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=3.055e^-4)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT 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

1727 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
3R	25245877	3R_25245877_DEL [dm3] 3R_29420155_DEL [dm6]	CTAAGCCCCAACTGACCAGC...	C	2.132e^-6	0.961	INTRON Ptp99A
3R	8433240	3R_8433240_SNP [dm3] 3R_12607518_SNP [dm6]	T	A	3.889e^-6	0.961	INTERGENIC
2R	14356798	2R_14356798_SNP [dm3] 2R_18469293_SNP [dm6]	C	T	6.111e^-6	0.961	INTRON CG30116	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	6225017	2R_6225017_SNP [dm3] 2R_10337512_SNP [dm6]	A	G	6.653e^-6	0.961	INTRON CG42732
3R	13043200	3R_13043200_SNP [dm3] 3R_17217478_SNP [dm6]	C	A	6.880e^-6	0.961	NON_SYNONYMOUS_CODING CG31262 UTR_3_PRIME CG31262	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	13676132	2L_13676132_SNP [dm3] 2L_13676132_SNP [dm6]	C	G	8.013e^-6	0.961	DOWNSTREAM CG31814 INTERGENIC
3L	1994648	3L_1994648_SNP [dm3] 3L_1994648_SNP [dm6]	A	T	9.454e^-6	0.961	INTERGENIC
2L	8664332	2L_8664332_SNP [dm3] 2L_8664332_SNP [dm6]	C	T	1.042e^-5	0.961	INTRON Sema-1a	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	18442505	2L_18442505_SNP [dm3] 2L_18442505_SNP [dm6]	T	A	1.049e^-5	0.961	SPLICE_SITE_REGION RpS26 UTR_3_PRIME RpS26 DOWNSTREAM RpS26	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	3418927	2L_3418927_SNP [dm3] 2L_3418927_SNP [dm6]	A	G	1.312e^-5	0.961	DOWNSTREAM CG31952 INTRON pgant2
2L	8664297	2L_8664297_SNP [dm3] 2L_8664297_SNP [dm6]	G	A	1.397e^-5	0.961	INTRON Sema-1a	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	8664347	2L_8664347_SNP [dm3] 2L_8664347_SNP [dm6]	T	C	1.397e^-5	0.961	INTRON Sema-1a	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	4662176	3R_4662176_SNP [dm3] 3R_8836454_SNP [dm6]	C	A	1.426e^-5	0.961	UTR_3_PRIME pyd INTRON pyd	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11447766	3L_11447766_SNP [dm3] 3L_11454666_SNP [dm6]	A	G	1.452e^-5	0.961	INTERGENIC
2L	18595778	2L_18595778_SNP [dm3] 2L_18595778_SNP [dm6]	C	T	1.595e^-5	0.961	DOWNSTREAM amos & 1 other INTERGENIC	regulatory region REDfly_CRMs
3L	8306711	3L_8306711_SNP [dm3] 3L_8313611_SNP [dm6]	A	C	1.626e^-5	0.961	INTRON CG7185
2R	17205839	2R_17205839_SNP [dm3] 2R_21318334_SNP [dm6]	G	A	1.888e^-5	0.961	SYNONYMOUS_CODING CG9485 UTR_3_PRIME CG33655
2L	11374401	2L_11374401_SNP [dm3] 2L_11374401_SNP [dm6]	C	T	1.969e^-5	0.961	DOWNSTREAM salr INTERGENIC
3R	25551240	3R_25551240_SNP [dm3] 3R_29725518_SNP [dm6]	A	G	2.012e^-5	0.961	SYNONYMOUS_CODING CG18731 UPSTREAM Kul & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	5527510	2R_5527510_SNP [dm3] 2R_9640005_SNP [dm6]	A	C	2.044e^-5	0.961	INTRON Mmp2
3L	5081051	3L_5081051_SNP [dm3] 3L_5081051_SNP [dm6]	C	G	2.121e^-5	0.961	INTERGENIC
3R	26881526	3R_26881526_SNP [dm3] 3R_31055804_SNP [dm6]	G	A	2.161e^-5	0.961	UTR_3_PRIME dco
2L	7221502	2L_7221502_SNP [dm3] 2L_7221502_SNP [dm6]	C	T	2.293e^-5	0.961	SYNONYMOUS_CODING ico DOWNSTREAM CR44989	TF binding site mE1_TFBS_sens
3L	5081101	3L_5081101_SNP [dm3] 3L_5081101_SNP [dm6]	A	T	2.350e^-5	0.961	INTERGENIC
2L	8812848	2L_8812848_SNP [dm3] 2L_8812848_SNP [dm6]	T	C	2.446e^-5	0.961	INTERGENIC	TF binding site mE1_TFBS_cad
3L	18630544	3L_18630544_SNP [dm3] 3L_18637444_SNP [dm6]	A	G	2.457e^-5	0.961	INTRON MYPT-75D
2L	16767626	2L_16767626_SNP [dm3] 2L_16767626_SNP [dm6]	T	A	2.543e^-5	0.961	UPSTREAM Mhc INTRON Mhc	regulatory region REDfly_CRMs
3R	25551481	3R_25551481_SNP [dm3] 3R_29725759_SNP [dm6]	A	G	2.738e^-5	0.961	UPSTREAM Kul & 1 other DOWNSTREAM CG18731 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	14416349	2R_14416349_SNP [dm3] 2R_18528844_SNP [dm6]	C	T	2.751e^-5	0.961	INTRON CG10924	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15232622	3R_15232622_SNP [dm3] 3R_19406900_SNP [dm6]	C	A	2.802e^-5	0.961	DOWNSTREAM CG5316 INTERGENIC
2R	16678770	2R_16678770_SNP [dm3] 2R_20791265_SNP [dm6]	G	A	2.884e^-5	0.961	UPSTREAM CG43677 DOWNSTREAM CG43668 INTERGENIC
2R	15823956	2R_15823956_SNP [dm3] 2R_19936451_SNP [dm6]	C	G	2.893e^-5	0.961	INTERGENIC
3L	5081021	3L_5081021_SNP [dm3] 3L_5081021_SNP [dm6]	A	G	2.944e^-5	0.961	INTERGENIC
3L	5122688	3L_5122688_SNP [dm3] 3L_5129588_SNP [dm6]	T	A	2.977e^-5	0.961	UPSTREAM CG4597 INTERGENIC
3L	5122699	3L_5122699_SNP [dm3] 3L_5129599_SNP [dm6]	C	T	2.977e^-5	0.961	UPSTREAM CG4597 INTERGENIC
X	12153632	X_12153632_SNP [dm3] X_12259599_SNP [dm6]	G	A	3.181e^-5	0.961	INTRON Ten-a
3L	6845479	3L_6845479_SNP [dm3] 3L_6852379_SNP [dm6]	T	C	3.402e^-5	0.961	INTERGENIC
3L	18853052	3L_18853052_SNP [dm3] 3L_18859952_SNP [dm6]	T	A	3.456e^-5	0.961	INTERGENIC
3L	5081072	3L_5081072_SNP [dm3] 3L_5081072_SNP [dm6]	C	A	3.462e^-5	0.961	INTERGENIC
3L	5081078	3L_5081078_MNP [dm3] 3L_5081078_MNP [dm6]	AAA	TTT	3.462e^-5	0.961	INTERGENIC
3L	5081082	3L_5081082_SNP [dm3] 3L_5081082_SNP [dm6]	C	T	3.462e^-5	0.961	INTERGENIC
2R	18791145	2R_18791145_SNP [dm3] 2R_22903622_SNP [dm6]	C	T	3.479e^-5	0.961	INTRON nahoda
3L	11407683	3L_11407683_SNP [dm3] 3L_11414583_SNP [dm6]	A	T	3.502e^-5	0.961	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16952522	2R_16952522_SNP [dm3] 2R_21065017_SNP [dm6]	G	T	3.535e^-5	0.961	UPSTREAM Cht12 DOWNSTREAM Cht4 INTERGENIC
3R	18630980	3R_18630980_SNP [dm3] 3R_22805258_SNP [dm6]	G	A	3.793e^-5	0.961	NON_SYNONYMOUS_CODING CG7031	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11557426	3L_11557426_SNP [dm3] 3L_11564326_SNP [dm6]	A	C	3.810e^-5	0.961	UPSTREAM CG33267 DOWNSTREAM CG7394 INTERGENIC
X	16961209	X_16961209_SNP [dm3] X_17067176_SNP [dm6]	A	T	3.894e^-5	0.961	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
3L	5912106	3L_5912106_SNP [dm3] 3L_5919006_SNP [dm6]	A	G	3.948e^-5	0.961	INTRON CG10483 EXON CR45167
3L	1416962	3L_1416962_SNP [dm3] 3L_1416962_SNP [dm6]	T	C	4.020e^-5	0.961	SYNONYMOUS_CODING FucTD INTRON Ptp61F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	1416974	3L_1416974_SNP [dm3] 3L_1416974_SNP [dm6]	C	A	4.020e^-5	0.961	SYNONYMOUS_CODING FucTD INTRON Ptp61F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	3100617	X_3100617_SNP [dm3] X_3206584_SNP [dm6]	T	A	4.030e^-5	0.961	INTRON dnc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14420145	2R_14420145_SNP [dm3] 2R_18532640_SNP [dm6]	C	T	4.043e^-5	0.961	INTRON CG10924	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	14420147	2R_14420147_SNP [dm3] 2R_18532642_SNP [dm6]	A	T	4.043e^-5	0.961	INTRON CG10924	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15819305	2R_15819305_SNP [dm3] 2R_19931800_SNP [dm6]	C	T	4.065e^-5	0.961	INTERGENIC
3L	12054994	3L_12054994_SNP [dm3] 3L_12061894_SNP [dm6]	C	T	4.203e^-5	0.961	SYNONYMOUS_CODING rols	TF binding site mE1_TFBS_cad
X	3100622	X_3100622_SNP [dm3] X_3206589_SNP [dm6]	A	T	4.568e^-5	0.961	INTRON dnc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11131199	3L_11131199_SNP [dm3] 3L_11138099_SNP [dm6]	A	G	4.607e^-5	0.961	INTRON CG32082
2L	9493003	2L_9493003_SNP [dm3] 2L_9493003_SNP [dm6]	G	A	4.630e^-5	0.961	SYNONYMOUS_CODING Gdi	TF binding site mE1_TFBS_cad
2R	15817219	2R_15817219_SNP [dm3] 2R_19929714_SNP [dm6]	C	A	4.686e^-5	0.961	INTERGENIC
2R	11703045	2R_11703045_SNP [dm3] 2R_15815540_SNP [dm6]	A	T	4.730e^-5	0.961	UPSTREAM Zasp52 INTRON tun & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	4094648	3L_4094648_SNP [dm3] 3L_4094648_SNP [dm6]	T	A	4.749e^-5	0.961	UTR_3_PRIME CG14995 DOWNSTREAM CG14990
3L	5081066	3L_5081066_SNP [dm3] 3L_5081066_SNP [dm6]	C	G	4.820e^-5	0.961	INTERGENIC
3L	8458011	3L_8458011_SNP [dm3] 3L_8464911_SNP [dm6]	T	C	4.903e^-5	0.961	SYNONYMOUS_CODING Gug	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	4661845	3L_4661845_INS [dm3] 3L_4661845_INS [dm6]	C	CC	4.926e^-5	0.961	INTRON axo
3L	14366814	3L_14366814_SNP [dm3] 3L_14373714_SNP [dm6]	C	T	4.927e^-5	0.961	INTERGENIC
X	16961245	X_16961245_SNP [dm3] X_17067212_SNP [dm6]	A	T	5.058e^-5	0.961	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
3L	18854045	3L_18854045_SNP [dm3] 3L_18860945_SNP [dm6]	G	C	5.062e^-5	0.961	UPSTREAM mir-315 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	6220781	2R_6220781_SNP [dm3] 2R_10333276_SNP [dm6]	A	G	5.121e^-5	0.961	INTRON CG42732
2R	15823928	2R_15823928_SNP [dm3] 2R_19936423_SNP [dm6]	C	T	5.206e^-5	0.961	INTERGENIC
3L	5081089	3L_5081089_SNP [dm3] 3L_5081089_SNP [dm6]	A	T	5.227e^-5	0.961	INTERGENIC
3R	27100952	3R_27100952_SNP [dm3] 3R_31275230_SNP [dm6]	C	A	5.245e^-5	0.961	INTERGENIC
2R	7532866	2R_7532866_SNP [dm3] 2R_11645361_SNP [dm6]	G	T	5.294e^-5	0.961	INTRON CG9003	TF binding site BDTNP1_TFBS_dl
3L	6845484	3L_6845484_SNP [dm3] 3L_6852384_SNP [dm6]	A	T	5.326e^-5	0.961	INTERGENIC
2L	7005341	2L_7005341_SNP [dm3] 2L_7005341_SNP [dm6]	A	C	5.360e^-5	0.961	INTRON uif
3R	14634152	3R_14634152_SNP [dm3] 3R_18808430_SNP [dm6]	C	G	5.390e^-5	0.961	INTRON CG18208
2L	11966881	2L_11966881_SNP [dm3] 2L_11966881_SNP [dm6]	G	A	5.597e^-5	0.961	INTRON CR43314
2L	8664271	2L_8664271_SNP [dm3] 2L_8664271_SNP [dm6]	T	A	5.680e^-5	0.961	INTRON Sema-1a	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	7023568	3L_7023568_SNP [dm3] 3L_7030468_SNP [dm6]	A	C	5.815e^-5	0.961	INTRON Mp
2R	17396979	2R_17396979_SNP [dm3] 2R_21509474_SNP [dm6]	T	C	5.913e^-5	0.961	INTRON MESK2
3L	11131251	3L_11131251_DEL [dm3] 3L_11138151_DEL [dm6]	TTTGGTTTG	T	6.046e^-5	0.961	INTRON CG32082
3L	11131262	3L_11131262_SNP [dm3] 3L_11138162_SNP [dm6]	T	A	6.046e^-5	0.961	INTRON CG32082
3L	5130096	3L_5130096_SNP [dm3] 3L_5136996_SNP [dm6]	A	G	6.223e^-5	0.961	SYNONYMOUS_CODING CG4611 UPSTREAM CG10674 DOWNSTREAM CR45160	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	17039531	3R_17039531_SNP [dm3] 3R_21213809_SNP [dm6]	C	A	6.250e^-5	0.961	UTR_3_PRIME SNF4Agamma	TF binding site BDTNP1_TFBS_dl
2R	5524192	2R_5524192_SNP [dm3] 2R_9636687_SNP [dm6]	C	G	6.261e^-5	0.961	DOWNSTREAM CR44070 INTRON Mmp2
3R	18266037	3R_18266037_SNP [dm3] 3R_22440315_SNP [dm6]	C	T	6.660e^-5	0.961	NON_SYNONYMOUS_CODING CG12499	TF binding site mE1_TFBS_cad
2R	18923662	2R_18923662_SNP [dm3] 2R_23036139_SNP [dm6]	T	C	6.730e^-5	0.961	INTRON twi & 1 other	TF binding site mE1_TFBS_inv
3R	25245831	3R_25245831_DEL [dm3] 3R_29420109_DEL [dm6]	AGCTTTCTTT	A	6.763e^-5	0.961	INTRON Ptp99A
3L	11131203	3L_11131203_SNP [dm3] 3L_11138103_SNP [dm6]	G	T	6.795e^-5	0.961	INTRON CG32082
X	9074311	X_9074311_SNP [dm3] X_9180278_SNP [dm6]	G	T	6.829e^-5	0.961	UTR_3_PRIME mei-P26
3R	26440609	3R_26440609_SNP [dm3] 3R_30614887_SNP [dm6]	C	T	6.845e^-5	0.961	EXON CR45571
3R	25532787	3R_25532787_INS [dm3] 3R_29707065_INS [dm6]	T	TAGCCAAGCTAAACAT...	6.899e^-5	0.961	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8720628	3R_8720628_SNP [dm3] 3R_12894906_SNP [dm6]	G	T	7.008e^-5	0.961	UPSTREAM CR33929 INTERGENIC
2R	12580798	2R_12580798_SNP [dm3] 2R_16693293_SNP [dm6]	T	C	7.058e^-5	0.961	SYNONYMOUS_CODING CG5210 INTRON CG30463	TF binding site mE1_TFBS_cad
2R	9683802	2R_9683802_SNP [dm3] 2R_13796297_SNP [dm6]	A	G	7.193e^-5	0.961	INTRON Cpr50Cb
2R	9683805	2R_9683805_SNP [dm3] 2R_13796300_SNP [dm6]	A	G	7.193e^-5	0.961	INTRON Cpr50Cb
2L	5860104	2L_5860104_SNP [dm3] 2L_5860104_SNP [dm6]	A	C	7.289e^-5	0.961	UTR_3_PRIME rau	TF binding site mE1_TFBS_cad
2R	14356525	2R_14356525_SNP [dm3] 2R_18469020_SNP [dm6]	T	A	7.465e^-5	0.961	INTRON CG30116
2R	14356542	2R_14356542_SNP [dm3] 2R_18469037_SNP [dm6]	G	A	7.693e^-5	0.961	INTRON CG30116
3R	17970150	3R_17970150_SNP [dm3] 3R_22144428_SNP [dm6]	G	T	7.748e^-5	0.961	INTRON SKIP
2L	3416411	2L_3416411_SNP [dm3] 2L_3416411_SNP [dm6]	C	T	7.820e^-5	0.961	UPSTREAM CG31952 INTRON pgant2

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By genomic position
Variant impact
Gene name

se_Glycogen phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results