTREAM NimC2	TF binding site mE1_TFBS_chinmo
2L	11886785	2L_11886785_SNP [dm3] 2L_11886785_SNP [dm6]	G	T	2.884e^-5	0.679	INTRON Pde1c
3L	10543884	3L_10543884_SNP [dm3] 3L_10550784_SNP [dm6]	A	G	2.891e^-5	0.679	INTRON A2bp1
X	16428953	X_16428953_SNP [dm3] X_16534920_SNP [dm6]	T	A	2.897e^-5	0.679	INTERGENIC
3L	10648718	3L_10648718_SNP [dm3] 3L_10655618_SNP [dm6]	T	A	3.008e^-5	0.694	INTRON CG32066
2R	17087207	2R_17087207_SNP [dm3] 2R_21199702_SNP [dm6]	C	G	3.036e^-5	0.694	UPSTREAM Glycogenin & 1 other DOWNSTREAM Lapsyn INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3L	10874563	3L_10874563_SNP [dm3] 3L_10881463_SNP [dm6]	T	G	3.175e^-5	0.709	SYNONYMOUS_CODING CG6409	TF binding site mE1_TFBS_chinmo
2L	8174010	2L_8174010_SNP [dm3] 2L_8174010_SNP [dm6]	T	A	3.223e^-5	0.709	INTRON Piezo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16916718	2R_16916718_SNP [dm3] 2R_21029213_SNP [dm6]	G	C	3.351e^-5	0.709	DOWNSTREAM CR45148 INTERGENIC
X	9254959	X_9254959_SNP [dm3] X_9360926_SNP [dm6]	T	C	3.368e^-5	0.709	SPLICE_SITE_REGION mgl INTRON mgl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	4120072	2R_4120072_SNP [dm3] 2R_8232567_SNP [dm6]	A	G	3.430e^-5	0.709	UPSTREAM dpn INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	4120102	2R_4120102_SNP [dm3] 2R_8232597_SNP [dm6]	G	T	3.430e^-5	0.709	UPSTREAM dpn INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	11116986	3L_11116986_SNP [dm3] 3L_11123886_SNP [dm6]	A	C	3.511e^-5	0.709	UPSTREAM Ufd1-like INTRON CG42575	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	16428952	X_16428952_SNP [dm3] X_16534919_SNP [dm6]	A	G	3.553e^-5	0.709	INTERGENIC
2R	6994881	2R_6994881_INS [dm3] 2R_11107376_INS [dm6]	T	TTT	3.559e^-5	0.709	UPSTREAM luna INTRON luna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	10555248	2L_10555248_SNP [dm3] 2L_10555248_SNP [dm6]	G	T	3.781e^-5	0.709	INTRON Trim9	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	4120059	2R_4120059_SNP [dm3] 2R_8232554_SNP [dm6]	A	T	3.800e^-5	0.709	UPSTREAM dpn INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	15782779	2R_15782779_SNP [dm3] 2R_19895274_SNP [dm6]	G	T	3.822e^-5	0.709	INTERGENIC
2R	14724388	2R_14724388_SNP [dm3] 2R_18836883_SNP [dm6]	C	T	3.853e^-5	0.709	UTR_3_PRIME CG15099 DOWNSTREAM CG15083
2L	4813763	2L_4813763_SNP [dm3] 2L_4813763_SNP [dm6]	C	T	3.855e^-5	0.709	INTRON CG15629
3L	8019464	3L_8019464_SNP [dm3] 3L_8026364_SNP [dm6]	T	C	3.877e^-5	0.709	INTRON nmo
3R	20662201	3R_20662201_SNP [dm3] 3R_24836479_SNP [dm6]	T	A	3.883e^-5	0.709	UPSTREAM sosie DOWNSTREAM CR45216 INTRON sosie
3L	2560217	3L_2560217_SNP [dm3] 3L_2560217_SNP [dm6]	G	A	3.909e^-5	0.709	SYNONYMOUS_CODING msn
3R	19042536	3R_19042536_SNP [dm3] 3R_23216814_SNP [dm6]	A	G	4.162e^-5	0.709	INTRON cnc

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By genomic position
Variant impact
Gene name

4μg/mL survivorship phenotype phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results