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=1.175e^-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_2L_t	0.044330
In_3R_K	0.009451

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.8945	0.0117
In_3R_K	6.5979	0.0369

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2253 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	16537615	2R_16537615_SNP [dm3] 2R_20650110_SNP [dm6]	A	T	2.310e^-7	0.433	INTRON Lrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2R	14011624	2R_14011624_SNP [dm3] 2R_18124119_SNP [dm6]	A	G	5.512e^-7	0.517	UPSTREAM stau INTRON stau	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1647129	3L_1647129_SNP [dm3] 3L_1647129_SNP [dm6]	A	G	9.257e^-7	0.579	NON_SYNONYMOUS_CODING CG17249 UPSTREAM Bro	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	2381060	3R_2381060_SNP [dm3] 3R_6555338_SNP [dm6]	C	A	3.664e^-6	0.82	INTRON dpr11
3R	23441415	3R_23441415_SNP [dm3] 3R_27615693_SNP [dm6]	A	C	4.068e^-6	0.82	INTRON Tusp
3R	7280728	3R_7280728_SNP [dm3] 3R_11455006_SNP [dm6]	T	A	4.460e^-6	0.82	UPSTREAM PGRP-LB INTRON CG17230 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	7278969	3R_7278969_SNP [dm3] 3R_11453247_SNP [dm6]	A	G	5.247e^-6	0.82	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	7278942	3R_7278942_SNP [dm3] 3R_11453220_SNP [dm6]	A	G	5.431e^-6	0.82	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo
3L	7278223	3L_7278223_SNP [dm3] 3L_7285123_SNP [dm6]	T	G	6.082e^-6	0.82	UTR_5_PRIME unc-13-4A	TF binding site mE1_TFBS_cad
3L	14356997	3L_14356997_SNP [dm3] 3L_14363897_SNP [dm6]	T	A	6.105e^-6	0.82	INTRON fz
2L	22020494	2L_22020494_SNP [dm3] 2L_22020494_SNP [dm6]	A	G	8.325e^-6	0.82	DOWNSTREAM CR33987 INTRON tio	TF binding site mE1_TFBS_Trl
3L	1647215	3L_1647215_SNP [dm3] 3L_1647215_SNP [dm6]	T	C	8.375e^-6	0.82	SYNONYMOUS_CODING CG17249 UPSTREAM Bro	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	5130756	3L_5130756_SNP [dm3] 3L_5137656_SNP [dm6]	G	T	8.629e^-6	0.82	SYNONYMOUS_CODING CG4611 DOWNSTREAM Prpk	TF binding site mE1_TFBS_chinmo
2R	16866762	2R_16866762_SNP [dm3] 2R_20979257_SNP [dm6]	A	T	9.226e^-6	0.82	START_GAINED CG9313 UTR_5_PRIME CG9313 UPSTREAM CG15650 & 1 other
3R	7279083	3R_7279083_SNP [dm3] 3R_11453361_SNP [dm6]	A	C	9.430e^-6	0.82	INTRON CG17230 & 1 other	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	25136442	3R_25136442_SNP [dm3] 3R_29310720_SNP [dm6]	A	G	9.864e^-6	0.82	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	1645303	3L_1645303_SNP [dm3] 3L_1645303_SNP [dm6]	A	T	1.179e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	11251034	2R_11251034_INS [dm3] 2R_15363529_INS [dm6]	A	ATA	1.197e^-5	0.82	INTRON unc-5
X	16052627	X_16052627_SNP [dm3] X_16158594_SNP [dm6]	T	C	1.241e^-5	0.82	INTERGENIC
3L	1645300	3L_1645300_SNP [dm3] 3L_1645300_SNP [dm6]	A	T	1.260e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	1645305	3L_1645305_SNP [dm3] 3L_1645305_SNP [dm6]	G	C	1.260e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	1645306	3L_1645306_SNP [dm3] 3L_1645306_SNP [dm6]	C	T	1.260e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	1645311	3L_1645311_DEL [dm3] 3L_1645311_DEL [dm6]	CA	C	1.260e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	21914973	2L_21914973_SNP [dm3] 2L_21914973_SNP [dm6]	T	C	1.305e^-5	0.82	SPLICE_SITE_REGION CG31600 INTRON CG31600
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	1.376e^-5	0.82	INTERGENIC
3R	16294815	3R_16294815_SNP [dm3] 3R_20469093_SNP [dm6]	G	A	1.380e^-5	0.82	INTRON Gfrl
3R	19625870	3R_19625870_SNP [dm3] 3R_23800148_SNP [dm6]	G	A	1.451e^-5	0.82	NON_SYNONYMOUS_CODING mbc
3R	7281547	3R_7281547_SNP [dm3] 3R_11455825_SNP [dm6]	G	A	1.491e^-5	0.82	INTRON CG17230 & 1 other
3L	722590	3L_722590_SNP [dm3] 3L_722590_SNP [dm6]	A	T	1.526e^-5	0.82	INTERGENIC
X	17062351	X_17062351_SNP [dm3] X_17168318_SNP [dm6]	T	A	1.628e^-5	0.82	INTRON baz
X	12021418	X_12021418_INS [dm3] X_12127385_INS [dm6]	A	AAA	1.647e^-5	0.82	UPSTREAM Ten-a INTRON Ten-a
3L	718515	3L_718515_SNP [dm3] 3L_718515_SNP [dm6]	A	C	1.691e^-5	0.82	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3417516	2L_3417516_SNP [dm3] 2L_3417516_SNP [dm6]	A	G	1.751e^-5	0.82	UTR_3_PRIME CG31952 INTRON pgant2
2L	18871899	2L_18871899_SNP [dm3] 2L_18871899_SNP [dm6]	T	C	1.813e^-5	0.82	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	22020382	2L_22020382_SNP [dm3] 2L_22020382_SNP [dm6]	G	T	1.843e^-5	0.82	DOWNSTREAM CR33987 INTRON tio	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	19570657	3R_19570657_SNP [dm3] 3R_23744935_SNP [dm6]	A	G	2.089e^-5	0.82	INTRON Hmgcr
3L	1646170	3L_1646170_SNP [dm3] 3L_1646170_SNP [dm6]	G	A	2.109e^-5	0.82	SYNONYMOUS_CODING CG17249 UPSTREAM alphaCOP DOWNSTREAM CG13919	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	8857647	3L_8857647_SNP [dm3] 3L_8864547_SNP [dm6]	A	G	2.212e^-5	0.82	INTRON dally
X	9500123	X_9500123_SNP [dm3] X_9606090_SNP [dm6]	C	T	2.289e^-5	0.82	UPSTREAM Lst8 DOWNSTREAM Aats-lys INTERGENIC
3L	13549586	3L_13549586_SNP [dm3] 3L_13556486_SNP [dm6]	C	A	2.347e^-5	0.82	INTRON bru-3
3L	10610526	3L_10610526_SNP [dm3] 3L_10617426_SNP [dm6]	C	G	2.449e^-5	0.82	INTERGENIC
3R	21491476	3R_21491476_SNP [dm3] 3R_25665754_SNP [dm6]	C	A	2.457e^-5	0.82	UPSTREAM Lgr3 DOWNSTREAM RASSF8 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	20909411	2R_20909411_SNP [dm3] 2R_25021888_SNP [dm6]	T	A	2.565e^-5	0.82	INTRON uzip
3L	8547231	3L_8547231_SNP [dm3] 3L_8554131_SNP [dm6]	C	A	2.648e^-5	0.82	INTRON rhea	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	5069599	X_5069599_INS [dm3] X_5175566_INS [dm6]	A	AACGCAA	2.665e^-5	0.82	CODON_INSERTION CG15465 UTR_5_PRIME rg INTRON rg	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12545177	2R_12545177_SNP [dm3] 2R_16657672_SNP [dm6]	C	T	2.738e^-5	0.82	INTRON Picot
2R	5805954	2R_5805954_SNP [dm3] 2R_9918449_SNP [dm6]	T	C	2.817e^-5	0.82	INTRON Mef2
3L	1646793	3L_1646793_SNP [dm3] 3L_1646793_SNP [dm6]	G	A	2.841e^-5	0.82	NON_SYNONYMOUS_CODING CG17249 DOWNSTREAM CG13919	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	8896256	X_8896256_SNP [dm3] X_9002223_SNP [dm6]	C	A	2.888e^-5	0.82	INTRON rdgA & 1 other
2R	5805963	2R_5805963_SNP [dm3] 2R_9918458_SNP [dm6]	G	T	2.999e^-5	0.82	INTRON Mef2
3L	1645310	3L_1645310_SNP [dm3] 3L_1645310_SNP [dm6]	C	T	3.011e^-5	0.82	UPSTREAM CG13919 & 1 other DOWNSTREAM CG17249 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	10204159	X_10204159_SNP [dm3] X_10310126_SNP [dm6]	C	A	3.096e^-5	0.82	INTRON alpha-Man-I
3R	7278960	3R_7278960_SNP [dm3] 3R_11453238_SNP [dm6]	G	A	3.104e^-5	0.82	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13549795	3L_13549795_SNP [dm3] 3L_13556695_SNP [dm6]	A	G	3.165e^-5	0.82	INTRON bru-3
3L	1646534	3L_1646534_SNP [dm3] 3L_1646534_SNP [dm6]	A	G	3.257e^-5	0.82	SYNONYMOUS_CODING CG17249 DOWNSTREAM CG13919	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	16866821	2R_16866821_SNP [dm3] 2R_20979316_SNP [dm6]	G	T	3.298e^-5	0.82	UTR_5_PRIME CG9313 UPSTREAM CG9313 & 1 other
2L	12111309	2L_12111309_SNP [dm3] 2L_12111309_SNP [dm6]	T	C	3.346e^-5	0.82	SYNONYMOUS_CODING Phae2 DOWNSTREAM Phae1	TF binding site mE1_TFBS_cad
3R	23441360	3R_23441360_SNP [dm3] 3R_27615638_SNP [dm6]	T	G	3.398e^-5	0.82	INTRON Tusp
2R	5805961	2R_5805961_SNP [dm3] 2R_9918456_SNP [dm6]	T	C	3.468e^-5	0.82	INTRON Mef2
2R	15394516	2R_15394516_SNP [dm3] 2R_19507011_SNP [dm6]	T	A	3.474e^-5	0.82	UPSTREAM tRNA:H:56E INTERGENIC
3R	24090091	3R_24090091_SNP [dm3] 3R_28264369_SNP [dm6]	A	G	3.530e^-5	0.82	NON_SYNONYMOUS_CODING CG43124 UPSTREAM CG43125
2L	11456327	2L_11456327_SNP [dm3] 2L_11456327_SNP [dm6]	A	C	3.564e^-5	0.82	INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2L	21998906	2L_21998906_SNP [dm3] 2L_21998906_SNP [dm6]	C	A	3.626e^-5	0.82	DOWNSTREAM CR44916 INTERGENIC	transposable element FlyBase
3R	7369247	3R_7369247_SNP [dm3] 3R_11543525_SNP [dm6]	T	A	3.699e^-5	0.82	UPSTREAM dpr4 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	24427748	3R_24427748_SNP [dm3] 3R_28602026_SNP [dm6]	A	T	3.752e^-5	0.82	UPSTREAM snoRNA:Psi28S-3405c & 2 others DOWNSTREAM snoRNA:Psi28S-3405a & 2 others INTRON Hrb98DE
3R	14616571	3R_14616571_SNP [dm3] 3R_18790849_SNP [dm6]	T	C	3.835e^-5	0.82	INTRON CG7720
3L	8316065	3L_8316065_SNP [dm3] 3L_8322965_SNP [dm6]	G	A	3.843e^-5	0.82	DOWNSTREAM CG13670 INTERGENIC
2L	12274966	2L_12274966_SNP [dm3] 2L_12274966_SNP [dm6]	G	T	3.860e^-5	0.82	INTRON aret
2L	19239503	2L_19239503_SNP [dm3] 2L_19239503_SNP [dm6]	A	G	3.907e^-5	0.82	INTERGENIC
3L	21393248	3L_21393248_SNP [dm3] 3L_21400148_SNP [dm6]	A	T	3.908e^-5	0.82	INTRON rgn
3L	12583095	3L_12583095_SNP [dm3] 3L_12589995_SNP [dm6]	A	T	3.922e^-5	0.82	INTRON ara	TF binding site BDTNP1_TFBS_twi
2L	8807137	2L_8807137_SNP [dm3] 2L_8807137_SNP [dm6]	T	C	3.925e^-5	0.82	INTERGENIC
2L	21914924	2L_21914924_SNP [dm3] 2L_21914924_SNP [dm6]	T	C	3.938e^-5	0.82	NON_SYNONYMOUS_CODING CG31600
2R	20355319	2R_20355319_SNP [dm3] 2R_24467796_SNP [dm6]	T	C	3.953e^-5	0.82	INTRON CG13579
3R	8591424	3R_8591424_SNP [dm3] 3R_12765702_SNP [dm6]	A	G	3.953e^-5	0.82	INTRON beat-Vc
2R	15394517	2R_15394517_SNP [dm3] 2R_19507012_SNP [dm6]	A	G	3.957e^-5	0.82	UPSTREAM tRNA:H:56E INTERGENIC
3L	9307271	3L_9307271_DEL [dm3] 3L_9314171_DEL [dm6]	ATGACCTTATTACGA...	A	4.014e^-5	0.82	INTERGENIC
2R	14028495	2R_14028495_SNP [dm3] 2R_18140990_SNP [dm6]	T	C	4.271e^-5	0.82	UPSTREAM pAbp DOWNSTREAM Pcl INTRON pAbp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl
X	17078271	X_17078271_SNP [dm3] X_17184238_SNP [dm6]	T	C	4.316e^-5	0.82	UPSTREAM CR44026 INTRON baz
3R	23519319	3R_23519319_SNP [dm3] 3R_27693597_SNP [dm6]	G	A	4.316e^-5	0.82	UPSTREAM CG43319 DOWNSTREAM CG12880 INTERGENIC
X	15738163	X_15738163_SNP [dm3] X_15844130_SNP [dm6]	C	A	4.369e^-5	0.82	START_GAINED Aats-arg UTR_5_PRIME Aats-arg UPSTREAM CG8578	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Ubx
2L	12294002	2L_12294002_SNP [dm3] 2L_12294002_SNP [dm6]	C	A	4.386e^-5	0.82	INTRON aret
3R	7276527	3R_7276527_SNP [dm3] 3R_11450805_SNP [dm6]	C	T	4.423e^-5	0.82	INTRON CG17230 & 1 other
2L	3839348	2L_3839348_SNP [dm3] 2L_3839348_SNP [dm6]	A	C	4.497e^-5	0.82	DOWNSTREAM slp2 INTERGENIC	regulatory region REDfly_CRMs
3R	5889411	3R_5889411_SNP [dm3] 3R_10063689_SNP [dm6]	C	A	4.555e^-5	0.82	UPSTREAM CG33631 DOWNSTREAM CG33630 INTERGENIC
3R	19073144	3R_19073144_SNP [dm3] 3R_23247422_SNP [dm6]	A	G	4.640e^-5	0.82	INTRON CG4467
2L	15386272	2L_15386272_INS [dm3] 2L_15386272_INS [dm6]	G	TTTC	4.660e^-5	0.82	INTERGENIC
2L	8506498	2L_8506498_SNP [dm3] 2L_8506498_SNP [dm6]	A	T	4.740e^-5	0.82	INTRON Dh31
3R	16295434	3R_16295434_SNP [dm3] 3R_20469712_SNP [dm6]	C	T	4.757e^-5	0.82	INTRON Gfrl
3R	7277793	3R_7277793_SNP [dm3] 3R_11452071_SNP [dm6]	T	C	4.775e^-5	0.82	UPSTREAM sals DOWNSTREAM PGRP-LB INTRON CG17230
3R	7277847	3R_7277847_DEL [dm3] 3R_11452125_DEL [dm6]	ATTAAAGTCTATGCCACTGC...	A	4.775e^-5	0.82	UPSTREAM sals DOWNSTREAM PGRP-LB INTRON CG17230
2L	3425135	2L_3425135_SNP [dm3] 2L_3425135_SNP [dm6]	C	G	4.859e^-5	0.82	INTRON pgant2
3L	12026303	3L_12026303_SNP [dm3] 3L_12033203_SNP [dm6]	G	C	4.865e^-5	0.82	DOWNSTREAM CG43993 INTRON rols
2R	16866778	2R_16866778_SNP [dm3] 2R_20979273_SNP [dm6]	G	T	4.867e^-5	0.82	UTR_5_PRIME CG9313 UPSTREAM CG15650 & 1 other
2L	21962090	2L_21962090_SNP [dm3] 2L_21962090_SNP [dm6]	A	G	4.930e^-5	0.82	INTERGENIC
2R	19822999	2R_19822999_SNP [dm3] 2R_23935476_SNP [dm6]	G	T	4.939e^-5	0.82	INTRON Ca-P60A
3R	19625641	3R_19625641_SNP [dm3] 3R_23799919_SNP [dm6]	G	A	4.996e^-5	0.82	SYNONYMOUS_CODING mbc
2R	13806936	2R_13806936_SNP [dm3] 2R_17919431_SNP [dm6]	G	T	5.069e^-5	0.82	INTRON Elk
X	9499586	X_9499586_SNP [dm3] X_9605553_SNP [dm6]	T	C	5.108e^-5	0.82	SYNONYMOUS_CODING Lst8 DOWNSTREAM Aats-lys	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	12112048	2L_12112048_SNP [dm3] 2L_12112048_SNP [dm6]	A	T	5.388e^-5	0.82	UTR_3_PRIME Phae2 DOWNSTREAM Phae2	TF binding site mE1_TFBS_cad

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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=9.659e^-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	0.01219

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.2315	0.0443
In_3R_K	5.6583	0.0591

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2174 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	15299750	3R_15299750_SNP [dm3] 3R_19474028_SNP [dm6]	T	A	1.503e^-6	0.825	INTRON Dys
2L	8809467	2L_8809467_INS [dm3] 2L_8809467_INS [dm6]	C	CC	1.939e^-6	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	3.131e^-6	0.825	INTERGENIC
2R	3077080	2R_3077080_INS [dm3] 2R_7189575_INS [dm6]	G	GGCAG	3.876e^-6	0.825	INTRON pk
3R	23513340	3R_23513340_SNP [dm3] 3R_27687618_SNP [dm6]	C	T	4.583e^-6	0.825	NON_SYNONYMOUS_CODING CG31055 INTRON CG12880	TF binding site mE1_TFBS_chinmo
2R	8914992	2R_8914992_SNP [dm3] 2R_13027487_SNP [dm6]	T	C	7.187e^-6	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	901595	2R_901595_INS [dm3] 2R_5014090_INS [dm6]	T	TAT	8.548e^-6	0.825	INTRON Ir41a
2L	21851919	2L_21851919_INS [dm3] 2L_21851919_INS [dm6]	T	TTCT	9.462e^-6	0.825	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	14388983	3R_14388983_SNP [dm3] 3R_18563261_SNP [dm6]	T	A	9.931e^-6	0.825	INTERGENIC
2R	15394517	2R_15394517_SNP [dm3] 2R_19507012_SNP [dm6]	A	G	1.012e^-5	0.825	UPSTREAM tRNA:H:56E INTERGENIC
2R	15394516	2R_15394516_SNP [dm3] 2R_19507011_SNP [dm6]	T	A	1.019e^-5	0.825	UPSTREAM tRNA:H:56E INTERGENIC
2R	16537615	2R_16537615_SNP [dm3] 2R_20650110_SNP [dm6]	A	T	1.092e^-5	0.825	INTRON Lrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	6100946	2L_6100946_SNP [dm3] 2L_6100946_SNP [dm6]	G	A	1.131e^-5	0.825	INTRON stai	TF binding site BDTNP1_TFBS_dl
2L	12274966	2L_12274966_SNP [dm3] 2L_12274966_SNP [dm6]	G	T	1.142e^-5	0.825	INTRON aret
2R	14011624	2R_14011624_SNP [dm3] 2R_18124119_SNP [dm6]	A	G	1.271e^-5	0.825	UPSTREAM stau INTRON stau	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10226967	2L_10226967_SNP [dm3] 2L_10226967_SNP [dm6]	A	G	1.273e^-5	0.825	UPSTREAM CG5708 DOWNSTREAM CG5694 INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	16989113	3R_16989113_SNP [dm3] 3R_21163391_SNP [dm6]	A	G	1.308e^-5	0.825	UPSTREAM CG5810 INTRON SNF4Agamma
3R	16989117	3R_16989117_SNP [dm3] 3R_21163395_SNP [dm6]	A	T	1.324e^-5	0.825	UPSTREAM CG5810 INTRON SNF4Agamma
2L	12294002	2L_12294002_SNP [dm3] 2L_12294002_SNP [dm6]	C	A	1.326e^-5	0.825	INTRON aret
2R	18453286	2R_18453286_SNP [dm3] 2R_22565781_SNP [dm6]	G	A	1.343e^-5	0.825	SYNONYMOUS_CODING dnr1	TF binding site mE1_TFBS_cad
3R	7278942	3R_7278942_SNP [dm3] 3R_11453220_SNP [dm6]	A	G	1.519e^-5	0.825	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo
3R	7366241	3R_7366241_SNP [dm3] 3R_11540519_SNP [dm6]	A	G	1.565e^-5	0.825	INTRON dpr4
2L	376777	2L_376777_SNP [dm3] 2L_376777_SNP [dm6]	G	A	1.583e^-5	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
X	9704731	X_9704731_SNP [dm3] X_9810698_SNP [dm6]	C	A	1.585e^-5	0.825	INTRON CG32698
2L	10226964	2L_10226964_SNP [dm3] 2L_10226964_SNP [dm6]	C	A	1.592e^-5	0.825	UPSTREAM CG5708 DOWNSTREAM CG5694 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	20889987	2R_20889987_INS [dm3] 2R_25002464_INS [dm6]	C	CAGTGTTAGTCTTACTTAAC...	1.625e^-5	0.825	INTRON zip
3R	23519319	3R_23519319_SNP [dm3] 3R_27693597_SNP [dm6]	G	A	1.685e^-5	0.825	UPSTREAM CG43319 DOWNSTREAM CG12880 INTERGENIC
2L	12294007	2L_12294007_SNP [dm3] 2L_12294007_SNP [dm6]	A	C	1.695e^-5	0.825	INTRON aret
2L	21866518	2L_21866518_SNP [dm3] 2L_21866518_SNP [dm6]	A	G	1.800e^-5	0.825	UPSTREAM CR44917 & 1 other DOWNSTREAM CR44919 INTRON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	6344151	3R_6344151_SNP [dm3] 3R_10518429_SNP [dm6]	A	T	1.817e^-5	0.825	INTRON hth	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	6101005	2L_6101005_SNP [dm3] 2L_6101005_SNP [dm6]	A	G	1.832e^-5	0.825	INTRON stai	TF binding site BDTNP1_TFBS_dl
3L	722590	3L_722590_SNP [dm3] 3L_722590_SNP [dm6]	A	T	1.867e^-5	0.825	INTERGENIC
X	17062351	X_17062351_SNP [dm3] X_17168318_SNP [dm6]	T	A	1.898e^-5	0.825	INTRON baz
3R	16295315	3R_16295315_SNP [dm3] 3R_20469593_SNP [dm6]	T	G	1.900e^-5	0.825	INTRON Gfrl
3R	10658738	3R_10658738_SNP [dm3] 3R_14833016_SNP [dm6]	G	C	1.929e^-5	0.825	INTRON btsz
3L	17185722	3L_17185722_SNP [dm3] 3L_17192622_SNP [dm6]	T	A	1.959e^-5	0.825	INTRON Rbp6
2L	8809372	2L_8809372_INS [dm3] 2L_8809372_INS [dm6]	C	CG	1.989e^-5	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi
2L	10482563	2L_10482563_SNP [dm3] 2L_10482563_SNP [dm6]	C	A	2.047e^-5	0.825	NON_SYNONYMOUS_CODING RluA-2 UTR_3_PRIME RluA-2 UPSTREAM Grip75	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens
2R	3079221	2R_3079221_SNP [dm3] 2R_7191716_SNP [dm6]	C	A	2.164e^-5	0.825	INTRON pk	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7831827	3L_7831827_SNP [dm3] 3L_7838727_SNP [dm6]	G	A	2.215e^-5	0.825	INTRON Pdp1	regulatory region REDfly_CRMs
3R	15059154	3R_15059154_SNP [dm3] 3R_19233432_SNP [dm6]	G	A	2.278e^-5	0.825	SYNONYMOUS_CODING unc79
3L	5829494	3L_5829494_SNP [dm3] 3L_5836394_SNP [dm6]	T	A	2.301e^-5	0.825	INTRON vn	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll mE1_TFBS_cad mE1_TFBS_HSA
3R	14388986	3R_14388986_SNP [dm3] 3R_18563264_SNP [dm6]	G	T	2.354e^-5	0.825	DOWNSTREAM CG43210 & 1 other INTERGENIC
3R	7280728	3R_7280728_SNP [dm3] 3R_11455006_SNP [dm6]	T	A	2.385e^-5	0.825	UPSTREAM PGRP-LB INTRON CG17230 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	2885564	2L_2885564_SNP [dm3] 2L_2885564_SNP [dm6]	A	T	2.390e^-5	0.825	UPSTREAM lilli & 1 other INTRON NTPase	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_en mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	5805963	2R_5805963_SNP [dm3] 2R_9918458_SNP [dm6]	G	T	2.418e^-5	0.825	INTRON Mef2
2L	15369702	2L_15369702_SNP [dm3] 2L_15369702_SNP [dm6]	G	A	2.451e^-5	0.825	INTERGENIC	TF binding site mE1_TFBS_D mE1_TFBS_HSA
3R	14388987	3R_14388987_SNP [dm3] 3R_18563265_SNP [dm6]	C	T	2.532e^-5	0.825	DOWNSTREAM CG43210 & 1 other INTERGENIC
3L	1647129	3L_1647129_SNP [dm3] 3L_1647129_SNP [dm6]	A	G	2.553e^-5	0.825	NON_SYNONYMOUS_CODING CG17249 UPSTREAM Bro	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
X	12416023	X_12416023_SNP [dm3] X_12521990_SNP [dm6]	C	T	2.565e^-5	0.825	SYNONYMOUS_CODING CG43921 UTR_5_PRIME CG43921	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
X	19871581	X_19871581_SNP [dm3] X_19977548_SNP [dm6]	T	G	2.605e^-5	0.825	INTERGENIC
2R	18063875	2R_18063875_SNP [dm3] 2R_22176370_SNP [dm6]	G	A	2.606e^-5	0.825	SYNONYMOUS_CODING CG6758 EXON CR45151	TF binding site mE1_TFBS_chinmo
2R	20024364	2R_20024364_SNP [dm3] 2R_24136841_SNP [dm6]	G	T	2.679e^-5	0.825	SYNONYMOUS_CODING CG4065	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	10658723	3R_10658723_SNP [dm3] 3R_14833001_SNP [dm6]	T	C	2.738e^-5	0.825	INTRON btsz
3R	6344146	3R_6344146_SNP [dm3] 3R_10518424_SNP [dm6]	T	G	2.752e^-5	0.825	INTRON hth	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	6347881	3R_6347881_SNP [dm3] 3R_10522159_SNP [dm6]	T	C	2.809e^-5	0.825	INTRON hth
2L	12293940	2L_12293940_SNP [dm3] 2L_12293940_SNP [dm6]	A	C	2.876e^-5	0.825	INTRON aret
2R	3077646	2R_3077646_SNP [dm3] 2R_7190141_SNP [dm6]	T	G	2.906e^-5	0.825	INTRON pk
2L	21879086	2L_21879086_SNP [dm3] 2L_21879086_SNP [dm6]	C	G	2.909e^-5	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15394537	2R_15394537_SNP [dm3] 2R_19507032_SNP [dm6]	G	C	2.933e^-5	0.825	UPSTREAM tRNA:H:56E INTERGENIC
3L	1646170	3L_1646170_SNP [dm3] 3L_1646170_SNP [dm6]	G	A	2.936e^-5	0.825	SYNONYMOUS_CODING CG17249 UPSTREAM alphaCOP DOWNSTREAM CG13919	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	21906159	2L_21906159_DEL [dm3] 2L_21906159_DEL [dm6]	TCGACA	T	2.972e^-5	0.825	UPSTREAM CG1428 INTERGENIC
2L	21906150	2L_21906150_DEL [dm3] 2L_21906150_DEL [dm6]	CACCTCTG	C	2.981e^-5	0.825	UPSTREAM CG1428 INTERGENIC
X	3559838	X_3559838_SNP [dm3] X_3665805_SNP [dm6]	A	T	3.039e^-5	0.825	UTR_3_PRIME AstA-R1
2L	21795611	2L_21795611_SNP [dm3] 2L_21795611_SNP [dm6]	C	G	3.170e^-5	0.825	UPSTREAM CG31612 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_ttk
2R	16789215	2R_16789215_SNP [dm3] 2R_20901710_SNP [dm6]	A	C	3.199e^-5	0.825	INTRON otp
2L	10482801	2L_10482801_SNP [dm3] 2L_10482801_SNP [dm6]	A	C	3.237e^-5	0.825	UPSTREAM Grip75 INTRON RluA-2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_sens
3L	7484492	3L_7484492_SNP [dm3] 3L_7491392_SNP [dm6]	G	T	3.244e^-5	0.825	UPSTREAM Cyp316a1 INTERGENIC
2R	10578635	2R_10578635_SNP [dm3] 2R_14691130_SNP [dm6]	T	C	3.253e^-5	0.825	INTRON mspo
2L	3997257	2L_3997257_INS [dm3] 2L_3997257_INS [dm6]	T	TGA	3.298e^-5	0.825	INTERGENIC
3L	1647215	3L_1647215_SNP [dm3] 3L_1647215_SNP [dm6]	T	C	3.306e^-5	0.825	SYNONYMOUS_CODING CG17249 UPSTREAM Bro	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	16923357	2R_16923357_SNP [dm3] 2R_21035852_SNP [dm6]	C	T	3.373e^-5	0.825	INTERGENIC
2L	12112048	2L_12112048_SNP [dm3] 2L_12112048_SNP [dm6]	A	T	3.387e^-5	0.825	UTR_3_PRIME Phae2 DOWNSTREAM Phae2	TF binding site mE1_TFBS_cad
2L	7586241	2L_7586241_DEL [dm3] 2L_7586241_DEL [dm6]	GG	G	3.420e^-5	0.825	INTERGENIC
3R	14030411	3R_14030411_SNP [dm3] 3R_18204689_SNP [dm6]	G	A	3.431e^-5	0.825	INTRON CG7985
2L	8809495	2L_8809495_SNP [dm3] 2L_8809495_SNP [dm6]	C	A	3.455e^-5	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	7278969	3R_7278969_SNP [dm3] 3R_11453247_SNP [dm6]	A	G	3.460e^-5	0.825	SYNONYMOUS_CODING PGRP-LB INTRON CG17230	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	718515	3L_718515_SNP [dm3] 3L_718515_SNP [dm6]	A	C	3.491e^-5	0.825	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4120278	3L_4120278_SNP [dm3] 3L_4120278_SNP [dm6]	T	C	3.522e^-5	0.825	INTRON Chd64	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_inv
2R	3008079	2R_3008079_SNP [dm3] 2R_7120574_SNP [dm6]	C	A	3.757e^-5	0.825	SYNONYMOUS_CODING esn
2L	12381038	2L_12381038_SNP [dm3] 2L_12381038_SNP [dm6]	C	G	3.805e^-5	0.825	INTRON bru-2
X	8735244	X_8735244_SNP [dm3] X_8841211_SNP [dm6]	T	G	3.842e^-5	0.825	INTRON CG12075
3R	11857631	3R_11857631_SNP [dm3] 3R_16031909_SNP [dm6]	A	C	3.884e^-5	0.825	INTRON pnr
2R	15895623	2R_15895623_SNP [dm3] 2R_20008118_SNP [dm6]	C	A	3.928e^-5	0.825	DOWNSTREAM CR44628 INTERGENIC
2R	15895632	2R_15895632_SNP [dm3] 2R_20008127_SNP [dm6]	T	G	3.928e^-5	0.825	DOWNSTREAM CR44628 INTERGENIC
2R	17731029	2R_17731029_SNP [dm3] 2R_21843524_SNP [dm6]	A	G	3.957e^-5	0.825	UPSTREAM tRNA:CR30407 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	390335	3L_390335_SNP [dm3] 3L_390335_SNP [dm6]	C	T	4.074e^-5	0.825	INTRON trh
3R	11857221	3R_11857221_SNP [dm3] 3R_16031499_SNP [dm6]	G	T	4.298e^-5	0.825	INTRON pnr
X	3559747	X_3559747_SNP [dm3] X_3665714_SNP [dm6]	A	G	4.361e^-5	0.825	UTR_3_PRIME AstA-R1
X	8160201	X_8160201_SNP [dm3] X_8266168_SNP [dm6]	A	T	4.376e^-5	0.825	SYNONYMOUS_CODING CG1632	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18740415	3R_18740415_INS [dm3] 3R_22914693_INS [dm6]	A	AGGCACA	4.405e^-5	0.825	INTRON klg
3L	3016342	3L_3016342_SNP [dm3] 3L_3016342_SNP [dm6]	A	G	4.468e^-5	0.825	SYNONYMOUS_CODING CG32487 UPSTREAM CG32488
2R	16923351	2R_16923351_DEL [dm3] 2R_21035846_DEL [dm6]	TT	T	4.530e^-5	0.825	INTERGENIC
2R	20889947	2R_20889947_SNP [dm3] 2R_25002424_SNP [dm6]	A	G	4.531e^-5	0.825	SYNONYMOUS_CODING zip
2R	20024436	2R_20024436_SNP [dm3] 2R_24136913_SNP [dm6]	G	A	4.575e^-5	0.825	SYNONYMOUS_CODING CG4065	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	20404418	2L_20404418_SNP [dm3] 2L_20404418_SNP [dm6]	G	A	4.617e^-5	0.825	INTRON CG10947
3R	16295434	3R_16295434_SNP [dm3] 3R_20469712_SNP [dm6]	C	T	4.670e^-5	0.825	INTRON Gfrl
2L	21805871	2L_21805871_SNP [dm3] 2L_21805871_SNP [dm6]	G	C	4.721e^-5	0.825	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	10915166	3R_10915166_SNP [dm3] 3R_15089444_SNP [dm6]	T	C	4.751e^-5	0.825	INTRON CG6966	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	2922161	2L_2922161_SNP [dm3] 2L_2922161_SNP [dm6]	T	A	4.761e^-5	0.825	INTRON lilli

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