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=1.504e^-2)
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

2613 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	27010374	3R_27010374_SNP [dm3] 3R_31184652_SNP [dm6]	T	C	1.141e^-6	0.688	SYNONYMOUS_CODING mesh
3L	5613631	3L_5613631_SNP [dm3] 3L_5620531_SNP [dm6]	C	T	1.208e^-6	0.688	INTERGENIC	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_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	7017394	2L_7017394_SNP [dm3] 2L_7017394_SNP [dm6]	G	A	2.013e^-6	0.688	SYNONYMOUS_CODING ade3 DOWNSTREAM ade3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	2495969	3R_2495969_SNP [dm3] 3R_6670247_SNP [dm6]	T	G	2.811e^-6	0.688	INTRON lab	regulatory region FlyBase REDfly_CRMs
2R	12806979	2R_12806979_SNP [dm3] 2R_16919474_SNP [dm6]	G	A	2.859e^-6	0.688	INTERGENIC
3L	6179603	3L_6179603_SNP [dm3] 3L_6186503_SNP [dm6]	G	A	3.000e^-6	0.688	SYNONYMOUS_CODING D19A DOWNSTREAM CG43293	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	14366400	3L_14366400_SNP [dm3] 3L_14373300_SNP [dm6]	C	A	3.834e^-6	0.688	INTERGENIC
3L	5314708	3L_5314708_SNP [dm3] 3L_5321608_SNP [dm6]	A	G	4.112e^-6	0.688	INTERGENIC
X	20358965	X_20358965_SNP [dm3] X_20487938_SNP [dm6]	T	A	4.873e^-6	0.688	INTRON RhoGAP19D
2L	9251474	2L_9251474_SNP [dm3] 2L_9251474_SNP [dm6]	A	T	5.733e^-6	0.688	UTR_3_PRIME borr UPSTREAM aust & 1 other
3R	8706189	3R_8706189_SNP [dm3] 3R_12880467_SNP [dm6]	G	A	5.836e^-6	0.688	INTERGENIC
3L	21153922	3L_21153922_SNP [dm3] 3L_21160822_SNP [dm6]	C	T	6.259e^-6	0.688	UTR_5_PRIME Ac78C
3L	11233537	3L_11233537_SNP [dm3] 3L_11240437_SNP [dm6]	T	C	6.417e^-6	0.688	INTERGENIC
3L	18112600	3L_18112600_SNP [dm3] 3L_18119500_SNP [dm6]	C	T	7.406e^-6	0.688	DOWNSTREAM CG32195 INTRON CG7341	TF binding site mE1_TFBS_cad
2R	14795174	2R_14795174_SNP [dm3] 2R_18907669_SNP [dm6]	C	G	7.806e^-6	0.688	INTRON sano	TF binding site mE1_TFBS_cad
3L	9334938	3L_9334938_SNP [dm3] 3L_9341838_SNP [dm6]	T	A	8.622e^-6	0.688	INTRON PGRP-LC	TF binding site mE1_TFBS_HSA
3L	12001375	3L_12001375_SNP [dm3] 3L_12008275_SNP [dm6]	G	T	9.787e^-6	0.688	UTR_3_PRIME rols DOWNSTREAM CG6928
3R	22713569	3R_22713569_SNP [dm3] 3R_26887847_SNP [dm6]	T	C	1.148e^-5	0.688	INTRON T48	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2R	19022162	2R_19022162_SNP [dm3] 2R_23134639_SNP [dm6]	G	A	1.246e^-5	0.688	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	6795946	2R_6795946_SNP [dm3] 2R_10908441_SNP [dm6]	G	C	1.264e^-5	0.688	INTERGENIC
3L	21153942	3L_21153942_SNP [dm3] 3L_21160842_SNP [dm6]	A	T	1.280e^-5	0.688	UTR_5_PRIME Ac78C
3L	9332008	3L_9332008_SNP [dm3] 3L_9338908_SNP [dm6]	G	T	1.309e^-5	0.688	DOWNSTREAM PGRP-LA INTRON PGRP-LC
2L	1178728	2L_1178728_SNP [dm3] 2L_1178728_SNP [dm6]	G	T	1.326e^-5	0.688	INTRON CG4896	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7017383	2L_7017383_SNP [dm3] 2L_7017383_SNP [dm6]	G	A	1.334e^-5	0.688	SYNONYMOUS_CODING ade3 DOWNSTREAM ade3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	27300122	3R_27300122_SNP [dm3] 3R_31474400_SNP [dm6]	A	T	1.367e^-5	0.688	DOWNSTREAM CR45555 INTERGENIC
2L	14094485	2L_14094485_SNP [dm3] 2L_14094485_SNP [dm6]	A	T	1.399e^-5	0.688	DOWNSTREAM nAChRalpha5 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2L	7017404	2L_7017404_SNP [dm3] 2L_7017404_SNP [dm6]	C	G	1.436e^-5	0.688	NON_SYNONYMOUS_CODING ade3 DOWNSTREAM ade3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	12189904	3R_12189904_SNP [dm3] 3R_16364182_SNP [dm6]	A	C	1.528e^-5	0.688	INTRON CG14880
3R	2350909	3R_2350909_SNP [dm3] 3R_6525187_SNP [dm6]	A	T	1.533e^-5	0.688	INTERGENIC
X	18642836	X_18642836_SNP [dm3] X_18748803_SNP [dm6]	T	G	1.591e^-5	0.688	UPSTREAM CG12609 INTERGENIC
2R	18573438	2R_18573438_DEL [dm3] 2R_22685933_DEL [dm6]	TATT	T	1.704e^-5	0.688	UTR_3_PRIME ppa	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	23625839	3R_23625839_SNP [dm3] 3R_27800117_SNP [dm6]	G	T	1.761e^-5	0.688	INTRON CG34353
2R	16774185	2R_16774185_SNP [dm3] 2R_20886680_SNP [dm6]	T	G	1.796e^-5	0.688	SYNONYMOUS_CODING otp
3L	20588872	3L_20588872_SNP [dm3] 3L_20595772_SNP [dm6]	A	G	1.800e^-5	0.688	INTERGENIC
2L	683988	2L_683988_SNP [dm3] 2L_683988_SNP [dm6]	G	T	1.806e^-5	0.688	INTRON ds	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	683989	2L_683989_SNP [dm3] 2L_683989_SNP [dm6]	T	A	1.806e^-5	0.688	INTRON ds	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25846387	3R_25846387_SNP [dm3] 3R_30020665_SNP [dm6]	A	T	1.848e^-5	0.688	INTRON Mgat2	TF binding site BDTNP1_TFBS_dl
3L	8074949	3L_8074949_SNP [dm3] 3L_8081849_SNP [dm6]	A	G	1.916e^-5	0.688	DOWNSTREAM CR43974 INTRON Ect4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	683994	2L_683994_SNP [dm3] 2L_683994_SNP [dm6]	G	A	1.947e^-5	0.688	INTRON ds	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	17972821	3R_17972821_SNP [dm3] 3R_22147099_SNP [dm6]	T	C	1.965e^-5	0.688	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
3L	1898203	3L_1898203_SNP [dm3] 3L_1898203_SNP [dm6]	G	A	2.004e^-5	0.688	UPSTREAM CG1887 INTRON CG1887
3R	15764947	3R_15764947_SNP [dm3] 3R_19939225_SNP [dm6]	C	A	2.039e^-5	0.688	INTRON Hs6st
3R	21061664	3R_21061664_SNP [dm3] 3R_25235942_SNP [dm6]	G	A	2.046e^-5	0.688	UPSTREAM CG10420 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15764938	3R_15764938_SNP [dm3] 3R_19939216_SNP [dm6]	C	T	2.047e^-5	0.688	INTRON Hs6st
2L	21335199	2L_21335199_SNP [dm3] 2L_21335199_SNP [dm6]	T	C	2.050e^-5	0.688	INTRON dimm
3R	17972809	3R_17972809_SNP [dm3] 3R_22147087_SNP [dm6]	A	T	2.089e^-5	0.688	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad
2R	14532301	2R_14532301_SNP [dm3] 2R_18644796_SNP [dm6]	C	A	2.090e^-5	0.688	INTRON SP2637	TF binding site BDTNP1_TFBS_da
3L	1021517	3L_1021517_SNP [dm3] 3L_1021517_SNP [dm6]	A	T	2.122e^-5	0.688	INTRON trio
3L	21144250	3L_21144250_SNP [dm3] 3L_21151150_SNP [dm6]	G	T	2.123e^-5	0.688	UPSTREAM Ac78C INTRON Ac78C
3L	8986615	3L_8986615_SNP [dm3] 3L_8993515_SNP [dm6]	A	G	2.125e^-5	0.688	SYNONYMOUS_CODING smg	TF binding site mE1_TFBS_cad
2R	16774017	2R_16774017_SNP [dm3] 2R_20886512_SNP [dm6]	T	G	2.160e^-5	0.688	INTRON otp
3R	24657763	3R_24657763_SNP [dm3] 3R_28832041_SNP [dm6]	A	G	2.222e^-5	0.688	UPSTREAM WASp DOWNSTREAM Apc INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	12504724	3L_12504724_SNP [dm3] 3L_12511624_SNP [dm6]	C	T	2.253e^-5	0.688	SYNONYMOUS_CODING sti
3R	2350925	3R_2350925_DEL [dm3] 3R_6525203_DEL [dm6]	GTG	AA	2.407e^-5	0.688	INTERGENIC
3L	18580888	3L_18580888_SNP [dm3] 3L_18587788_SNP [dm6]	C	G	2.462e^-5	0.688	UPSTREAM CG7271 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	19022085	2R_19022085_SNP [dm3] 2R_23134562_SNP [dm6]	T	A	2.483e^-5	0.688	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	17128919	2R_17128919_SNP [dm3] 2R_21241414_SNP [dm6]	A	G	2.560e^-5	0.688	INTRON ASPP
3R	26754631	3R_26754631_SNP [dm3] 3R_30928909_SNP [dm6]	A	C	2.575e^-5	0.688	INTRON Ptx1	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
3R	17972810	3R_17972810_SNP [dm3] 3R_22147088_SNP [dm6]	A	C	2.584e^-5	0.688	INTRON SKIP	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_cad
X	15294540	X_15294540_SNP [dm3] X_15400507_SNP [dm6]	A	T	2.658e^-5	0.688	INTRON Cngl
2L	7626997	2L_7626997_SNP [dm3] 2L_7626997_SNP [dm6]	A	T	2.678e^-5	0.688	INTERGENIC
X	18636517	X_18636517_INS [dm3] X_18742484_INS [dm6]	A	ATTGCGA	2.745e^-5	0.688	INTERGENIC
3L	14109883	3L_14109883_SNP [dm3] 3L_14116783_SNP [dm6]	C	T	2.820e^-5	0.688	INTRON Sox21b
X	5725046	X_5725046_SNP [dm3] X_5831013_SNP [dm6]	A	T	2.866e^-5	0.688	DOWNSTREAM CR43264 INTRON CG15765
X	5725128	X_5725128_SNP [dm3] X_5831095_SNP [dm6]	G	C	2.866e^-5	0.688	DOWNSTREAM CR43264 INTRON CG15765
3R	17143883	3R_17143883_SNP [dm3] 3R_21318161_SNP [dm6]	T	A	2.920e^-5	0.688	DOWNSTREAM CG16791 & 1 other INTERGENIC
X	10459204	X_10459204_SNP [dm3] X_10565171_SNP [dm6]	T	A	2.964e^-5	0.688	DOWNSTREAM CG15296 INTRON spri
2L	2483881	2L_2483881_DEL [dm3] 2L_2483881_DEL [dm6]	ACACACA	A	2.998e^-5	0.688	INTERGENIC	enhancer FlyBase regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3R	21086869	3R_21086869_SNP [dm3] 3R_25261147_SNP [dm6]	A	T	3.031e^-5	0.688	UTR_3_PRIME CG10425 DOWNSTREAM CG11857
3L	12693301	3L_12693301_SNP [dm3] 3L_12700201_SNP [dm6]	G	A	3.142e^-5	0.688	INTRON mirr	TF binding site BDTNP1_TFBS_twi
2R	19022105	2R_19022105_SNP [dm3] 2R_23134582_SNP [dm6]	T	A	3.153e^-5	0.688	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	14447694	2R_14447694_SNP [dm3] 2R_18560189_SNP [dm6]	G	T	3.250e^-5	0.688	SYNONYMOUS_CODING GEFmeso	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14609240	2R_14609240_SNP [dm3] 2R_18721735_SNP [dm6]	C	A	3.289e^-5	0.688	INTRON Hs3st-A
3R	10012571	3R_10012571_SNP [dm3] 3R_14186849_SNP [dm6]	G	C	3.298e^-5	0.688	INTRON Dop1R1
3L	21057156	3L_21057156_SNP [dm3] 3L_21064056_SNP [dm6]	G	C	3.302e^-5	0.688	UTR_5_PRIME siz INTRON siz
2L	9250844	2L_9250844_SNP [dm3] 2L_9250844_SNP [dm6]	G	A	3.387e^-5	0.688	SYNONYMOUS_CODING aust DOWNSTREAM CR43734 & 2 others	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	20588877	3L_20588877_SNP [dm3] 3L_20595777_SNP [dm6]	A	C	3.411e^-5	0.688	INTERGENIC
3R	27213948	3R_27213948_SNP [dm3] 3R_31388226_SNP [dm6]	G	A	3.564e^-5	0.688	INTRON CG1607	TF binding site mE1_TFBS_cad
2R	9741877	2R_9741877_SNP [dm3] 2R_13854372_SNP [dm6]	A	T	3.566e^-5	0.688	UPSTREAM CR44367 & 1 other DOWNSTREAM CG6553 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	5613313	3L_5613313_SNP [dm3] 3L_5620213_SNP [dm6]	A	C	3.601e^-5	0.688	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	21061701	3R_21061701_SNP [dm3] 3R_25235979_SNP [dm6]	A	G	3.655e^-5	0.688	UPSTREAM CG10420 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	13056978	2L_13056978_SNP [dm3] 2L_13056978_SNP [dm6]	A	C	3.658e^-5	0.688	INTRON CG9932
2L	7902481	2L_7902481_SNP [dm3] 2L_7902481_SNP [dm6]	G	C	3.683e^-5	0.688	INTRON Snoo
3R	11159918	3R_11159918_SNP [dm3] 3R_15334196_SNP [dm6]	G	A	3.719e^-5	0.688	SYNONYMOUS_CODING Sra-1	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
X	20359023	X_20359023_SNP [dm3] X_20487996_SNP [dm6]	G	C	3.818e^-5	0.688	INTRON RhoGAP19D
3R	24959269	3R_24959269_SNP [dm3] 3R_29133547_SNP [dm6]	C	T	3.819e^-5	0.688	INTRON Vha100-1
3L	11233539	3L_11233539_SNP [dm3] 3L_11240439_SNP [dm6]	A	G	3.875e^-5	0.688	INTERGENIC
2R	14439504	2R_14439504_SNP [dm3] 2R_18551999_SNP [dm6]	T	A	3.877e^-5	0.688	INTERGENIC
3R	19262866	3R_19262866_SNP [dm3] 3R_23437144_SNP [dm6]	G	A	3.916e^-5	0.688	INTRON CG4374
2L	4918222	2L_4918222_SNP [dm3] 2L_4918222_SNP [dm6]	T	C	3.918e^-5	0.688	INTRON hoe1
X	13055757	X_13055757_SNP [dm3] X_13161724_SNP [dm6]	G	T	4.015e^-5	0.688	UTR_3_PRIME CG12096 & 1 other DOWNSTREAM CG12096
X	15294627	X_15294627_SNP [dm3] X_15400594_SNP [dm6]	T	C	4.016e^-5	0.688	INTRON Cngl
2R	14609238	2R_14609238_SNP [dm3] 2R_18721733_SNP [dm6]	T	A	4.045e^-5	0.688	INTRON Hs3st-A
3L	6179646	3L_6179646_SNP [dm3] 3L_6186546_SNP [dm6]	C	T	4.135e^-5	0.688	SYNONYMOUS_CODING D19A DOWNSTREAM CG43293	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	14520875	3R_14520875_SNP [dm3] 3R_18695153_SNP [dm6]	A	T	4.214e^-5	0.688	UPSTREAM CG34282 INTERGENIC
3L	5280751	3L_5280751_SNP [dm3] 3L_5287651_SNP [dm6]	A	T	4.302e^-5	0.688	INTERGENIC
X	7250110	X_7250110_INS [dm3] X_7356077_INS [dm6]	G	GC	4.304e^-5	0.688	INTRON CR44357 & 1 other
2L	14764504	2L_14764504_SNP [dm3] 2L_14764504_SNP [dm6]	C	A	4.321e^-5	0.688	DOWNSTREAM CSN1a INTERGENIC
2L	7901123	2L_7901123_SNP [dm3] 2L_7901123_SNP [dm6]	C	G	4.352e^-5	0.688	INTRON Snoo
2R	12284091	2R_12284091_SNP [dm3] 2R_16396586_SNP [dm6]	T	A	4.354e^-5	0.688	INTRON Sema-2b

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By genomic position
Variant impact
Gene name

Week 2 mean ascension (cm) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results