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=3.608e^-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

773 significant hits at p-value < 0.001.

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	13731031	3L_13731031_SNP [dm3] 3L_13737931_SNP [dm6]	A	T	1.106e^-8	0.006	INTRON bru-3
3R	16131712	3R_16131712_SNP [dm3] 3R_20305990_SNP [dm6]	T	C	1.564e^-8	0.006	DOWNSTREAM CG4362 INTERGENIC
3R	16131716	3R_16131716_SNP [dm3] 3R_20305994_SNP [dm6]	A	G	1.564e^-8	0.006	DOWNSTREAM CG4362 INTERGENIC	transposable element FlyBase
2R	16944984	2R_16944984_SNP [dm3] 2R_21057479_SNP [dm6]	A	C	2.212e^-8	0.006	UPSTREAM cpa & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
3L	1666516	3L_1666516_SNP [dm3] 3L_1666516_SNP [dm6]	C	G	2.212e^-8	0.006	UTR_3_PRIME CG7974 DOWNSTREAM snoRNA:Me28S-A2634b & 3 others INTRON Uhg7 EXON snoRNA:Me28S-A2634c	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_zfh1
3L	8915057	3L_8915057_SNP [dm3] 3L_8921957_SNP [dm6]	G	T	2.212e^-8	0.006	INTRON Tsp66E
2L	11360287	2L_11360287_SNP [dm3] 2L_11360287_SNP [dm6]	T	G	9.047e^-5	0.828	INTRON salr	regulatory region REDfly_CRMs
3R	16091202	3R_16091202_DEL [dm3] 3R_20265480_DEL [dm6]	GCAG	G	9.047e^-5	0.828	INTRON cic
2R	16388634	2R_16388634_SNP [dm3] 2R_20501129_SNP [dm6]	G	T	1.156e^-4	0.828	INTERGENIC	regulatory region REDfly_CRMs
2R	19668908	2R_19668908_SNP [dm3] 2R_23781385_SNP [dm6]	G	T	1.156e^-4	0.828	INTRON CG9850
3L	13239962	3L_13239962_SNP [dm3] 3L_13246862_SNP [dm6]	G	T	1.156e^-4	0.828	DOWNSTREAM CG32119 INTRON caps
3L	14203099	3L_14203099_SNP [dm3] 3L_14209999_SNP [dm6]	G	A	1.156e^-4	0.828	INTRON nuf
3L	14205740	3L_14205740_SNP [dm3] 3L_14212640_SNP [dm6]	G	T	1.156e^-4	0.828	INTRON nuf	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_run
3L	15505935	3L_15505935_SNP [dm3] 3L_15512835_SNP [dm6]	C	T	1.156e^-4	0.828	SYNONYMOUS_CODING Eip71CD UTR_3_PRIME Eip71CD	TF binding site mE1_TFBS_cad mE1_TFBS_sens mE1_TFBS_Trl
3L	23887033	3L_23887033_SNP [dm3] 3L_23893933_SNP [dm6]	C	G	1.156e^-4	0.828	INTRON CG40470
3L	5881190	3L_5881190_SNP [dm3] 3L_5888090_SNP [dm6]	T	A	1.156e^-4	0.828	INTERGENIC
3L	8914948	3L_8914948_SNP [dm3] 3L_8921848_SNP [dm6]	G	C	1.156e^-4	0.828	INTRON Tsp66E
3R	13010414	3R_13010414_SNP [dm3] 3R_17184692_SNP [dm6]	G	T	1.156e^-4	0.828	INTRON Mur89F
3R	15367170	3R_15367170_SNP [dm3] 3R_19541448_SNP [dm6]	T	G	1.156e^-4	0.828	INTRON Dys
X	20774213	X_20774213_INS [dm3] X_20903186_INS [dm6]	G	GTGTGAGTG	1.156e^-4	0.828	INTRON shakB
X	2169556	X_2169556_SNP [dm3] X_2275523_SNP [dm6]	G	A	1.156e^-4	0.828	UPSTREAM CG2918 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA
X	2180469	X_2180469_SNP [dm3] X_2286436_SNP [dm6]	G	A	1.156e^-4	0.828	INTRON CG2865	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	2180470	X_2180470_DEL [dm3] X_2286437_DEL [dm6]	GAGAA	G	1.156e^-4	0.828	INTRON CG2865	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	2180478	X_2180478_SNP [dm3] X_2286445_SNP [dm6]	A	G	1.156e^-4	0.828	INTRON CG2865	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	8469228	X_8469228_SNP [dm3] X_8575195_SNP [dm6]	T	A	1.156e^-4	0.828	INTRON CG12065	TF binding site BDTNP1_TFBS_dl
2L	17587962	2L_17587962_SNP [dm3] 2L_17587962_SNP [dm6]	A	T	1.356e^-4	0.828	DOWNSTREAM CR44411 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3109409	2L_3109409_DEL [dm3] 2L_3109409_DEL [dm6]	TT	A	1.795e^-4	0.828	UPSTREAM PpD6 INTRON toc	TF binding site mE1_TFBS_inv
2L	7586069	2L_7586069_SNP [dm3] 2L_7586069_SNP [dm6]	A	G	1.795e^-4	0.828	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	8094331	2L_8094331_SNP [dm3] 2L_8094331_SNP [dm6]	A	T	1.795e^-4	0.828	INTRON Bsg	TF binding site BDTNP1_TFBS_twi
2R	10008361	2R_10008361_SNP [dm3] 2R_14120856_SNP [dm6]	C	G	1.795e^-4	0.828	INTRON Prosap	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	18568931	3L_18568931_SNP [dm3] 3L_18575831_SNP [dm6]	T	C	1.795e^-4	0.828	UTR_3_PRIME AstC-R1
3L	18568935	3L_18568935_SNP [dm3] 3L_18575835_SNP [dm6]	T	C	1.795e^-4	0.828	UTR_3_PRIME AstC-R1
2L	3054961	2L_3054961_SNP [dm3] 2L_3054961_SNP [dm6]	T	G	1.891e^-4	0.828	INTRON v_2_k05816
2L	5842018	2L_5842018_SNP [dm3] 2L_5842018_SNP [dm6]	A	T	1.891e^-4	0.828	INTRON TrissinR
2L	5959143	2L_5959143_SNP [dm3] 2L_5959143_SNP [dm6]	G	C	1.891e^-4	0.828	UPSTREAM Vm26Ac DOWNSTREAM Vm26Aa INTERGENIC	TF binding site mE1_TFBS_cad
2L	8165871	2L_8165871_SNP [dm3] 2L_8165871_SNP [dm6]	T	C	1.891e^-4	0.828	INTRON Piezo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	11059627	2R_11059627_SNP [dm3] 2R_15172122_SNP [dm6]	C	A	1.891e^-4	0.828	INTRON igl
2R	13571570	2R_13571570_SNP [dm3] 2R_17684065_SNP [dm6]	A	T	1.891e^-4	0.828	UPSTREAM Sema-1b & 1 other INTRON HPS4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	13571581	2R_13571581_SNP [dm3] 2R_17684076_SNP [dm6]	A	G	1.891e^-4	0.828	UPSTREAM Sema-1b & 1 other INTRON HPS4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	13615952	2R_13615952_SNP [dm3] 2R_17728447_SNP [dm6]	C	G	1.891e^-4	0.828	START_GAINED CG4984 UTR_5_PRIME CG4984 UTR_3_PRIME CG4975 UPSTREAM CG4984
2R	15722324	2R_15722324_SNP [dm3] 2R_19834819_SNP [dm6]	G	C	1.891e^-4	0.828	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	17768719	2R_17768719_SNP [dm3] 2R_21881214_SNP [dm6]	A	G	1.891e^-4	0.828	DOWNSTREAM PpN58A INTRON Fili
2R	6917977	2R_6917977_SNP [dm3] 2R_11030472_SNP [dm6]	C	T	1.891e^-4	0.828	INTRON luna
3L	11018664	3L_11018664_SNP [dm3] 3L_11025564_SNP [dm6]	C	G	1.891e^-4	0.828	NON_SYNONYMOUS_CODING CG32079 DOWNSTREAM Fad2
3L	15271860	3L_15271860_SNP [dm3] 3L_15278760_SNP [dm6]	T	A	1.891e^-4	0.828	INTERGENIC
3L	15271861	3L_15271861_SNP [dm3] 3L_15278761_SNP [dm6]	G	A	1.891e^-4	0.828	INTERGENIC
3L	2925603	3L_2925603_SNP [dm3] 3L_2925603_SNP [dm6]	G	A	1.891e^-4	0.828	INTRON Shab
3L	7826296	3L_7826296_SNP [dm3] 3L_7833196_SNP [dm6]	C	T	1.891e^-4	0.828	UPSTREAM Pdp1 INTRON Pdp1
X	2343523	X_2343523_SNP [dm3] X_2449490_SNP [dm6]	G	C	1.891e^-4	0.828	SYNONYMOUS_CODING z INTRON boi	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2L	10087305	2L_10087305_SNP [dm3] 2L_10087305_SNP [dm6]	G	C	2.423e^-4	0.828	INTRON CG44153	TF binding site mE1_TFBS_chinmo
2L	1035854	2L_1035854_SNP [dm3] 2L_1035854_SNP [dm6]	G	C	2.423e^-4	0.828	INTRON IA-2
2L	1042190	2L_1042190_SNP [dm3] 2L_1042190_SNP [dm6]	G	A	2.423e^-4	0.828	INTRON IA-2
2L	1057068	2L_1057068_SNP [dm3] 2L_1057068_SNP [dm6]	G	A	2.423e^-4	0.828	INTRON S
2L	10795910	2L_10795910_SNP [dm3] 2L_10795910_SNP [dm6]	G	A	2.423e^-4	0.828	INTRON CG31869
2L	13500829	2L_13500829_SNP [dm3] 2L_13500829_SNP [dm6]	G	A	2.423e^-4	0.828	UTR_3_PRIME B4 DOWNSTREAM CG42784	TF binding site mE1_TFBS_bab1
2L	1451515	2L_1451515_SNP [dm3] 2L_1451515_SNP [dm6]	C	A	2.423e^-4	0.828	INTERGENIC
2L	1451524	2L_1451524_SNP [dm3] 2L_1451524_SNP [dm6]	G	T	2.423e^-4	0.828	INTERGENIC
2L	18883415	2L_18883415_SNP [dm3] 2L_18883415_SNP [dm6]	T	A	2.423e^-4	0.828	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	19878032	2L_19878032_SNP [dm3] 2L_19878032_SNP [dm6]	G	C	2.423e^-4	0.828	INTRON sick
2L	2738874	2L_2738874_SNP [dm3] 2L_2738874_SNP [dm6]	C	T	2.423e^-4	0.828	SYNONYMOUS_CODING CG31689
2L	2739781	2L_2739781_SNP [dm3] 2L_2739781_SNP [dm6]	A	T	2.423e^-4	0.828	UTR_3_PRIME CG31689 UPSTREAM Hrs	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4348934	2L_4348934_SNP [dm3] 2L_4348934_SNP [dm6]	A	T	2.423e^-4	0.828	UPSTREAM CR44699 DOWNSTREAM CR44697 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	5936045	2L_5936045_DEL [dm3] 2L_5936045_DEL [dm6]	GTACGCTTTGTTTATTATAA...	G	2.423e^-4	0.828	INTRON dsf	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	6161970	2L_6161970_SNP [dm3] 2L_6161970_SNP [dm6]	G	A	2.423e^-4	0.828	DOWNSTREAM CG13989 INTERGENIC
2L	6760553	2L_6760553_SNP [dm3] 2L_6760553_SNP [dm6]	C	G	2.423e^-4	0.828	SPLICE_SITE_REGION CG11321 UPSTREAM CG11322 INTRON CG11321	TF binding site BDTNP1_TFBS_twi
2L	6760557	2L_6760557_SNP [dm3] 2L_6760557_SNP [dm6]	T	C	2.423e^-4	0.828	SPLICE_SITE_REGION CG11321 UPSTREAM CG11322 INTRON CG11321	TF binding site BDTNP1_TFBS_twi
2L	7752125	2L_7752125_SNP [dm3] 2L_7752125_SNP [dm6]	T	G	2.423e^-4	0.828	DOWNSTREAM CG7203 INTERGENIC
2R	10418162	2R_10418162_SNP [dm3] 2R_14530657_SNP [dm6]	C	T	2.423e^-4	0.828	INTRON ttv
2R	11850232	2R_11850232_SNP [dm3] 2R_15962727_SNP [dm6]	G	A	2.423e^-4	0.828	SYNONYMOUS_CODING Strn-Mlck INTRON Strn-Mlck	TF binding site mE1_TFBS_cad
2R	11850274	2R_11850274_SNP [dm3] 2R_15962769_SNP [dm6]	T	G	2.423e^-4	0.828	SYNONYMOUS_CODING Strn-Mlck INTRON Strn-Mlck	TF binding site mE1_TFBS_cad
2R	11874557	2R_11874557_SNP [dm3] 2R_15987052_SNP [dm6]	T	G	2.423e^-4	0.828	UPSTREAM CR45021 INTRON Strn-Mlck
2R	12044726	2R_12044726_SNP [dm3] 2R_16157221_SNP [dm6]	A	C	2.423e^-4	0.828	DOWNSTREAM CG10734 INTRON lbk	TF binding site BDTNP1_TFBS_prd
2R	12044766	2R_12044766_SNP [dm3] 2R_16157261_SNP [dm6]	C	T	2.423e^-4	0.828	DOWNSTREAM CG10734 INTRON lbk
2R	12044770	2R_12044770_SNP [dm3] 2R_16157265_SNP [dm6]	T	A	2.423e^-4	0.828	DOWNSTREAM CG10734 INTRON lbk
2R	12302067	2R_12302067_SNP [dm3] 2R_16414562_SNP [dm6]	C	T	2.423e^-4	0.828	DOWNSTREAM Menl-2 & 1 other INTRON Sema-2b
2R	12667658	2R_12667658_SNP [dm3] 2R_16780153_SNP [dm6]	T	A	2.423e^-4	0.828	UTR_5_PRIME resilin UPSTREAM resilin	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	14136876	2R_14136876_SNP [dm3] 2R_18249371_SNP [dm6]	T	C	2.423e^-4	0.828	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
2R	14323884	2R_14323884_SNP [dm3] 2R_18436379_SNP [dm6]	C	T	2.423e^-4	0.828	INTRON CG30118	TF binding site BDTNP1_TFBS_dl
2R	14451281	2R_14451281_SNP [dm3] 2R_18563776_SNP [dm6]	A	T	2.423e^-4	0.828	INTRON GEFmeso	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2R	15230138	2R_15230138_SNP [dm3] 2R_19342633_SNP [dm6]	G	C	2.423e^-4	0.828	SYNONYMOUS_CODING CG9975 INTRON Rgk1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
2R	15533323	2R_15533323_SNP [dm3] 2R_19645818_SNP [dm6]	C	T	2.423e^-4	0.828	DOWNSTREAM CG15905 INTERGENIC
2R	15533526	2R_15533526_SNP [dm3] 2R_19646021_SNP [dm6]	G	T	2.423e^-4	0.828	DOWNSTREAM CG15905 INTERGENIC
2R	16388542	2R_16388542_SNP [dm3] 2R_20501037_SNP [dm6]	T	A	2.423e^-4	0.828	INTERGENIC	regulatory region REDfly_CRMs
2R	16388612	2R_16388612_SNP [dm3] 2R_20501107_SNP [dm6]	G	C	2.423e^-4	0.828	INTERGENIC	regulatory region REDfly_CRMs
2R	16388697	2R_16388697_SNP [dm3] 2R_20501192_SNP [dm6]	T	A	2.423e^-4	0.828	INTERGENIC	regulatory region REDfly_CRMs
2R	16440782	2R_16440782_SNP [dm3] 2R_20553277_SNP [dm6]	C	T	2.423e^-4	0.828	INTERGENIC
2R	16440783	2R_16440783_SNP [dm3] 2R_20553278_SNP [dm6]	A	C	2.423e^-4	0.828	INTERGENIC
2R	16577840	2R_16577840_SNP [dm3] 2R_20690335_SNP [dm6]	T	C	2.423e^-4	0.828	INTERGENIC
2R	16804337	2R_16804337_SNP [dm3] 2R_20916832_SNP [dm6]	T	C	2.423e^-4	0.828	UTR_5_PRIME Rx	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	16818156	2R_16818156_SNP [dm3] 2R_20930651_SNP [dm6]	C	G	2.423e^-4	0.828	INTRON Rx
2R	17360161	2R_17360161_SNP [dm3] 2R_21472656_SNP [dm6]	G	A	2.423e^-4	0.828	INTRON Sdc
2R	17360167	2R_17360167_SNP [dm3] 2R_21472662_SNP [dm6]	T	A	2.423e^-4	0.828	INTRON Sdc
2R	17476800	2R_17476800_SNP [dm3] 2R_21589295_SNP [dm6]	T	A	2.423e^-4	0.828	UPSTREAM CG33225 INTERGENIC
2R	17672086	2R_17672086_SNP [dm3] 2R_21784581_SNP [dm6]	T	A	2.423e^-4	0.828	INTERGENIC
2R	18205508	2R_18205508_INS [dm3] 2R_22318003_INS [dm6]	C	CC	2.423e^-4	0.828	UPSTREAM Gp150 DOWNSTREAM CR44756 INTRON Gp150	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2R	18206395	2R_18206395_SNP [dm3] 2R_22318890_SNP [dm6]	C	T	2.423e^-4	0.828	DOWNSTREAM CR44756 INTRON Gp150	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Trl mE1_TFBS_zfh1
2R	18335168	2R_18335168_SNP [dm3] 2R_22447663_SNP [dm6]	C	A	2.423e^-4	0.828	INTERGENIC
2R	19099753	2R_19099753_SNP [dm3] 2R_23212230_SNP [dm6]	G	T	2.423e^-4	0.828	UPSTREAM LS2 INTERGENIC	TF binding site mE1_TFBS_inv
2R	19203190	2R_19203190_SNP [dm3] 2R_23315667_SNP [dm6]	A	G	2.423e^-4	0.828	INTERGENIC
2R	19260654	2R_19260654_SNP [dm3] 2R_23373131_SNP [dm6]	T	C	2.423e^-4	0.828	SYNONYMOUS_CODING Golgin245	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo

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Gene name

RPL32C phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results