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=1.645e^-19)
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

Covariate	p-value	Significance
In_3R_P	<
In_3R_K	<
In_3R_Mo	<

Kruskal-Wallis test

Covariate	χ²	p-value
In_3R_P	16.1262	0.0003
In_3R_K	27.462	1.0882e-06
In_3R_Mo	10.4084	0.0055

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4631 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
2L	15182170	2L_15182170_INS [dm3] 2L_15182170_INS [dm6]	T	TCTT	4.350e^-8	0.046	INTRON CG4168
3L	14384514	3L_14384514_SNP [dm3] 3L_14391414_SNP [dm6]	C	T	4.869e^-8	0.046	INTERGENIC
3L	473509	3L_473509_INS [dm3] 3L_473509_INS [dm6]	C	CTTTTC	1.026e^-7	0.064	INTRON klar
3R	14752837	3R_14752837_SNP [dm3] 3R_18927115_SNP [dm6]	A	G	2.985e^-7	0.093	UTR_3_PRIME Mpc1 DOWNSTREAM Xrp1
3R	14752822	3R_14752822_SNP [dm3] 3R_18927100_SNP [dm6]	G	T	4.142e^-7	0.093	UTR_3_PRIME Mpc1 DOWNSTREAM Xrp1
3R	11252079	3R_11252079_DEL [dm3] 3R_15426357_DEL [dm6]	GCTC	G	4.805e^-7	0.093	INTRON CG6118
3R	9552543	3R_9552543_DEL [dm3] 3R_13726821_DEL [dm6]	TAAATG	T	5.082e^-7	0.093	INTRON CG34383
3R	14669930	3R_14669930_SNP [dm3] 3R_18844208_SNP [dm6]	G	A	5.509e^-7	0.093	INTRON CG18208
3R	9552564	3R_9552564_DEL [dm3] 3R_13726842_DEL [dm6]	AGTCT	A	6.581e^-7	0.093	INTRON CG34383
3R	14812422	3R_14812422_SNP [dm3] 3R_18986700_SNP [dm6]	G	A	6.726e^-7	0.093	INTRON gukh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	9050782	X_9050782_SNP [dm3] X_9156749_SNP [dm6]	G	A	8.305e^-7	0.093	UPSTREAM His3.3B DOWNSTREAM Ost48 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA
2R	6175206	2R_6175206_INS [dm3] 2R_10287701_INS [dm6]	A	AA	8.559e^-7	0.093	UPSTREAM CAP INTRON CAP
3R	10628531	3R_10628531_SNP [dm3] 3R_14802809_SNP [dm6]	C	A	8.946e^-7	0.093	SYNONYMOUS_CODING CG14857
3L	12065886	3L_12065886_SNP [dm3] 3L_12072786_SNP [dm6]	T	A	8.971e^-7	0.093	INTRON Sema-5c	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
3L	12109684	3L_12109684_SNP [dm3] 3L_12116584_SNP [dm6]	A	G	9.164e^-7	0.093	INTRON l_3_j2D3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	11605427	3R_11605427_DEL [dm3] 3R_15779705_DEL [dm6]	AGAGTGGCCAATAAAATTCG...	A	9.464e^-7	0.093	UPSTREAM CG5614 INTERGENIC
3R	11721982	3R_11721982_INS [dm3] 3R_15896260_INS [dm6]	G	GGCTG	9.562e^-7	0.093	UPSTREAM CG14877 DOWNSTREAM glob1 INTERGENIC
2L	20962196	2L_20962196_SNP [dm3] 2L_20962196_SNP [dm6]	T	C	9.625e^-7	0.093	INTERGENIC
3R	9552551	3R_9552551_DEL [dm3] 3R_13726829_DEL [dm6]	TG	T	9.929e^-7	0.093	INTRON CG34383
X	21946825	X_21946825_INS [dm3] X_22544989_INS [dm6]	G	GG	1.036e^-6	0.093	UPSTREAM CG17599 INTERGENIC
3R	9552554	3R_9552554_DEL [dm3] 3R_13726832_DEL [dm6]	TAAA	T	1.084e^-6	0.093	INTRON CG34383
3R	9552654	3R_9552654_SNP [dm3] 3R_13726932_SNP [dm6]	C	A	1.177e^-6	0.093	INTRON CG34383
X	794279	X_794279_SNP [dm3] X_900246_SNP [dm6]	T	C	1.189e^-6	0.093	UPSTREAM CG43867 INTRON CG43867	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z
3L	14384699	3L_14384699_SNP [dm3] 3L_14391599_SNP [dm6]	A	G	1.338e^-6	0.093	INTERGENIC
3L	3427015	3L_3427015_SNP [dm3] 3L_3427015_SNP [dm6]	C	T	1.345e^-6	0.093	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14709622	3R_14709622_SNP [dm3] 3R_18883900_SNP [dm6]	T	C	1.384e^-6	0.093	INTERGENIC
X	15578022	X_15578022_DEL [dm3] X_15683989_DEL [dm6]	ATGTGTCAC	A	1.431e^-6	0.093	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23837085	3R_23837085_SNP [dm3] 3R_28011363_SNP [dm6]	A	G	1.517e^-6	0.093	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	14147591	3R_14147591_SNP [dm3] 3R_18321869_SNP [dm6]	T	A	1.606e^-6	0.093	INTRON CG31235
X	15578017	X_15578017_DEL [dm3] X_15683984_DEL [dm6]	TC	T	1.654e^-6	0.093	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23861845	3R_23861845_SNP [dm3] 3R_28036123_SNP [dm6]	C	T	1.782e^-6	0.093	INTRON CG34362
3R	23859298	3R_23859298_SNP [dm3] 3R_28033576_SNP [dm6]	A	C	1.846e^-6	0.093	INTRON CG34362
X	15578098	X_15578098_SNP [dm3] X_15684065_SNP [dm6]	T	G	1.939e^-6	0.093	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9552529	3R_9552529_SNP [dm3] 3R_13726807_SNP [dm6]	T	G	2.076e^-6	0.093	INTRON CG34383
X	7682833	X_7682833_SNP [dm3] X_7788800_SNP [dm6]	A	T	2.137e^-6	0.093	INTERGENIC
X	15578111	X_15578111_SNP [dm3] X_15684078_SNP [dm6]	C	T	2.181e^-6	0.093	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	5764164	3R_5764164_DEL [dm3] 3R_9938442_DEL [dm6]	AACTC	A	2.187e^-6	0.093	INTRON Glut4EF	TF binding site mE1_TFBS_cad
3L	5306407	3L_5306407_DEL [dm3] 3L_5313307_DEL [dm6]	AA	A	2.192e^-6	0.093	INTERGENIC
3R	14777575	3R_14777575_SNP [dm3] 3R_18951853_SNP [dm6]	G	A	2.239e^-6	0.093	INTRON CG42613 & 1 other
3R	14775380	3R_14775380_SNP [dm3] 3R_18949658_SNP [dm6]	A	G	2.259e^-6	0.093	UPSTREAM CG42613 & 1 other INTRON CG42613
3L	14386254	3L_14386254_SNP [dm3] 3L_14393154_SNP [dm6]	A	T	2.306e^-6	0.093	INTERGENIC
3R	11323982	3R_11323982_SNP [dm3] 3R_15498260_SNP [dm6]	A	G	2.327e^-6	0.093	INTERGENIC
X	7682834	X_7682834_SNP [dm3] X_7788801_SNP [dm6]	T	G	2.369e^-6	0.093	INTERGENIC
3R	10887670	3R_10887670_SNP [dm3] 3R_15061948_SNP [dm6]	G	T	2.373e^-6	0.093	INTRON dpr9
3R	14700335	3R_14700335_SNP [dm3] 3R_18874613_SNP [dm6]	G	A	2.430e^-6	0.093	UPSTREAM CG14298 INTERGENIC
3L	12107226	3L_12107226_SNP [dm3] 3L_12114126_SNP [dm6]	T	A	2.475e^-6	0.093	INTERGENIC
2L	13956401	2L_13956401_SNP [dm3] 2L_13956401_SNP [dm6]	G	A	2.479e^-6	0.093	DOWNSTREAM Ance-3 INTERGENIC
3R	14704441	3R_14704441_SNP [dm3] 3R_18878719_SNP [dm6]	C	T	2.524e^-6	0.093	INTERGENIC
3R	23902220	3R_23902220_SNP [dm3] 3R_28076498_SNP [dm6]	T	A	2.557e^-6	0.093	INTRON CG34362	TF binding site mE1_TFBS_inv
3L	924500	3L_924500_SNP [dm3] 3L_924500_SNP [dm6]	A	C	2.572e^-6	0.093	INTRON Glut1
2L	18532269	2L_18532269_SNP [dm3] 2L_18532269_SNP [dm6]	C	T	2.588e^-6	0.093	UTR_3_PRIME Pde11 DOWNSTREAM Pde11 & 1 other
X	14259821	X_14259821_SNP [dm3] X_14365788_SNP [dm6]	G	A	2.681e^-6	0.093	INTRON dpr8
2L	20962076	2L_20962076_SNP [dm3] 2L_20962076_SNP [dm6]	G	A	2.702e^-6	0.093	INTERGENIC
3R	14673376	3R_14673376_SNP [dm3] 3R_18847654_SNP [dm6]	G	A	2.731e^-6	0.093	SYNONYMOUS_CODING CG18208	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24020069	3R_24020069_SNP [dm3] 3R_28194347_SNP [dm6]	A	T	2.744e^-6	0.093	INTRON CG34354
X	15578013	X_15578013_SNP [dm3] X_15683980_SNP [dm6]	C	T	2.788e^-6	0.093	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	17597830	2L_17597830_DEL [dm3] 2L_17597830_DEL [dm6]	TAT	A	2.869e^-6	0.093	INTRON Sytalpha
X	14321291	X_14321291_SNP [dm3] X_14427258_SNP [dm6]	C	A	2.891e^-6	0.093	INTRON dpr8
X	3471683	X_3471683_SNP [dm3] X_3577650_SNP [dm6]	G	T	2.930e^-6	0.093	INTRON AstA-R1
3L	14219632	3L_14219632_DEL [dm3] 3L_14226532_DEL [dm6]	CTA	G	3.079e^-6	0.096	INTRON nuf	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	18503519	3L_18503519_INS [dm3] 3L_18510419_INS [dm6]	G	GGGT	3.206e^-6	0.097	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
3R	14771263	3R_14771263_SNP [dm3] 3R_18945541_SNP [dm6]	T	C	3.252e^-6	0.097	INTRON CG42613
2L	14078423	2L_14078423_SNP [dm3] 2L_14078423_SNP [dm6]	C	A	3.267e^-6	0.097	INTRON nAChRalpha5
3L	8568403	3L_8568403_SNP [dm3] 3L_8575303_SNP [dm6]	G	T	3.403e^-6	0.098	NON_SYNONYMOUS_CODING CG6638 DOWNSTREAM rhea	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	12108869	3L_12108869_INS [dm3] 3L_12115769_INS [dm6]	C	CC	3.534e^-6	0.098	UPSTREAM l_3_j2D3 INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	10182386	2R_10182386_DEL [dm3] 2R_14294881_DEL [dm6]	TGCTTTAAAGGGACTAGGCA...	T	3.569e^-6	0.098	UTR_3_PRIME Ih INTRON Ih
3R	14700183	3R_14700183_SNP [dm3] 3R_18874461_SNP [dm6]	G	T	3.573e^-6	0.098	INTERGENIC
3R	16209629	3R_16209629_INS [dm3] 3R_20383907_INS [dm6]	T	TTAATTATTT	3.587e^-6	0.098	INTRON Gfrl
X	11479413	X_11479413_SNP [dm3] X_11585380_SNP [dm6]	C	G	3.603e^-6	0.098	NON_SYNONYMOUS_CODING nod UPSTREAM CR43217	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	11545663	3R_11545663_SNP [dm3] 3R_15719941_SNP [dm6]	C	T	3.692e^-6	0.099	INTERGENIC
3R	14674342	3R_14674342_SNP [dm3] 3R_18848620_SNP [dm6]	A	G	3.941e^-6	0.102	UTR_5_PRIME CG18208	TF binding site mE1_TFBS_cad
3R	14748021	3R_14748021_SNP [dm3] 3R_18922299_SNP [dm6]	C	A	3.956e^-6	0.102	INTRON Xrp1	TF binding site BDTNP1_TFBS_dl
3R	11311519	3R_11311519_SNP [dm3] 3R_15485797_SNP [dm6]	T	C	4.172e^-6	0.102	UPSTREAM CG5205 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv
3R	14738957	3R_14738957_INS [dm3] 3R_18913235_INS [dm6]	A	AA	4.190e^-6	0.102	UPSTREAM CG14291 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_Trl
3R	14706865	3R_14706865_SNP [dm3] 3R_18881143_SNP [dm6]	G	A	4.210e^-6	0.102	INTERGENIC
3R	4127454	3R_4127454_SNP [dm3] 3R_8301732_SNP [dm6]	C	T	4.355e^-6	0.102	UPSTREAM CG9626 DOWNSTREAM nac INTRON mRpL1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	14711340	3R_14711340_SNP [dm3] 3R_18885618_SNP [dm6]	T	C	4.360e^-6	0.102	INTERGENIC
3R	15180912	3R_15180912_INS [dm3] 3R_19355190_INS [dm6]	T	TGTGAGAAACTGATACTCAC...	4.370e^-6	0.102	DOWNSTREAM CG43203 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr
3R	9552603	3R_9552603_SNP [dm3] 3R_13726881_SNP [dm6]	T	A	4.411e^-6	0.102	INTRON CG34383
3R	14700164	3R_14700164_SNP [dm3] 3R_18874442_SNP [dm6]	C	G	4.432e^-6	0.102	INTERGENIC
3R	14748054	3R_14748054_SNP [dm3] 3R_18922332_SNP [dm6]	A	T	4.515e^-6	0.102	INTRON Xrp1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	9552585	3R_9552585_SNP [dm3] 3R_13726863_SNP [dm6]	A	T	4.592e^-6	0.102	INTRON CG34383
3R	14771437	3R_14771437_SNP [dm3] 3R_18945715_SNP [dm6]	G	T	4.645e^-6	0.102	INTRON CG42613
2L	4336566	2L_4336566_DEL [dm3] 2L_4336566_DEL [dm6]	AAA	A	4.671e^-6	0.102	UTR_5_PRIME Atet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	14078418	2L_14078418_SNP [dm3] 2L_14078418_SNP [dm6]	C	T	4.692e^-6	0.102	INTRON nAChRalpha5
3R	9552684	3R_9552684_SNP [dm3] 3R_13726962_SNP [dm6]	G	A	4.716e^-6	0.102	INTRON CG34383
X	15578115	X_15578115_SNP [dm3] X_15684082_SNP [dm6]	G	A	4.756e^-6	0.102	DOWNSTREAM CG15599 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23841644	3R_23841644_SNP [dm3] 3R_28015922_SNP [dm6]	C	G	4.798e^-6	0.102	INTERGENIC
3R	14750157	3R_14750157_SNP [dm3] 3R_18924435_SNP [dm6]	T	C	4.912e^-6	0.104	INTRON Xrp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	24041344	3R_24041344_SNP [dm3] 3R_28215622_SNP [dm6]	C	T	5.091e^-6	0.106	INTRON CG34354	TF binding site BDTNP1_TFBS_twi
3L	14386240	3L_14386240_SNP [dm3] 3L_14393140_SNP [dm6]	T	A	5.298e^-6	0.107	INTERGENIC
3R	14771444	3R_14771444_SNP [dm3] 3R_18945722_SNP [dm6]	C	A	5.318e^-6	0.107	INTRON CG42613
3R	15886276	3R_15886276_SNP [dm3] 3R_20060554_SNP [dm6]	A	G	5.356e^-6	0.107	UPSTREAM CG4390 INTERGENIC
X	21112429	X_21112429_INS [dm3] X_21241402_INS [dm6]	G	GCTCCGAGGGGATG...	5.452e^-6	0.107	INTRON CG32521
3R	14147693	3R_14147693_SNP [dm3] 3R_18321971_SNP [dm6]	G	T	5.478e^-6	0.107	INTRON CG31235
2L	7595046	2L_7595046_SNP [dm3] 2L_7595046_SNP [dm6]	G	A	5.515e^-6	0.107	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9552594	3R_9552594_SNP [dm3] 3R_13726872_SNP [dm6]	C	A	5.545e^-6	0.107	INTRON CG34383
3R	9391751	3R_9391751_MNP [dm3] 3R_13566029_MNP [dm6]	TTG	AAC	5.690e^-6	0.107	INTERGENIC
3L	14384492	3L_14384492_SNP [dm3] 3L_14391392_SNP [dm6]	C	T	5.842e^-6	0.107	INTERGENIC
3L	15945603	3L_15945603_SNP [dm3] 3L_15952503_SNP [dm6]	C	T	5.889e^-6	0.107	UTR_5_PRIME Pka-C3 INTRON Pka-C3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_3R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results