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=1.337e^-3)
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

Covariate	χ²	p-value	Significance
wolba	3.2303	0.0723

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1971 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
3L	6960692	3L_6960692_SNP [dm3] 3L_6967592_SNP [dm6]	A	G	1.871e^-6	0.897	SYNONYMOUS_CODING CG10064 DOWNSTREAM Mis12	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	18025266	X_18025266_SNP [dm3] X_18131233_SNP [dm6]	T	A	3.053e^-6	0.897	UTR_3_PRIME ari-1 DOWNSTREAM ari-1
2R	17976167	2R_17976167_SNP [dm3] 2R_22088662_SNP [dm6]	C	T	4.117e^-6	0.897	UTR_5_PRIME CG13502 DOWNSTREAM CG43393
2R	17976170	2R_17976170_SNP [dm3] 2R_22088665_SNP [dm6]	G	C	4.117e^-6	0.897	UTR_5_PRIME CG13502 DOWNSTREAM CG43393
3R	13976534	3R_13976534_SNP [dm3] 3R_18150812_SNP [dm6]	C	A	4.243e^-6	0.897	INTERGENIC
3R	5312697	3R_5312697_SNP [dm3] 3R_9486975_SNP [dm6]	T	G	6.218e^-6	0.897	UTR_5_PRIME CG16779
2L	4335627	2L_4335627_SNP [dm3] 2L_4335627_SNP [dm6]	C	G	8.042e^-6	0.897	INTRON Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	13198339	2L_13198339_SNP [dm3] 2L_13198339_SNP [dm6]	C	T	8.265e^-6	0.897	SPLICE_SITE_REGION CG16972 INTRON CG16972	TF binding site mE1_TFBS_cad
3L	1531315	3L_1531315_SNP [dm3] 3L_1531315_SNP [dm6]	C	G	9.786e^-6	0.897	UPSTREAM Ir62a INTRON CG12090	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	1822115	X_1822115_SNP [dm3] X_1928082_SNP [dm6]	G	A	1.041e^-5	0.897	UPSTREAM CG11596 DOWNSTREAM Ocrl INTRON CG11596	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens
3R	9550253	3R_9550253_INS [dm3] 3R_13724531_INS [dm6]	C	CGAACC	1.245e^-5	0.897	INTRON CG34383	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens
X	15818480	X_15818480_SNP [dm3] X_15924447_SNP [dm6]	T	C	1.258e^-5	0.897	SYNONYMOUS_CODING CG8916 UPSTREAM Lcch3
3L	1107836	3L_1107836_SNP [dm3] 3L_1107836_SNP [dm6]	G	A	1.293e^-5	0.897	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	12615993	2R_12615993_SNP [dm3] 2R_16728488_SNP [dm6]	T	C	1.368e^-5	0.897	INTRON CG30463
X	16565339	X_16565339_SNP [dm3] X_16671306_SNP [dm6]	T	C	1.454e^-5	0.897	INTRON CG13012	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	4859287	3R_4859287_SNP [dm3] 3R_9033565_SNP [dm6]	A	T	1.457e^-5	0.897	UTR_5_PRIME neur INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_Dll mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
X	18843974	X_18843974_SNP [dm3] X_18949941_SNP [dm6]	T	C	1.484e^-5	0.897	INTRON CG43759
3R	23986624	3R_23986624_SNP [dm3] 3R_28160902_SNP [dm6]	G	C	1.518e^-5	0.897	INTRON CG34354
2L	5064447	2L_5064447_SNP [dm3] 2L_5064447_SNP [dm6]	C	T	1.858e^-5	0.897	UTR_5_PRIME qtc INTRON qtc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	3773851	3R_3773851_SNP [dm3] 3R_7948129_SNP [dm6]	C	T	1.863e^-5	0.897	INTRON dsx	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Trl
2L	6189489	2L_6189489_SNP [dm3] 2L_6189489_SNP [dm6]	A	G	1.897e^-5	0.897	INTRON CG34380	TF binding site BDTNP1_TFBS_prd mE1_TFBS_chinmo mE1_TFBS_HSA
2L	4333473	2L_4333473_SNP [dm3] 2L_4333473_SNP [dm6]	G	T	1.930e^-5	0.897	UPSTREAM Atet INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	4792282	3L_4792282_SNP [dm3] 3L_4792282_SNP [dm6]	C	G	1.957e^-5	0.897	SYNONYMOUS_CODING RhoGEF64C	TF binding site BDTNP1_TFBS_Mad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	20503929	2R_20503929_SNP [dm3] 2R_24616406_SNP [dm6]	T	C	2.012e^-5	0.897	INTRON CG13594
2R	8444367	2R_8444367_SNP [dm3] 2R_12556862_SNP [dm6]	C	T	2.041e^-5	0.897	SYNONYMOUS_CODING fra	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	4858555	3R_4858555_SNP [dm3] 3R_9032833_SNP [dm6]	A	T	2.260e^-5	0.897	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	4858813	3R_4858813_SNP [dm3] 3R_9033091_SNP [dm6]	G	C	2.260e^-5	0.897	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23983828	3R_23983828_INS [dm3] 3R_28158106_INS [dm6]	A	AATCAAGCTAG...	2.404e^-5	0.897	INTRON CG34354	TF binding site mE1_TFBS_inv
3L	14900108	3L_14900108_SNP [dm3] 3L_14907008_SNP [dm6]	C	A	2.427e^-5	0.897	INTRON DCX-EMAP
2L	7510288	2L_7510288_SNP [dm3] 2L_7510288_SNP [dm6]	C	T	2.570e^-5	0.897	INTRON RapGAP1
X	1819533	X_1819533_SNP [dm3] X_1925500_SNP [dm6]	T	C	2.622e^-5	0.897	SPLICE_SITE_REGION Ocrl INTRON Ocrl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	17575922	X_17575922_SNP [dm3] X_17681889_SNP [dm6]	T	A	2.693e^-5	0.897	INTRON chas	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	6617870	3L_6617870_SNP [dm3] 3L_6624770_SNP [dm6]	G	A	2.908e^-5	0.897	INTRON GluRIA
3R	15444024	3R_15444024_SNP [dm3] 3R_19618302_SNP [dm6]	T	A	3.224e^-5	0.897	INTRON CG6231
3R	23965546	3R_23965546_SNP [dm3] 3R_28139824_SNP [dm6]	C	G	3.290e^-5	0.897	INTERGENIC
3L	12854288	3L_12854288_SNP [dm3] 3L_12861188_SNP [dm6]	C	A	3.290e^-5	0.897	NON_SYNONYMOUS_CODING CG32107 DOWNSTREAM CG10943	TF binding site mE1_TFBS_bab1
3R	22888958	3R_22888958_SNP [dm3] 3R_27063236_SNP [dm6]	C	T	3.525e^-5	0.897	DOWNSTREAM CG34292 INTRON Nep5
3R	23984245	3R_23984245_SNP [dm3] 3R_28158523_SNP [dm6]	T	A	3.532e^-5	0.897	INTRON CG34354
3R	26441982	3R_26441982_SNP [dm3] 3R_30616260_SNP [dm6]	G	A	3.532e^-5	0.897	DOWNSTREAM CR45571 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14454533	X_14454533_SNP [dm3] X_14560500_SNP [dm6]	C	G	3.745e^-5	0.897	INTERGENIC
2L	11950629	2L_11950629_SNP [dm3] 2L_11950629_SNP [dm6]	T	C	3.768e^-5	0.897	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11950690	2L_11950690_SNP [dm3] 2L_11950690_SNP [dm6]	A	T	3.768e^-5	0.897	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	6129525	2R_6129525_SNP [dm3] 2R_10242020_SNP [dm6]	C	T	3.782e^-5	0.897	SYNONYMOUS_CODING Hdc	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13305859	3L_13305859_SNP [dm3] 3L_13312759_SNP [dm6]	T	G	3.797e^-5	0.897	INTERGENIC
3R	14979690	3R_14979690_SNP [dm3] 3R_19153968_SNP [dm6]	T	C	3.987e^-5	0.897	UPSTREAM CG5835 DOWNSTREAM CG11779 INTERGENIC
3L	13305965	3L_13305965_SNP [dm3] 3L_13312865_SNP [dm6]	T	A	3.992e^-5	0.897	INTERGENIC
2L	7175809	2L_7175809_SNP [dm3] 2L_7175809_SNP [dm6]	T	A	4.015e^-5	0.897	INTERGENIC
3L	11327849	3L_11327849_SNP [dm3] 3L_11334749_SNP [dm6]	G	A	4.026e^-5	0.897	INTERGENIC
2R	17154760	2R_17154760_SNP [dm3] 2R_21267255_SNP [dm6]	C	T	4.090e^-5	0.897	SYNONYMOUS_CODING CG30393 UPSTREAM CG30391 INTRON Rgk3	TF binding site mE1_TFBS_chinmo
3L	17816161	3L_17816161_SNP [dm3] 3L_17823061_SNP [dm6]	A	G	4.122e^-5	0.897	UPSTREAM Grd & 1 other INTERGENIC
2L	2466176	2L_2466176_SNP [dm3] 2L_2466176_SNP [dm6]	G	C	4.269e^-5	0.897	INTERGENIC	enhancer FlyBase
2R	18758054	2R_18758054_SNP [dm3] 2R_22870531_SNP [dm6]	T	C	4.321e^-5	0.897	UTR_3_PRIME fd59A UPSTREAM CG13532	TF binding site mE1_TFBS_cad
3R	26845665	3R_26845665_SNP [dm3] 3R_31019943_SNP [dm6]	T	C	4.380e^-5	0.897	INTERGENIC	TF binding site mE1_TFBS_inv
3L	21728117	3L_21728117_SNP [dm3] 3L_21735017_SNP [dm6]	C	T	4.462e^-5	0.897	UPSTREAM CR43888 DOWNSTREAM CG14573 INTERGENIC
2L	10412180	2L_10412180_SNP [dm3] 2L_10412180_SNP [dm6]	T	C	4.494e^-5	0.897	INTRON CG5355
2L	4335778	2L_4335778_SNP [dm3] 2L_4335778_SNP [dm6]	T	A	4.524e^-5	0.897	INTRON Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14979055	3R_14979055_SNP [dm3] 3R_19153333_SNP [dm6]	C	A	4.685e^-5	0.897	DOWNSTREAM CG11779 INTRON CG5835
2R	18746028	2R_18746028_SNP [dm3] 2R_22858505_SNP [dm6]	G	A	4.736e^-5	0.897	INTRON inaD
2R	18746029	2R_18746029_SNP [dm3] 2R_22858506_SNP [dm6]	G	A	4.736e^-5	0.897	INTRON inaD
3R	21044138	3R_21044138_SNP [dm3] 3R_25218416_SNP [dm6]	A	G	4.888e^-5	0.897	SYNONYMOUS_CODING CG31106 UPSTREAM CG31103
3L	14185603	3L_14185603_SNP [dm3] 3L_14192503_SNP [dm6]	C	T	4.892e^-5	0.897	INTRON nuf	TF binding site BDTNP1_TFBS_dl
3L	4416330	3L_4416330_SNP [dm3] 3L_4416330_SNP [dm6]	C	T	5.118e^-5	0.897	INTRON DOR
3L	2018577	3L_2018577_SNP [dm3] 3L_2018577_SNP [dm6]	C	T	5.169e^-5	0.897	INTERGENIC
2L	11376614	2L_11376614_INS [dm3] 2L_11376614_INS [dm6]	A	GC	5.182e^-5	0.897	INTERGENIC	regulatory region REDfly_CRMs
3R	23984456	3R_23984456_SNP [dm3] 3R_28158734_SNP [dm6]	G	C	5.216e^-5	0.897	INTRON CG34354
2L	15739547	2L_15739547_SNP [dm3] 2L_15739547_SNP [dm6]	G	A	5.223e^-5	0.897	INTRON CycE	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13305938	3L_13305938_SNP [dm3] 3L_13312838_SNP [dm6]	A	T	5.305e^-5	0.897	INTERGENIC
3L	13305953	3L_13305953_SNP [dm3] 3L_13312853_SNP [dm6]	C	T	5.305e^-5	0.897	INTERGENIC
3L	13305958	3L_13305958_SNP [dm3] 3L_13312858_SNP [dm6]	C	T	5.305e^-5	0.897	INTERGENIC
3L	13305967	3L_13305967_SNP [dm3] 3L_13312867_SNP [dm6]	A	T	5.305e^-5	0.897	INTERGENIC
3L	13305978	3L_13305978_SNP [dm3] 3L_13312878_SNP [dm6]	T	A	5.305e^-5	0.897	INTERGENIC
3L	13306014	3L_13306014_SNP [dm3] 3L_13312914_SNP [dm6]	C	T	5.305e^-5	0.897	INTERGENIC
2R	7805876	2R_7805876_SNP [dm3] 2R_11918371_SNP [dm6]	G	T	5.318e^-5	0.897	EXON CR44305
2R	12700082	2R_12700082_SNP [dm3] 2R_16812577_SNP [dm6]	C	T	5.424e^-5	0.897	EXON CR44379
2R	15390420	2R_15390420_SNP [dm3] 2R_19502915_SNP [dm6]	T	G	5.491e^-5	0.897	UPSTREAM CG11007 INTERGENIC	TF binding site mE1_TFBS_Ubx
X	1194700	X_1194700_SNP [dm3] X_1300667_SNP [dm6]	C	T	5.588e^-5	0.897	INTRON DAAM
2R	17174382	2R_17174382_SNP [dm3] 2R_21286877_SNP [dm6]	T	G	5.594e^-5	0.897	SYNONYMOUS_CODING CG10505	TF binding site mE1_TFBS_chinmo
3L	9299715	3L_9299715_SNP [dm3] 3L_9306615_SNP [dm6]	G	A	5.688e^-5	0.897	INTERGENIC
3R	23970432	3R_23970432_SNP [dm3] 3R_28144710_SNP [dm6]	T	C	5.865e^-5	0.897	INTERGENIC
X	15369912	X_15369912_SNP [dm3] X_15475879_SNP [dm6]	C	T	5.871e^-5	0.897	UPSTREAM CG6324 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_Ubx
X	17192711	X_17192711_SNP [dm3] X_17298678_SNP [dm6]	T	C	5.871e^-5	0.897	INTRON CG5445 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	17193957	X_17193957_SNP [dm3] X_17299924_SNP [dm6]	C	T	5.871e^-5	0.897	INTRON CG5445 & 1 other	TF binding site BDTNP1_TFBS_dl
X	17194537	X_17194537_SNP [dm3] X_17300504_SNP [dm6]	C	T	5.871e^-5	0.897	INTRON CG5445 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	1819782	X_1819782_SNP [dm3] X_1925749_SNP [dm6]	C	T	5.900e^-5	0.897	SYNONYMOUS_CODING Ocrl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5333948	2L_5333948_SNP [dm3] 2L_5333948_SNP [dm6]	C	T	6.018e^-5	0.897	INTRON fusl
3R	23967838	3R_23967838_SNP [dm3] 3R_28142116_SNP [dm6]	G	A	6.035e^-5	0.897	INTERGENIC
3R	23968105	3R_23968105_SNP [dm3] 3R_28142383_SNP [dm6]	T	C	6.035e^-5	0.897	INTERGENIC
3R	23969487	3R_23969487_SNP [dm3] 3R_28143765_SNP [dm6]	A	T	6.035e^-5	0.897	INTERGENIC
X	18041505	X_18041505_SNP [dm3] X_18147472_SNP [dm6]	T	G	6.102e^-5	0.897	INTERGENIC
2R	18346740	2R_18346740_SNP [dm3] 2R_22459235_SNP [dm6]	G	A	6.161e^-5	0.897	INTRON CG10384
3L	12306706	3L_12306706_SNP [dm3] 3L_12313606_SNP [dm6]	G	A	6.206e^-5	0.897	INTERGENIC
2R	5803049	2R_5803049_DEL [dm3] 2R_9915544_DEL [dm6]	GTTG	G	6.240e^-5	0.897	UTR_3_PRIME Mef2 DOWNSTREAM Mef2
X	14454530	X_14454530_SNP [dm3] X_14560497_SNP [dm6]	T	C	6.259e^-5	0.897	INTERGENIC
2R	18746172	2R_18746172_SNP [dm3] 2R_22858649_SNP [dm6]	C	A	6.264e^-5	0.897	UTR_5_PRIME inaD
3L	12306692	3L_12306692_SNP [dm3] 3L_12313592_SNP [dm6]	G	T	6.313e^-5	0.897	INTERGENIC
3R	10594934	3R_10594934_SNP [dm3] 3R_14769212_SNP [dm6]	C	A	6.343e^-5	0.897	INTRON jvl
2L	8075797	2L_8075797_SNP [dm3] 2L_8075797_SNP [dm6]	C	T	6.401e^-5	0.897	SYNONYMOUS_CODING Mcr
3R	23983839	3R_23983839_SNP [dm3] 3R_28158117_SNP [dm6]	C	T	6.545e^-5	0.897	INTRON CG34354	TF binding site mE1_TFBS_inv
3R	23983842	3R_23983842_SNP [dm3] 3R_28158120_SNP [dm6]	C	T	6.545e^-5	0.897	INTRON CG34354	TF binding site mE1_TFBS_inv
2L	11950777	2L_11950777_SNP [dm3] 2L_11950777_SNP [dm6]	T	C	6.568e^-5	0.897	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

pc_FLCN_Hobo_HS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results