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=4.735e^-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	0.06516

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	5.3699	0.0682

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1914 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
X	21280862	X_21280862_INS [dm3] X_21409835_INS [dm6]	G	GG	4.315e^-7	0.809	EXON CR45003
3R	23799951	3R_23799951_SNP [dm3] 3R_27974229_SNP [dm6]	C	G	1.514e^-6	0.917	SYNONYMOUS_CODING betaTub97EF	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5649544	2R_5649544_SNP [dm3] 2R_9762039_SNP [dm6]	T	C	2.097e^-6	0.917	SPLICE_SITE_REGION trpl INTRON trpl	TF binding site mE1_TFBS_cad
3R	23494766	3R_23494766_SNP [dm3] 3R_27669044_SNP [dm6]	G	A	2.739e^-6	0.917	SYNONYMOUS_CODING unc80	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	21280854	X_21280854_SNP [dm3] X_21409827_SNP [dm6]	T	C	3.199e^-6	0.917	EXON CR45003
3R	10171644	3R_10171644_SNP [dm3] 3R_14345922_SNP [dm6]	C	A	4.107e^-6	0.917	INTRON NK7.1
3R	10409395	3R_10409395_SNP [dm3] 3R_14583673_SNP [dm6]	T	C	4.891e^-6	0.917	INTRON stumps
2L	12281930	2L_12281930_SNP [dm3] 2L_12281930_SNP [dm6]	T	C	5.277e^-6	0.917	INTRON aret
3L	683252	3L_683252_SNP [dm3] 3L_683252_SNP [dm6]	G	T	6.255e^-6	0.917	SYNONYMOUS_CODING ebd1 UPSTREAM CG3386	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	6968839	2L_6968839_SNP [dm3] 2L_6968839_SNP [dm6]	G	A	7.223e^-6	0.917	UTR_3_PRIME snRNP-U1-70K DOWNSTREAM snRNP-U1-70K	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	21902872	X_21902872_SNP [dm3] X_22501036_SNP [dm6]	T	A	7.578e^-6	0.917	NON_SYNONYMOUS_CODING l_1_G0196 INTRON l_1_G0196
2L	7495110	2L_7495110_SNP [dm3] 2L_7495110_SNP [dm6]	A	C	7.601e^-6	0.917	INTRON Ziz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	16955833	2L_16955833_SNP [dm3] 2L_16955833_SNP [dm6]	T	G	7.968e^-6	0.917	INTERGENIC
2R	16549085	2R_16549085_SNP [dm3] 2R_20661580_SNP [dm6]	C	G	8.409e^-6	0.917	UPSTREAM CG13437 DOWNSTREAM Lrt & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
3R	17941991	3R_17941991_SNP [dm3] 3R_22116269_SNP [dm6]	A	G	8.435e^-6	0.917	SYNONYMOUS_CODING Ir94b
2L	6965613	2L_6965613_SNP [dm3] 2L_6965613_SNP [dm6]	G	A	9.171e^-6	0.917	SYNONYMOUS_CODING Coprox	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	21280957	X_21280957_SNP [dm3] X_21409930_SNP [dm6]	T	C	1.051e^-5	0.917	SPLICE_SITE_REGION CR45003 EXON CR45003
2L	6969567	2L_6969567_SNP [dm3] 2L_6969567_SNP [dm6]	C	A	1.075e^-5	0.917	UTR_3_PRIME snRNP-U1-70K DOWNSTREAM snRNP-U1-70K	TF binding site mE1_TFBS_sens
2L	6968350	2L_6968350_SNP [dm3] 2L_6968350_SNP [dm6]	G	A	1.080e^-5	0.917	UPSTREAM smt3 DOWNSTREAM snRNP-U1-70K INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx
2L	8989513	2L_8989513_SNP [dm3] 2L_8989513_SNP [dm6]	G	C	1.114e^-5	0.917	UTR_5_PRIME rost UPSTREAM rost
3L	19524744	3L_19524744_SNP [dm3] 3L_19531644_SNP [dm6]	A	T	1.180e^-5	0.917	INTERGENIC
3L	13385094	3L_13385094_SNP [dm3] 3L_13391994_SNP [dm6]	C	G	1.191e^-5	0.917	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	16880183	3R_16880183_SNP [dm3] 3R_21054461_SNP [dm6]	A	G	1.226e^-5	0.917	DOWNSTREAM Mvl INTRON Mvl	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	23003397	3R_23003397_SNP [dm3] 3R_27177675_SNP [dm6]	C	A	1.270e^-5	0.917	INTRON Ser	TF binding site mE1_TFBS_cad
X	3731271	X_3731271_SNP [dm3] X_3837238_SNP [dm6]	T	C	1.345e^-5	0.917	INTRON ec	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	11659510	X_11659510_SNP [dm3] X_11765477_SNP [dm6]	C	G	1.361e^-5	0.917	UPSTREAM CG9360 INTRON m	TF binding site mE1_TFBS_cnc
X	21282846	X_21282846_SNP [dm3] X_21411819_SNP [dm6]	G	C	1.406e^-5	0.917	INTERGENIC
2R	17396974	2R_17396974_SNP [dm3] 2R_21509469_SNP [dm6]	G	A	1.474e^-5	0.917	INTRON MESK2
X	14757014	X_14757014_SNP [dm3] X_14862981_SNP [dm6]	T	G	1.677e^-5	0.917	DOWNSTREAM CG9518 INTRON Flo2
3R	19901238	3R_19901238_SNP [dm3] 3R_24075516_SNP [dm6]	C	A	1.682e^-5	0.917	INTRON 4EHP
3L	13365418	3L_13365418_SNP [dm3] 3L_13372318_SNP [dm6]	G	A	1.713e^-5	0.917	INTERGENIC
2L	7498096	2L_7498096_SNP [dm3] 2L_7498096_SNP [dm6]	A	T	1.728e^-5	0.917	UTR_3_PRIME RapGAP1 UPSTREAM Obp28a
3L	683279	3L_683279_SNP [dm3] 3L_683279_SNP [dm6]	C	G	1.767e^-5	0.917	NON_SYNONYMOUS_CODING ebd1 UPSTREAM CG3386	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	7373651	2L_7373651_DEL [dm3] 2L_7373651_DEL [dm6]	GAGATCGGG	G	1.782e^-5	0.917	INTRON Wnt10	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3292704	3L_3292704_SNP [dm3] 3L_3292704_SNP [dm6]	G	A	1.868e^-5	0.917	INTRON CG12009
2L	549912	2L_549912_SNP [dm3] 2L_549912_SNP [dm6]	T	C	1.921e^-5	0.917	UPSTREAM Ets21C INTRON Ets21C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	23003428	3R_23003428_SNP [dm3] 3R_27177706_SNP [dm6]	A	C	1.933e^-5	0.917	INTRON Ser	TF binding site mE1_TFBS_cad
3L	22540042	3L_22540042_SNP [dm3] 3L_22546942_SNP [dm6]	T	A	1.935e^-5	0.917	INTERGENIC
X	14757015	X_14757015_SNP [dm3] X_14862982_SNP [dm6]	T	C	1.979e^-5	0.917	DOWNSTREAM CG9518 INTRON Flo2
3R	23494660	3R_23494660_SNP [dm3] 3R_27668938_SNP [dm6]	C	T	1.985e^-5	0.917	INTRON unc80	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	4565614	3L_4565614_SNP [dm3] 3L_4565614_SNP [dm6]	A	G	2.005e^-5	0.917	INTRON CG42540	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	10413110	3R_10413110_INS [dm3] 3R_14587388_INS [dm6]	T	TAATGT	2.210e^-5	0.933	INTRON stumps	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	21280814	X_21280814_SNP [dm3] X_21409787_SNP [dm6]	A	G	2.353e^-5	0.933	EXON CR45003
3R	26713324	3R_26713324_SNP [dm3] 3R_30887602_SNP [dm6]	T	A	2.415e^-5	0.933	INTRON Sap-r
3R	25624104	3R_25624104_SNP [dm3] 3R_29798382_SNP [dm6]	A	G	2.415e^-5	0.933	SYNONYMOUS_CODING CG7837	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8347780	2L_8347780_SNP [dm3] 2L_8347780_SNP [dm6]	G	T	2.434e^-5	0.933	INTRON CG7778
3L	12157902	3L_12157902_SNP [dm3] 3L_12164802_SNP [dm6]	T	A	2.537e^-5	0.933	UTR_3_PRIME Rh7
2R	5663854	2R_5663854_DEL [dm3] 2R_9776349_DEL [dm6]	ATAATAATTTTCTA...	A	2.551e^-5	0.933	INTRON CG1688 EXON CR44207
3R	10172068	3R_10172068_SNP [dm3] 3R_14346346_SNP [dm6]	A	G	2.563e^-5	0.933	INTRON NK7.1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14278150	2L_14278150_SNP [dm3] 2L_14278150_SNP [dm6]	A	T	2.564e^-5	0.933	DOWNSTREAM CG32971 INTRON wb
3R	26729549	3R_26729549_SNP [dm3] 3R_30903827_SNP [dm6]	G	A	2.623e^-5	0.933	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	17658807	X_17658807_SNP [dm3] X_17764774_SNP [dm6]	C	G	2.634e^-5	0.933	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	22055432	X_22055432_SNP [dm3] X_22653596_SNP [dm6]	C	G	2.635e^-5	0.933	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19524747	3L_19524747_SNP [dm3] 3L_19531647_SNP [dm6]	G	A	2.698e^-5	0.937	INTERGENIC
3R	19964611	3R_19964611_SNP [dm3] 3R_24138889_SNP [dm6]	C	A	2.813e^-5	0.94	INTRON Npc2f	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	17943965	3R_17943965_SNP [dm3] 3R_22118243_SNP [dm6]	G	A	2.879e^-5	0.94	SYNONYMOUS_CODING Ir94c UPSTREAM Ir94b
2L	13081656	2L_13081656_SNP [dm3] 2L_13081656_SNP [dm6]	T	G	2.917e^-5	0.94	INTERGENIC
3R	23003416	3R_23003416_DEL [dm3] 3R_27177694_DEL [dm6]	ATA	A	2.961e^-5	0.94	INTRON Ser	TF binding site mE1_TFBS_cad
3R	23003431	3R_23003431_SNP [dm3] 3R_27177709_SNP [dm6]	T	G	2.961e^-5	0.94	INTRON Ser	TF binding site mE1_TFBS_cad
X	19099065	X_19099065_SNP [dm3] X_19205032_SNP [dm6]	G	A	3.101e^-5	0.94	INTRON Ulp1
3R	23003446	3R_23003446_SNP [dm3] 3R_27177724_SNP [dm6]	A	T	3.269e^-5	0.94	INTRON Ser	TF binding site mE1_TFBS_cad
2L	777869	2L_777869_SNP [dm3] 2L_777869_SNP [dm6]	C	T	3.277e^-5	0.94	DOWNSTREAM CG13946 INTERGENIC
3R	20493348	3R_20493348_SNP [dm3] 3R_24667626_SNP [dm6]	C	T	3.523e^-5	0.94	UPSTREAM slo INTRON slo	regulatory region REDfly_CRMs
3L	3800564	3L_3800564_SNP [dm3] 3L_3800564_SNP [dm6]	A	G	3.534e^-5	0.94	UTR_5_PRIME CG32264 INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10172974	3R_10172974_INS [dm3] 3R_14347252_INS [dm6]	G	GAG	3.556e^-5	0.94	INTRON NK7.1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	6965902	2L_6965902_SNP [dm3] 2L_6965902_SNP [dm6]	A	T	3.604e^-5	0.94	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	7453397	2L_7453397_SNP [dm3] 2L_7453397_SNP [dm6]	G	T	3.653e^-5	0.94	INTRON Gr28a
3L	3907783	3L_3907783_DEL [dm3] 3L_3907783_DEL [dm6]	TT	T	3.696e^-5	0.94	UTR_3_PRIME ida DOWNSTREAM mge
3R	21033739	3R_21033739_SNP [dm3] 3R_25208017_SNP [dm6]	G	A	3.706e^-5	0.94	INTRON CG13654 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	2105746	3L_2105746_SNP [dm3] 3L_2105746_SNP [dm6]	A	G	3.758e^-5	0.94	SYNONYMOUS_CODING sls	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	18781527	3L_18781527_SNP [dm3] 3L_18788427_SNP [dm6]	C	T	3.782e^-5	0.94	INTRON ftz-f1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	22540043	3L_22540043_SNP [dm3] 3L_22546943_SNP [dm6]	C	T	3.899e^-5	0.94	INTERGENIC
3R	26723629	3R_26723629_SNP [dm3] 3R_30897907_SNP [dm6]	C	G	3.899e^-5	0.94	NON_SYNONYMOUS_CODING Cyp4c3
3R	10492726	3R_10492726_SNP [dm3] 3R_14667004_SNP [dm6]	A	G	3.944e^-5	0.94	SYNONYMOUS_CODING Meltrin DOWNSTREAM Meltrin	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	21126037	3R_21126037_SNP [dm3] 3R_25300315_SNP [dm6]	G	T	3.959e^-5	0.94	UPSTREAM CG31288 & 1 other INTERGENIC
3L	15391612	3L_15391612_SNP [dm3] 3L_15398512_SNP [dm6]	A	G	3.977e^-5	0.94	INTERGENIC
3R	17943956	3R_17943956_SNP [dm3] 3R_22118234_SNP [dm6]	C	T	4.006e^-5	0.94	SYNONYMOUS_CODING Ir94c UPSTREAM Ir94b
3L	16605774	3L_16605774_SNP [dm3] 3L_16612674_SNP [dm6]	G	T	4.116e^-5	0.94	SYNONYMOUS_CODING CG4101 UPSTREAM Su_P_ DOWNSTREAM Mo25	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med
X	22055499	X_22055499_SNP [dm3] X_22653663_SNP [dm6]	A	C	4.124e^-5	0.94	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23263751	3R_23263751_SNP [dm3] 3R_27438029_SNP [dm6]	G	A	4.208e^-5	0.94	UPSTREAM side DOWNSTREAM CG44290 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	19347489	3L_19347489_SNP [dm3] 3L_19354389_SNP [dm6]	G	T	4.259e^-5	0.94	INTRON CG32206
3R	23003425	3R_23003425_SNP [dm3] 3R_27177703_SNP [dm6]	T	C	4.440e^-5	0.94	INTRON Ser	TF binding site mE1_TFBS_cad
X	8714909	X_8714909_DEL [dm3] X_8820876_DEL [dm6]	CC	C	4.503e^-5	0.94	INTERGENIC
2R	16023742	2R_16023742_SNP [dm3] 2R_20136237_SNP [dm6]	G	C	4.694e^-5	0.94	DOWNSTREAM CR44634 INTERGENIC
3L	682872	3L_682872_SNP [dm3] 3L_682872_SNP [dm6]	T	A	4.703e^-5	0.94	UPSTREAM CG3386 DOWNSTREAM ebd1 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	12021444	X_12021444_SNP [dm3] X_12127411_SNP [dm6]	G	A	4.723e^-5	0.94	UPSTREAM Ten-a INTRON Ten-a
3R	17031798	3R_17031798_DEL [dm3] 3R_21206076_DEL [dm6]	GGAGTTGTATAATATATGTC...	T	4.745e^-5	0.94	INTRON SNF4Agamma	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	19901147	3R_19901147_SNP [dm3] 3R_24075425_SNP [dm6]	G	A	4.879e^-5	0.94	INTRON 4EHP
2R	13074576	2R_13074576_SNP [dm3] 2R_17187071_SNP [dm6]	C	A	4.894e^-5	0.94	DOWNSTREAM CR44388 INTERGENIC	TF binding site BDTNP1_TFBS_z
X	13809632	X_13809632_SNP [dm3] X_13915599_SNP [dm6]	T	C	4.961e^-5	0.94	INTRON mamo
3R	23799635	3R_23799635_SNP [dm3] 3R_27973913_SNP [dm6]	C	T	4.986e^-5	0.94	INTRON betaTub97EF
2L	12153175	2L_12153175_SNP [dm3] 2L_12153175_SNP [dm6]	A	G	5.050e^-5	0.94	INTRON CG31760
3R	10997129	3R_10997129_SNP [dm3] 3R_15171407_SNP [dm6]	T	G	5.067e^-5	0.94	INTRON Gyc88E & 1 other
X	21280848	X_21280848_SNP [dm3] X_21409821_SNP [dm6]	G	A	5.076e^-5	0.94	EXON CR45003
3R	18252843	3R_18252843_SNP [dm3] 3R_22427121_SNP [dm6]	A	G	5.128e^-5	0.94	SYNONYMOUS_CODING CG13847	TF binding site mE1_TFBS_chinmo
3L	18866643	3L_18866643_SNP [dm3] 3L_18873543_SNP [dm6]	C	T	5.170e^-5	0.94	SYNONYMOUS_CODING Ugt UPSTREAM Rad9	TF binding site mE1_TFBS_sens
2R	2709554	2R_2709554_SNP [dm3] 2R_6822049_SNP [dm6]	T	A	5.189e^-5	0.94	EXON CR44442
2L	6965897	2L_6965897_SNP [dm3] 2L_6965897_SNP [dm6]	G	A	5.307e^-5	0.94	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	106859	2L_106859_SNP [dm3] 2L_106859_SNP [dm6]	A	G	5.379e^-5	0.94	UPSTREAM Sam-S & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
X	3860164	X_3860164_SNP [dm3] X_3966131_SNP [dm6]	A	G	5.399e^-5	0.94	SYNONYMOUS_CODING CG6428 UPSTREAM lva	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens

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By genomic position
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totalLength phenotype

Phenotype distribution and association to known covariates

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GWAS results