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=6.153e^-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
wolba	0.03624
In_2L_t	0.05683
In_3R_P	0.04460

Kruskal-Wallis test

Covariate	χ²	p-value
wolba	5.9024	0.0151
In_2L_t	8.876	0.0118
In_3R_P	7.5843	0.0225

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3530 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	18594107	2R_18594107_SNP [dm3] 2R_22706602_SNP [dm6]	T	C	7.852e^-8	0.11	UPSTREAM Obp58d DOWNSTREAM Obp58b INTRON Obp58c	TF binding site mE1_TFBS_inv
3R	25624104	3R_25624104_SNP [dm3] 3R_29798382_SNP [dm6]	A	G	1.176e^-7	0.11	SYNONYMOUS_CODING CG7837	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	1976285	3R_1976285_INS [dm3] 3R_6150563_INS [dm6]	T	TGGGACT	3.826e^-7	0.239	UTR_3_PRIME CG31559
2R	16614246	2R_16614246_SNP [dm3] 2R_20726741_SNP [dm6]	T	G	6.268e^-7	0.24	INTRON dpr
3R	24099073	3R_24099073_SNP [dm3] 3R_28273351_SNP [dm6]	A	G	6.411e^-7	0.24	INTERGENIC
3L	12157902	3L_12157902_SNP [dm3] 3L_12164802_SNP [dm6]	T	A	8.895e^-7	0.278	UTR_3_PRIME Rh7
2R	6141475	2R_6141475_SNP [dm3] 2R_10253970_SNP [dm6]	G	A	1.097e^-6	0.294	SYNONYMOUS_CODING CG12913	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	3800755	3L_3800755_SNP [dm3] 3L_3800755_SNP [dm6]	T	C	1.439e^-6	0.3	UTR_5_PRIME CG32264 INTRON CG32264	TF binding site mE1_TFBS_cad
3R	7869981	3R_7869981_SNP [dm3] 3R_12044259_SNP [dm6]	T	C	1.440e^-6	0.3	DOWNSTREAM CG14736 INTERGENIC
3L	3800564	3L_3800564_SNP [dm3] 3L_3800564_SNP [dm6]	A	G	1.838e^-6	0.329	UTR_5_PRIME CG32264 INTRON CG32264	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	6571967	3L_6571967_SNP [dm3] 3L_6578867_SNP [dm6]	T	A	1.929e^-6	0.329	INTRON CG18769 & 1 other
3R	12616309	3R_12616309_SNP [dm3] 3R_16790587_SNP [dm6]	G	A	2.148e^-6	0.336	DOWNSTREAM Glut3 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	4585691	3R_4585691_SNP [dm3] 3R_8759969_SNP [dm6]	C	T	2.591e^-6	0.343	INTRON CG11768 & 1 other
3R	7864531	3R_7864531_SNP [dm3] 3R_12038809_SNP [dm6]	A	T	2.653e^-6	0.343	INTERGENIC
3R	14689182	3R_14689182_SNP [dm3] 3R_18863460_SNP [dm6]	A	G	2.744e^-6	0.343	INTERGENIC
3R	7875049	3R_7875049_SNP [dm3] 3R_12049327_SNP [dm6]	A	T	3.774e^-6	0.373	UPSTREAM CG14739 INTERGENIC
3L	10048571	3L_10048571_SNP [dm3] 3L_10055471_SNP [dm6]	A	G	4.057e^-6	0.373	INTRON dpr6
2R	17432382	2R_17432382_DEL [dm3] 2R_21544877_DEL [dm6]	GTTCTAAG	G	4.257e^-6	0.373	INTRON Egfr	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	7864479	3R_7864479_SNP [dm3] 3R_12038757_SNP [dm6]	G	A	4.892e^-6	0.373	INTERGENIC
3R	4588298	3R_4588298_SNP [dm3] 3R_8762576_SNP [dm6]	G	T	5.044e^-6	0.373	INTRON CG11768 & 1 other
2R	19452755	2R_19452755_SNP [dm3] 2R_23565232_SNP [dm6]	T	A	5.079e^-6	0.373	DOWNSTREAM CG30184 INTRON apt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	1977798	3R_1977798_SNP [dm3] 3R_6152076_SNP [dm6]	T	C	5.365e^-6	0.373	INTRON CG31559
3R	4587212	3R_4587212_SNP [dm3] 3R_8761490_SNP [dm6]	G	A	5.383e^-6	0.373	INTRON CG11768 & 1 other
3R	7864521	3R_7864521_SNP [dm3] 3R_12038799_SNP [dm6]	C	G	5.634e^-6	0.373	INTERGENIC
2R	17579695	2R_17579695_SNP [dm3] 2R_21692190_SNP [dm6]	G	A	5.763e^-6	0.373	DOWNSTREAM CngB INTRON Ppcdc & 1 other	TF binding site mE1_TFBS_cad
3R	24103455	3R_24103455_SNP [dm3] 3R_28277733_SNP [dm6]	T	C	5.778e^-6	0.373	INTERGENIC
3R	25030065	3R_25030065_SNP [dm3] 3R_29204343_SNP [dm6]	C	T	5.837e^-6	0.373	UPSTREAM CG14508 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	1830797	3R_1830797_SNP [dm3] 3R_6005075_SNP [dm6]	G	A	6.088e^-6	0.373	SYNONYMOUS_CODING Rm62
3R	7061924	3R_7061924_SNP [dm3] 3R_11236202_SNP [dm6]	T	A	6.194e^-6	0.373	UPSTREAM CG31441 DOWNSTREAM CG17721 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
3R	7864690	3R_7864690_DEL [dm3] 3R_12038968_DEL [dm6]	CCCCAAAAACCGACC...	C	6.361e^-6	0.373	INTERGENIC
2R	15859013	2R_15859013_SNP [dm3] 2R_19971508_SNP [dm6]	C	T	6.549e^-6	0.373	INTERGENIC
3R	13913739	3R_13913739_SNP [dm3] 3R_18088017_SNP [dm6]	T	C	7.047e^-6	0.373	INTERGENIC
3L	9011625	3L_9011625_SNP [dm3] 3L_9018525_SNP [dm6]	A	G	7.134e^-6	0.373	INTRON Doc2	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2L	1025357	2L_1025357_SNP [dm3] 2L_1025357_SNP [dm6]	C	T	7.730e^-6	0.373	DOWNSTREAM CG4375 INTRON IA-2	TF binding site mE1_TFBS_chinmo
3R	17930630	3R_17930630_SNP [dm3] 3R_22104908_SNP [dm6]	T	C	8.172e^-6	0.373	NON_SYNONYMOUS_CODING CG13407 INTRON CG5778
X	8372637	X_8372637_SNP [dm3] X_8478604_SNP [dm6]	G	A	8.232e^-6	0.373	UPSTREAM Cp36 DOWNSTREAM Cp7Fc INTRON CG33223	regulatory region REDfly_CRMs
2R	16155689	2R_16155689_SNP [dm3] 2R_20268184_SNP [dm6]	C	T	8.926e^-6	0.373	SYNONYMOUS_CODING CG8908	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	20108068	2R_20108068_SNP [dm3] 2R_24220545_SNP [dm6]	C	G	9.062e^-6	0.373	INTRON CG30419
3R	3277742	3R_3277742_SNP [dm3] 3R_7452020_SNP [dm6]	T	A	9.085e^-6	0.373	UPSTREAM tRNA:V3b:84Da DOWNSTREAM tRNA:V3b:84Db & 1 other INTERGENIC
3R	4603905	3R_4603905_SNP [dm3] 3R_8778183_SNP [dm6]	A	G	9.132e^-6	0.373	DOWNSTREAM CG33191 INTRON Pif1B & 1 other
2L	936735	2L_936735_SNP [dm3] 2L_936735_SNP [dm6]	A	G	9.145e^-6	0.373	INTRON CG4341
3R	7864459	3R_7864459_DEL [dm3] 3R_12038737_DEL [dm6]	CAGCCCCACC	C	9.203e^-6	0.373	INTERGENIC
2R	19452742	2R_19452742_SNP [dm3] 2R_23565219_SNP [dm6]	T	G	9.359e^-6	0.373	DOWNSTREAM CG30184 INTRON apt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	8372671	X_8372671_SNP [dm3] X_8478638_SNP [dm6]	T	C	1.008e^-5	0.373	UPSTREAM Cp36 DOWNSTREAM Cp7Fc INTRON CG33223	regulatory region REDfly_CRMs
3R	24234813	3R_24234813_SNP [dm3] 3R_28409091_SNP [dm6]	C	G	1.022e^-5	0.373	INTERGENIC
2R	931248	2R_931248_SNP [dm3] 2R_5043743_SNP [dm6]	G	T	1.031e^-5	0.373	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	24103479	3R_24103479_SNP [dm3] 3R_28277757_SNP [dm6]	T	C	1.054e^-5	0.373	INTERGENIC
3R	7870284	3R_7870284_SNP [dm3] 3R_12044562_SNP [dm6]	C	A	1.059e^-5	0.373	INTERGENIC
3R	19908685	3R_19908685_SNP [dm3] 3R_24082963_SNP [dm6]	A	C	1.160e^-5	0.373	INTRON 4EHP
3L	5132760	3L_5132760_SNP [dm3] 3L_5139660_SNP [dm6]	C	T	1.171e^-5	0.373	UTR_5_PRIME CHMP2B UPSTREAM Prpk DOWNSTREAM CG4611 & 1 other	TF binding site BDTNP1_TFBS_dl
3R	4587935	3R_4587935_SNP [dm3] 3R_8762213_SNP [dm6]	C	A	1.171e^-5	0.373	INTRON CG11768 & 1 other
3L	3802875	3L_3802875_SNP [dm3] 3L_3802875_SNP [dm6]	C	G	1.174e^-5	0.373	DOWNSTREAM ntc INTRON CG32264
3L	5132495	3L_5132495_SNP [dm3] 3L_5139395_SNP [dm6]	A	C	1.178e^-5	0.373	UTR_5_PRIME Prpk UPSTREAM CHMP2B DOWNSTREAM CG4611	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	9011594	3L_9011594_SNP [dm3] 3L_9018494_SNP [dm6]	G	A	1.188e^-5	0.373	INTRON Doc2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2R	15859032	2R_15859032_SNP [dm3] 2R_19971527_SNP [dm6]	G	T	1.267e^-5	0.373	INTERGENIC
3R	4573431	3R_4573431_SNP [dm3] 3R_8747709_SNP [dm6]	G	A	1.270e^-5	0.373	UPSTREAM CG8223 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3R	4570763	3R_4570763_SNP [dm3] 3R_8745041_SNP [dm6]	G	A	1.274e^-5	0.373	INTRON CG9801
X	8372626	X_8372626_SNP [dm3] X_8478593_SNP [dm6]	A	G	1.282e^-5	0.373	UPSTREAM Cp36 DOWNSTREAM Cp7Fc INTRON CG33223	regulatory region REDfly_CRMs
3L	3802889	3L_3802889_SNP [dm3] 3L_3802889_SNP [dm6]	G	A	1.311e^-5	0.373	DOWNSTREAM ntc INTRON CG32264
X	8372545	X_8372545_INS [dm3] X_8478512_INS [dm6]	A	AAGCTTCAAA	1.345e^-5	0.373	UPSTREAM Cp36 DOWNSTREAM Cp7Fc INTRON CG33223	regulatory region REDfly_CRMs
3R	7873175	3R_7873175_SNP [dm3] 3R_12047453_SNP [dm6]	T	C	1.348e^-5	0.373	DOWNSTREAM CG14739 INTERGENIC
3L	7013663	3L_7013663_SNP [dm3] 3L_7020563_SNP [dm6]	A	T	1.351e^-5	0.373	INTRON Mp
3R	17184439	3R_17184439_SNP [dm3] 3R_21358717_SNP [dm6]	C	T	1.358e^-5	0.373	UTR_5_PRIME pre-mod_mdg4_-I & 3 others UTR_3_PRIME pre-mod_mdg4_-K & 1 other INTRON mod_mdg4_ & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	12044951	3R_12044951_SNP [dm3] 3R_16219229_SNP [dm6]	A	T	1.437e^-5	0.373	INTERGENIC
3R	15277412	3R_15277412_SNP [dm3] 3R_19451690_SNP [dm6]	A	G	1.444e^-5	0.373	INTRON CG31221
2L	2660905	2L_2660905_SNP [dm3] 2L_2660905_SNP [dm6]	T	G	1.458e^-5	0.373	INTERGENIC
3L	5132481	3L_5132481_SNP [dm3] 3L_5139381_SNP [dm6]	T	C	1.495e^-5	0.373	UTR_5_PRIME Prpk UPSTREAM CHMP2B DOWNSTREAM CG4611	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	19407914	2R_19407914_SNP [dm3] 2R_23520391_SNP [dm6]	G	A	1.568e^-5	0.373	SYNONYMOUS_CODING RabX1
3R	7871772	3R_7871772_DEL [dm3] 3R_12046050_DEL [dm6]	GTGGAACTCCT...	G	1.638e^-5	0.373	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	4589049	3R_4589049_SNP [dm3] 3R_8763327_SNP [dm6]	T	G	1.686e^-5	0.373	INTRON CG11768 & 1 other
3R	7869980	3R_7869980_SNP [dm3] 3R_12044258_SNP [dm6]	G	A	1.711e^-5	0.373	DOWNSTREAM CG14736 INTERGENIC
3R	7864931	3R_7864931_SNP [dm3] 3R_12039209_SNP [dm6]	C	G	1.725e^-5	0.373	INTERGENIC
X	13864391	X_13864391_SNP [dm3] X_13970358_SNP [dm6]	C	T	1.797e^-5	0.373	INTRON mamo
3R	16755540	3R_16755540_SNP [dm3] 3R_20929818_SNP [dm6]	G	A	1.807e^-5	0.373	DOWNSTREAM hdly INTRON CG31191
3L	5132755	3L_5132755_SNP [dm3] 3L_5139655_SNP [dm6]	C	T	1.814e^-5	0.373	START_GAINED CHMP2B UTR_5_PRIME CHMP2B UPSTREAM Prpk DOWNSTREAM CG4611 & 1 other	TF binding site BDTNP1_TFBS_dl
3R	19300763	3R_19300763_SNP [dm3] 3R_23475041_SNP [dm6]	G	A	1.857e^-5	0.373	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3R	733482	3R_733482_SNP [dm3] 3R_4907760_SNP [dm6]	G	A	1.887e^-5	0.373	SYNONYMOUS_CODING Gnf1
3L	5132557	3L_5132557_INS [dm3] 3L_5139457_INS [dm6]	T	TAT	1.927e^-5	0.373	UPSTREAM CHMP2B & 1 other DOWNSTREAM CG4611 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	5883774	3L_5883774_SNP [dm3] 3L_5890674_SNP [dm6]	C	A	1.964e^-5	0.373	INTERGENIC
3R	6113572	3R_6113572_SNP [dm3] 3R_10287850_SNP [dm6]	A	C	1.993e^-5	0.373	INTRON CG43143
3R	1189028	3R_1189028_SNP [dm3] 3R_5363306_SNP [dm6]	C	A	1.994e^-5	0.373	INTRON Cerk
3L	5132527	3L_5132527_SNP [dm3] 3L_5139427_SNP [dm6]	A	G	2.017e^-5	0.373	UPSTREAM CHMP2B & 1 other DOWNSTREAM CG4611 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	22905163	3R_22905163_SNP [dm3] 3R_27079441_SNP [dm6]	C	T	2.033e^-5	0.373	INTRON CG14257	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	6678865	2R_6678865_SNP [dm3] 2R_10791360_SNP [dm6]	A	C	2.040e^-5	0.373	UPSTREAM mthl13 INTRON CG33144
3L	5883845	3L_5883845_SNP [dm3] 3L_5890745_SNP [dm6]	G	C	2.046e^-5	0.373	INTERGENIC
3R	13930771	3R_13930771_SNP [dm3] 3R_18105049_SNP [dm6]	T	A	2.083e^-5	0.373	INTRON sr
3R	12044869	3R_12044869_SNP [dm3] 3R_16219147_SNP [dm6]	G	A	2.110e^-5	0.373	INTERGENIC
3L	7121510	3L_7121510_SNP [dm3] 3L_7128410_SNP [dm6]	G	C	2.150e^-5	0.373	UPSTREAM CG15829 & 1 other DOWNSTREAM BBS1 INTERGENIC
3L	5132545	3L_5132545_SNP [dm3] 3L_5139445_SNP [dm6]	G	A	2.174e^-5	0.373	UPSTREAM CHMP2B & 1 other DOWNSTREAM CG4611 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	1683374	3L_1683374_SNP [dm3] 3L_1683374_SNP [dm6]	G	C	2.182e^-5	0.373	INTRON CG7991
3R	7870534	3R_7870534_SNP [dm3] 3R_12044812_SNP [dm6]	C	A	2.201e^-5	0.373	INTERGENIC
3R	6116239	3R_6116239_SNP [dm3] 3R_10290517_SNP [dm6]	A	C	2.227e^-5	0.373	UPSTREAM CG43143 INTRON CG43143
3L	3907783	3L_3907783_DEL [dm3] 3L_3907783_DEL [dm6]	TT	T	2.267e^-5	0.373	UTR_3_PRIME ida DOWNSTREAM mge
3L	4631088	3L_4631088_SNP [dm3] 3L_4631088_SNP [dm6]	C	T	2.273e^-5	0.373	INTRON axo
3R	26720384	3R_26720384_SNP [dm3] 3R_30894662_SNP [dm6]	C	T	2.313e^-5	0.373	INTRON Cyp4c3	TF binding site mE1_TFBS_HSA
2R	6141545	2R_6141545_SNP [dm3] 2R_10254040_SNP [dm6]	C	T	2.315e^-5	0.373	INTRON CG12913	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	15207504	2L_15207504_SNP [dm3] 2L_15207504_SNP [dm6]	C	G	2.359e^-5	0.373	UPSTREAM CR44196 INTERGENIC
3R	12044890	3R_12044890_SNP [dm3] 3R_16219168_SNP [dm6]	A	G	2.370e^-5	0.373	INTERGENIC
2R	17579888	2R_17579888_SNP [dm3] 2R_21692383_SNP [dm6]	G	A	2.379e^-5	0.373	DOWNSTREAM CngB INTRON Ppcdc & 1 other	TF binding site mE1_TFBS_cad
3R	7870917	3R_7870917_SNP [dm3] 3R_12045195_SNP [dm6]	C	A	2.385e^-5	0.373	INTERGENIC

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By genomic position
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middleLength phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results