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=1.957e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2461 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	6105874	2L_6105874_SNP [dm3] 2L_6105874_SNP [dm6]	T	C	6.312e^-7	0.512	INTRON stai
X	18851129	X_18851129_INS [dm3] X_18957096_INS [dm6]	A	ACAAATATTG	7.679e^-7	0.512	INTRON CG43759
2L	1561541	2L_1561541_SNP [dm3] 2L_1561541_SNP [dm6]	T	A	9.826e^-7	0.512	INTRON haf
3L	16037490	3L_16037490_SNP [dm3] 3L_16044390_SNP [dm6]	T	C	1.128e^-6	0.512	INTRON th	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_Trl
2L	8583625	2L_8583625_SNP [dm3] 2L_8583625_SNP [dm6]	C	T	1.766e^-6	0.642	INTRON Sema-1a
3R	19211784	3R_19211784_SNP [dm3] 3R_23386062_SNP [dm6]	T	C	2.299e^-6	0.658	INTERGENIC	TF binding site mE1_TFBS_Trl
2R	12379912	2R_12379912_SNP [dm3] 2R_16492407_SNP [dm6]	T	C	2.535e^-6	0.658	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	563223	2L_563223_SNP [dm3] 2L_563223_SNP [dm6]	T	C	3.047e^-6	0.665	START_GAINED CG11835 UTR_5_PRIME CG11835 UPSTREAM CG2794 INTRON CG11835	TF binding site mE1_TFBS_chinmo
X	20396880	X_20396880_SNP [dm3] X_20525853_SNP [dm6]	G	A	3.704e^-6	0.665	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
2L	2866098	2L_2866098_SNP [dm3] 2L_2866098_SNP [dm6]	A	G	6.239e^-6	0.665	INTRON CG2991
3L	2105093	3L_2105093_SNP [dm3] 3L_2105093_SNP [dm6]	G	C	7.581e^-6	0.665	INTRON sls	TF binding site mE1_TFBS_chinmo
2L	2797921	2L_2797921_SNP [dm3] 2L_2797921_SNP [dm6]	T	G	9.112e^-6	0.665	INTRON Syt1 EXON CR43821	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	4261013	2L_4261013_SNP [dm3] 2L_4261013_SNP [dm6]	T	C	9.261e^-6	0.665	INTRON CR44080
2L	6106168	2L_6106168_INS [dm3] 2L_6106168_INS [dm6]	G	CT	9.332e^-6	0.665	INTRON stai
2L	6106172	2L_6106172_INS [dm3] 2L_6106172_INS [dm6]	T	TAAGCTA	9.332e^-6	0.665	INTRON stai
2L	22931363	2L_22931363_SNP [dm3] 2L_23038631_SNP [dm6]	T	G	9.999e^-6	0.665	INTERGENIC
2R	2348113	2R_2348113_SNP [dm3] 2R_6460608_SNP [dm6]	C	A	1.005e^-5	0.665	INTERGENIC
2R	17877171	2R_17877171_SNP [dm3] 2R_21989666_SNP [dm6]	C	T	1.027e^-5	0.665	SYNONYMOUS_CODING CG34370	TF binding site mE1_TFBS_cad
3L	16037555	3L_16037555_SNP [dm3] 3L_16044455_SNP [dm6]	A	G	1.065e^-5	0.665	INTRON th	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_Trl
2R	18444112	2R_18444112_SNP [dm3] 2R_22556607_SNP [dm6]	T	C	1.096e^-5	0.665	SYNONYMOUS_CODING px	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12705144	3L_12705144_INS [dm3] 3L_12712044_INS [dm6]	T	TGAAATATA	1.147e^-5	0.665	INTERGENIC	TF binding site mE1_TFBS_D
3L	12705165	3L_12705165_DEL [dm3] 3L_12712065_DEL [dm6]	AG	A	1.147e^-5	0.665	INTERGENIC	TF binding site mE1_TFBS_D
3L	12705307	3L_12705307_SNP [dm3] 3L_12712207_SNP [dm6]	T	G	1.147e^-5	0.665	INTERGENIC
3L	12705308	3L_12705308_SNP [dm3] 3L_12712208_SNP [dm6]	T	A	1.147e^-5	0.665	INTERGENIC
3L	12705369	3L_12705369_SNP [dm3] 3L_12712269_SNP [dm6]	G	C	1.149e^-5	0.665	INTERGENIC
3L	3499847	3L_3499847_SNP [dm3] 3L_3499847_SNP [dm6]	G	T	1.189e^-5	0.665	INTRON CG42324
3L	13656806	3L_13656806_SNP [dm3] 3L_13663706_SNP [dm6]	T	C	1.204e^-5	0.665	INTRON bru-3
2R	1922669	2R_1922669_SNP [dm3] 2R_6035164_SNP [dm6]	T	C	1.255e^-5	0.665	INTRON SCAP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16071254	X_16071254_SNP [dm3] X_16177221_SNP [dm6]	A	C	1.284e^-5	0.665	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	2397947	2R_2397947_SNP [dm3] 2R_6510442_SNP [dm6]	G	T	1.296e^-5	0.665	UPSTREAM CR45127 INTRON jing	TF binding site BDTNP1_TFBS_dl
3R	19250659	3R_19250659_SNP [dm3] 3R_23424937_SNP [dm6]	C	T	1.368e^-5	0.665	DOWNSTREAM CG43694 INTRON CG4374
2L	554505	2L_554505_SNP [dm3] 2L_554505_SNP [dm6]	T	C	1.477e^-5	0.665	SYNONYMOUS_CODING rempA
X	16510329	X_16510329_SNP [dm3] X_16616296_SNP [dm6]	A	G	1.507e^-5	0.665	SYNONYMOUS_CODING CG9782	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	2105215	3L_2105215_SNP [dm3] 3L_2105215_SNP [dm6]	T	C	1.538e^-5	0.665	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
2R	1922700	2R_1922700_SNP [dm3] 2R_6035195_SNP [dm6]	T	C	1.555e^-5	0.665	INTRON SCAP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12705141	3L_12705141_INS [dm3] 3L_12712041_INS [dm6]	T	TA	1.563e^-5	0.665	INTERGENIC	TF binding site mE1_TFBS_D mE1_TFBS_HSA
3L	12705146	3L_12705146_SNP [dm3] 3L_12712046_SNP [dm6]	G	A	1.563e^-5	0.665	INTERGENIC	TF binding site mE1_TFBS_D
2L	22446523	2L_22446523_DEL [dm3] 2L_22553791_DEL [dm6]	ATAGCCTGG	A	1.572e^-5	0.665	UTR_3_PRIME CG17493	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	15274440	2L_15274440_SNP [dm3] 2L_15274440_SNP [dm6]	A	T	1.604e^-5	0.665	INTRON UK114	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15208408	2R_15208408_SNP [dm3] 2R_19320903_SNP [dm6]	G	A	1.672e^-5	0.665	INTRON Rgk1
3L	12705303	3L_12705303_INS [dm3] 3L_12712203_INS [dm6]	C	CCTT	1.768e^-5	0.665	INTERGENIC
2R	15074883	2R_15074883_SNP [dm3] 2R_19187378_SNP [dm6]	A	G	1.959e^-5	0.665	INTRON hppy
2L	9079208	2L_9079208_SNP [dm3] 2L_9079208_SNP [dm6]	T	A	2.080e^-5	0.665	INTERGENIC
2L	9079278	2L_9079278_SNP [dm3] 2L_9079278_SNP [dm6]	A	T	2.080e^-5	0.665	INTERGENIC
2L	827721	2L_827721_SNP [dm3] 2L_827721_SNP [dm6]	G	A	2.151e^-5	0.665	INTRON dock	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	554520	2L_554520_SNP [dm3] 2L_554520_SNP [dm6]	A	G	2.226e^-5	0.665	SYNONYMOUS_CODING rempA
X	20396870	X_20396870_SNP [dm3] X_20525843_SNP [dm6]	G	A	2.233e^-5	0.665	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
X	20396871	X_20396871_SNP [dm3] X_20525844_SNP [dm6]	G	A	2.233e^-5	0.665	UPSTREAM Tak1 INTERGENIC	TF binding site mE1_TFBS_zfh1
3R	9476474	3R_9476474_SNP [dm3] 3R_13650752_SNP [dm6]	A	C	2.305e^-5	0.665	INTRON rin
3R	9476494	3R_9476494_SNP [dm3] 3R_13650772_SNP [dm6]	A	T	2.305e^-5	0.665	INTRON rin
3R	9476516	3R_9476516_SNP [dm3] 3R_13650794_SNP [dm6]	G	C	2.305e^-5	0.665	INTRON rin
3L	3499962	3L_3499962_SNP [dm3] 3L_3499962_SNP [dm6]	C	T	2.400e^-5	0.665	INTRON CG42324
2L	7333251	2L_7333251_SNP [dm3] 2L_7333251_SNP [dm6]	T	A	2.465e^-5	0.665	UPSTREAM Wnt6 INTERGENIC
3L	2105204	3L_2105204_SNP [dm3] 3L_2105204_SNP [dm6]	T	C	2.495e^-5	0.665	NON_SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3R	8517999	3R_8517999_SNP [dm3] 3R_12692277_SNP [dm6]	G	T	2.524e^-5	0.665	SYNONYMOUS_CODING CG31347 UPSTREAM Su_fu_ INTRON Arp1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	12474432	2R_12474432_INS [dm3] 2R_16586927_INS [dm6]	T	TT	2.563e^-5	0.665	DOWNSTREAM CG8311 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	9235815	2L_9235815_SNP [dm3] 2L_9235815_SNP [dm6]	T	A	2.564e^-5	0.665	DOWNSTREAM tRNA:CR31885 INTRON tai
2R	1928321	2R_1928321_SNP [dm3] 2R_6040816_SNP [dm6]	T	A	2.564e^-5	0.665	UPSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	1928456	2R_1928456_SNP [dm3] 2R_6040951_SNP [dm6]	C	G	2.564e^-5	0.665	UPSTREAM CG14591 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	12705311	3L_12705311_SNP [dm3] 3L_12712211_SNP [dm6]	A	G	2.565e^-5	0.665	INTERGENIC
2R	2035245	2R_2035245_SNP [dm3] 2R_6147740_SNP [dm6]	C	G	2.568e^-5	0.665	INTRON EcR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	2035267	2R_2035267_SNP [dm3] 2R_6147762_SNP [dm6]	T	C	2.568e^-5	0.665	INTRON EcR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9151139	2L_9151139_INS [dm3] 2L_9151139_INS [dm6]	A	AA	2.575e^-5	0.665	UPSTREAM CG32982 INTRON CG32982	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	4635922	3L_4635922_SNP [dm3] 3L_4635922_SNP [dm6]	C	A	2.632e^-5	0.665	DOWNSTREAM axo INTRON axo	TF binding site mE1_TFBS_hkb
X	17949594	X_17949594_SNP [dm3] X_18055561_SNP [dm6]	C	G	2.637e^-5	0.665	INTRON Sh
2L	22524909	2L_22524909_SNP [dm3] 2L_22632177_SNP [dm6]	C	A	2.673e^-5	0.665	INTRON CG40006
2R	800295	2R_800295_SNP [dm3] 2R_4912790_SNP [dm6]	G	A	2.678e^-5	0.665	INTERGENIC	transposable element FlyBase
2R	6746413	2R_6746413_SNP [dm3] 2R_10858908_SNP [dm6]	A	G	2.706e^-5	0.665	UPSTREAM CR44302 INTRON CG30015
2L	14107422	2L_14107422_SNP [dm3] 2L_14107422_SNP [dm6]	T	C	2.709e^-5	0.665	UTR_3_PRIME CG16879 DOWNSTREAM CG16879 & 1 other
2L	22931397	2L_22931397_SNP [dm3] 2L_23038665_SNP [dm6]	T	A	2.723e^-5	0.665	INTERGENIC
2L	22980612	2L_22980612_DEL [dm3] 2L_23087880_DEL [dm6]	CATATGCAGCGACTGTGTAT...	C	2.723e^-5	0.665	INTERGENIC
X	11164903	X_11164903_SNP [dm3] X_11270870_SNP [dm6]	T	C	2.725e^-5	0.665	INTRON CG44422
X	8878082	X_8878082_SNP [dm3] X_8984049_SNP [dm6]	G	A	2.749e^-5	0.665	SYNONYMOUS_CODING CG12662 INTRON rdgA & 1 other
2R	5195024	2R_5195024_SNP [dm3] 2R_9307519_SNP [dm6]	G	A	2.768e^-5	0.665	SYNONYMOUS_CODING Myd88	TF binding site mE1_TFBS_cad
2L	9079121	2L_9079121_SNP [dm3] 2L_9079121_SNP [dm6]	C	T	2.845e^-5	0.665	INTERGENIC
2R	19823033	2R_19823033_SNP [dm3] 2R_23935510_SNP [dm6]	T	A	2.888e^-5	0.665	INTRON Ca-P60A
2L	22450549	2L_22450549_SNP [dm3] 2L_22557817_SNP [dm6]	G	A	3.208e^-5	0.665	INTERGENIC
2L	9087754	2L_9087754_SNP [dm3] 2L_9087754_SNP [dm6]	T	C	3.324e^-5	0.665	SYNONYMOUS_CODING Toll-4	TF binding site BDTNP1_TFBS_twi
2L	2797927	2L_2797927_SNP [dm3] 2L_2797927_SNP [dm6]	T	G	3.342e^-5	0.665	INTRON Syt1 EXON CR43821	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	4478083	2L_4478083_SNP [dm3] 2L_4478083_SNP [dm6]	T	C	3.410e^-5	0.665	UTR_3_PRIME dp
X	17943498	X_17943498_SNP [dm3] X_18049465_SNP [dm6]	C	G	3.460e^-5	0.665	DOWNSTREAM CG15373 INTRON Sh
2R	13693541	2R_13693541_SNP [dm3] 2R_17806036_SNP [dm6]	A	T	3.501e^-5	0.665	INTRON grh	TF binding site BDTNP1_TFBS_dl
X	17949626	X_17949626_SNP [dm3] X_18055593_SNP [dm6]	A	T	3.614e^-5	0.665	INTRON Sh
3R	26599617	3R_26599617_SNP [dm3] 3R_30773895_SNP [dm6]	G	A	3.700e^-5	0.665	INTRON zfh1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2L	14920274	2L_14920274_SNP [dm3] 2L_14920274_SNP [dm6]	G	T	3.709e^-5	0.665	INTRON CG42313
3R	26659694	3R_26659694_SNP [dm3] 3R_30833972_SNP [dm6]	C	A	3.747e^-5	0.665	INTRON CG15544
X	2908486	X_2908486_SNP [dm3] X_3014453_SNP [dm6]	A	C	3.771e^-5	0.665	INTRON kirre
3R	26963771	3R_26963771_SNP [dm3] 3R_31138049_SNP [dm6]	A	T	3.790e^-5	0.665	INTRON Gycbeta100B
2R	10624769	2R_10624769_INS [dm3] 2R_14737264_INS [dm6]	C	CAA	3.794e^-5	0.665	DOWNSTREAM CR43428 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	1759415	3L_1759415_SNP [dm3] 3L_1759415_SNP [dm6]	G	A	3.803e^-5	0.665	SYNONYMOUS_CODING Dhc62B DOWNSTREAM CG8001	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13968410	3L_13968410_SNP [dm3] 3L_13975310_SNP [dm6]	A	G	3.805e^-5	0.665	INTRON Hsc70-1
2L	9985299	2L_9985299_SNP [dm3] 2L_9985299_SNP [dm6]	T	A	3.819e^-5	0.665	UPSTREAM CR13130 INTRON bib	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	12705191	3L_12705191_DEL [dm3] 3L_12712091_DEL [dm6]	AAATATCCTA	A	3.820e^-5	0.665	INTERGENIC
2L	13425332	2L_13425332_SNP [dm3] 2L_13425332_SNP [dm6]	C	A	3.908e^-5	0.665	INTRON CG42784
X	14708245	X_14708245_SNP [dm3] X_14814212_SNP [dm6]	T	C	3.911e^-5	0.665	INTRON rut
X	6115489	X_6115489_SNP [dm3] X_6221456_SNP [dm6]	G	A	4.104e^-5	0.665	SYNONYMOUS_CODING Efr
X	4293670	X_4293670_SNP [dm3] X_4399637_SNP [dm6]	A	T	4.132e^-5	0.665	INTRON CR32773
2R	7561373	2R_7561373_SNP [dm3] 2R_11673868_SNP [dm6]	T	A	4.147e^-5	0.665	INTRON Roc2 & 1 other
3R	26963749	3R_26963749_SNP [dm3] 3R_31138027_SNP [dm6]	T	C	4.181e^-5	0.665	INTRON Gycbeta100B
3R	16067745	3R_16067745_SNP [dm3] 3R_20242023_SNP [dm6]	A	C	4.182e^-5	0.665	INTRON Nlg4

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Missing results

By genomic position
Variant impact
Gene name

CN_Hobo_TEMP phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results