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=5.269e^-6)
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
In_2R_NS	5.0168	0.0814

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2002 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	8078685	2R_8078685_SNP [dm3] 2R_12191180_SNP [dm6]	G	A	1.485e^-7	0.208	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8089676	2R_8089676_SNP [dm3] 2R_12202171_SNP [dm6]	A	T	3.750e^-7	0.208	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	9031423	3R_9031423_SNP [dm3] 3R_13205701_SNP [dm6]	G	T	3.784e^-7	0.208	INTERGENIC
3R	24571138	3R_24571138_SNP [dm3] 3R_28745416_SNP [dm6]	T	A	4.680e^-7	0.208	UPSTREAM AstA-R2 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	8988335	3R_8988335_SNP [dm3] 3R_13162613_SNP [dm6]	C	G	5.692e^-7	0.208	NON_SYNONYMOUS_CODING timeout
2R	8091687	2R_8091687_SNP [dm3] 2R_12204182_SNP [dm6]	A	G	7.731e^-7	0.208	INTERGENIC
2R	8078974	2R_8078974_SNP [dm3] 2R_12191469_SNP [dm6]	G	C	7.761e^-7	0.208	NON_SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
X	15551588	X_15551588_SNP [dm3] X_15657555_SNP [dm6]	C	A	1.278e^-6	0.289	INTERGENIC	TF binding site mE1_TFBS_Kr
2R	8078684	2R_8078684_SNP [dm3] 2R_12191179_SNP [dm6]	A	G	1.387e^-6	0.289	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8090564	2R_8090564_SNP [dm3] 2R_12203059_SNP [dm6]	G	A	1.671e^-6	0.313	INTERGENIC
3R	8988291	3R_8988291_INS [dm3] 3R_13162569_INS [dm6]	G	TGGA	2.168e^-6	0.347
3L	13349801	3L_13349801_SNP [dm3] 3L_13356701_SNP [dm6]	A	G	2.218e^-6	0.347	INTRON Nplp2
3R	9031928	3R_9031928_SNP [dm3] 3R_13206206_SNP [dm6]	C	T	2.602e^-6	0.375	INTERGENIC
3R	24625737	3R_24625737_SNP [dm3] 3R_28800015_SNP [dm6]	T	A	3.032e^-6	0.399	INTERGENIC
2R	8091181	2R_8091181_SNP [dm3] 2R_12203676_SNP [dm6]	A	C	3.320e^-6	0.399	INTERGENIC
2R	10576575	2R_10576575_SNP [dm3] 2R_14689070_SNP [dm6]	G	C	3.413e^-6	0.399	INTRON mspo
2R	8100594	2R_8100594_SNP [dm3] 2R_12213089_SNP [dm6]	G	A	3.858e^-6	0.399	UPSTREAM Sr-CII & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	8072884	2R_8072884_INS [dm3] 2R_12185379_INS [dm6]	G	GAGTTACGGGTGCCTCCGTT...	4.495e^-6	0.399	UTR_3_PRIME CG13175 & 1 other UPSTREAM Cyp6g1	regulatory region REDfly_CRMs
3R	9078765	3R_9078765_SNP [dm3] 3R_13253043_SNP [dm6]	C	T	4.551e^-6	0.399	INTRON Ace
2R	8090560	2R_8090560_SNP [dm3] 2R_12203055_SNP [dm6]	A	T	4.565e^-6	0.399	INTERGENIC
X	15551571	X_15551571_DEL [dm3] X_15657538_DEL [dm6]	TT	T	4.565e^-6	0.399	INTERGENIC	TF binding site mE1_TFBS_Kr
2R	12132532	2R_12132532_SNP [dm3] 2R_16245027_SNP [dm6]	A	G	4.820e^-6	0.399	SYNONYMOUS_CODING CngA	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10576602	2R_10576602_SNP [dm3] 2R_14689097_SNP [dm6]	G	T	4.895e^-6	0.399	INTRON mspo
2R	8098232	2R_8098232_SNP [dm3] 2R_12210727_SNP [dm6]	G	A	5.194e^-6	0.406	SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	15551401	X_15551401_SNP [dm3] X_15657368_SNP [dm6]	C	A	6.138e^-6	0.46	INTERGENIC
3R	14146935	3R_14146935_SNP [dm3] 3R_18321213_SNP [dm6]	C	G	7.132e^-6	0.491	INTRON CG31235
X	15551480	X_15551480_SNP [dm3] X_15657447_SNP [dm6]	C	A	7.467e^-6	0.491	INTERGENIC
2R	8091158	2R_8091158_SNP [dm3] 2R_12203653_SNP [dm6]	G	C	7.996e^-6	0.491	INTERGENIC
3R	14146932	3R_14146932_SNP [dm3] 3R_18321210_SNP [dm6]	G	A	8.101e^-6	0.491	INTRON CG31235
3L	12346892	3L_12346892_SNP [dm3] 3L_12353792_SNP [dm6]	A	T	8.166e^-6	0.491	INTERGENIC
3R	9031918	3R_9031918_SNP [dm3] 3R_13206196_SNP [dm6]	C	A	8.414e^-6	0.491	INTERGENIC
2R	8095372	2R_8095372_INS [dm3] 2R_12207867_INS [dm6]	T	TT	8.562e^-6	0.491	DOWNSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	14146933	3R_14146933_SNP [dm3] 3R_18321211_SNP [dm6]	C	A	8.635e^-6	0.491	INTRON CG31235
3L	12346886	3L_12346886_SNP [dm3] 3L_12353786_SNP [dm6]	C	T	8.896e^-6	0.491	INTERGENIC
2L	9318682	2L_9318682_SNP [dm3] 2L_9318682_SNP [dm6]	G	A	9.944e^-6	0.533	INTERGENIC
3R	9031458	3R_9031458_SNP [dm3] 3R_13205736_SNP [dm6]	G	C	1.028e^-5	0.535	INTERGENIC
2R	8092269	2R_8092269_SNP [dm3] 2R_12204764_SNP [dm6]	T	A	1.184e^-5	0.6	INTERGENIC
3L	17243503	3L_17243503_SNP [dm3] 3L_17250403_SNP [dm6]	G	A	1.224e^-5	0.6	INTRON CR43870
2L	9966721	2L_9966721_SNP [dm3] 2L_9966721_SNP [dm6]	C	T	1.297e^-5	0.6	SYNONYMOUS_CODING Dref UPSTREAM RpL13	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	18936651	3R_18936651_SNP [dm3] 3R_23110929_SNP [dm6]	G	A	1.301e^-5	0.6	INTRON CG13830
2L	7153581	2L_7153581_SNP [dm3] 2L_7153581_SNP [dm6]	G	C	1.313e^-5	0.6	INTRON Pvf3
3R	24667321	3R_24667321_SNP [dm3] 3R_28841599_SNP [dm6]	T	G	1.355e^-5	0.605	INTRON Apc	TF binding site BDTNP1_TFBS_twi
2R	10013361	2R_10013361_SNP [dm3] 2R_14125856_SNP [dm6]	A	C	1.429e^-5	0.623	INTRON Prosap
3R	14146927	3R_14146927_SNP [dm3] 3R_18321205_SNP [dm6]	A	T	1.524e^-5	0.634	INTRON CG31235
2R	17188582	2R_17188582_SNP [dm3] 2R_21301077_SNP [dm6]	A	T	1.545e^-5	0.634	UPSTREAM CG42672 INTRON CG42672
2R	17326783	2R_17326783_SNP [dm3] 2R_21439278_SNP [dm6]	C	A	1.556e^-5	0.634	INTRON Sdc
2L	8606105	2L_8606105_SNP [dm3] 2L_8606105_SNP [dm6]	G	C	1.657e^-5	0.661	INTRON Sema-1a
2R	10576572	2R_10576572_SNP [dm3] 2R_14689067_SNP [dm6]	A	G	1.742e^-5	0.669	INTRON mspo
2R	8100454	2R_8100454_SNP [dm3] 2R_12212949_SNP [dm6]	G	T	1.747e^-5	0.669	UPSTREAM Sr-CII INTERGENIC
2R	19675962	2R_19675962_SNP [dm3] 2R_23788439_SNP [dm6]	T	G	1.905e^-5	0.676	INTRON CG9850
2R	8092306	2R_8092306_SNP [dm3] 2R_12204801_SNP [dm6]	C	T	1.936e^-5	0.676	INTERGENIC
2L	12156636	2L_12156636_SNP [dm3] 2L_12156636_SNP [dm6]	G	A	1.946e^-5	0.676	INTRON CG31760
3R	17076358	3R_17076358_SNP [dm3] 3R_21250636_SNP [dm6]	T	G	1.955e^-5	0.676	INTRON ETHR
3L	10403943	3L_10403943_SNP [dm3] 3L_10410843_SNP [dm6]	A	T	2.006e^-5	0.676	DOWNSTREAM CR44543 INTERGENIC
2R	11143571	2R_11143571_SNP [dm3] 2R_15256066_SNP [dm6]	C	T	2.031e^-5	0.676	SPLICE_SITE_REGION scb INTRON scb	TF binding site mE1_TFBS_cad
2R	8091180	2R_8091180_SNP [dm3] 2R_12203675_SNP [dm6]	C	A	2.064e^-5	0.676	INTERGENIC
2R	8077706	2R_8077706_SNP [dm3] 2R_12190201_SNP [dm6]	G	T	2.066e^-5	0.676	SYNONYMOUS_CODING Cyp6g2 UPSTREAM Cyp6t3	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	13825555	X_13825555_SNP [dm3] X_13931522_SNP [dm6]	A	G	2.112e^-5	0.676	INTRON mamo
3R	21822107	3R_21822107_SNP [dm3] 3R_25996385_SNP [dm6]	C	T	2.128e^-5	0.676	NON_SYNONYMOUS_CODING CG43116 DOWNSTREAM Nf1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5518333	3L_5518333_SNP [dm3] 3L_5525233_SNP [dm6]	G	T	2.166e^-5	0.676	INTRON Lkr
2R	10576605	2R_10576605_SNP [dm3] 2R_14689100_SNP [dm6]	A	T	2.210e^-5	0.676	INTRON mspo
X	14154195	X_14154195_SNP [dm3] X_14260162_SNP [dm6]	C	T	2.263e^-5	0.676	INTERGENIC
2L	4222485	2L_4222485_SNP [dm3] 2L_4222485_SNP [dm6]	G	C	2.272e^-5	0.676	UPSTREAM ft INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_Stat92E mE1_TFBS_Trl
3R	8988821	3R_8988821_SNP [dm3] 3R_13163099_SNP [dm6]	G	A	2.395e^-5	0.697	SYNONYMOUS_CODING timeout
2L	1485693	2L_1485693_SNP [dm3] 2L_1485693_SNP [dm6]	T	C	2.530e^-5	0.697	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
2R	17623680	2R_17623680_SNP [dm3] 2R_21736175_SNP [dm6]	C	G	2.564e^-5	0.697	INTERGENIC
3L	12357247	3L_12357247_SNP [dm3] 3L_12364147_SNP [dm6]	T	A	2.601e^-5	0.697	INTERGENIC
3R	9124849	3R_9124849_SNP [dm3] 3R_13299127_SNP [dm6]	C	A	2.612e^-5	0.697	SYNONYMOUS_CODING CG8774 UTR_5_PRIME CG8774 DOWNSTREAM CG8773	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
2R	8090749	2R_8090749_SNP [dm3] 2R_12203244_SNP [dm6]	T	A	2.638e^-5	0.697	INTERGENIC
2L	1485719	2L_1485719_INS [dm3] 2L_1485719_INS [dm6]	C	CTTC	2.654e^-5	0.697	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
2R	13941175	2R_13941175_SNP [dm3] 2R_18053670_SNP [dm6]	T	G	2.678e^-5	0.697	NON_SYNONYMOUS_CODING CG10911
3R	18784574	3R_18784574_SNP [dm3] 3R_22958852_SNP [dm6]	T	G	2.710e^-5	0.697	INTRON klg	TF binding site mE1_TFBS_cad
2R	14189546	2R_14189546_SNP [dm3] 2R_18302041_SNP [dm6]	G	A	2.714e^-5	0.697	DOWNSTREAM CG14505 INTRON sbb
3R	8986186	3R_8986186_SNP [dm3] 3R_13160464_SNP [dm6]	T	A	2.763e^-5	0.7	INTRON timeout
X	4505991	X_4505991_SNP [dm3] X_4611958_SNP [dm6]	A	G	2.928e^-5	0.732	UPSTREAM CR32773 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	9114055	3R_9114055_SNP [dm3] 3R_13288333_SNP [dm6]	A	T	3.089e^-5	0.759	INTRON CG15887	TF binding site mE1_TFBS_inv
2L	9965324	2L_9965324_SNP [dm3] 2L_9965324_SNP [dm6]	T	A	3.115e^-5	0.759	INTRON Dref	TF binding site mE1_TFBS_sens
2R	16474918	2R_16474918_SNP [dm3] 2R_20587413_SNP [dm6]	G	T	3.289e^-5	0.791	UPSTREAM bl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
3R	24571403	3R_24571403_SNP [dm3] 3R_28745681_SNP [dm6]	G	A	3.440e^-5	0.8	UPSTREAM AstA-R2 INTERGENIC
2L	9965613	2L_9965613_SNP [dm3] 2L_9965613_SNP [dm6]	C	G	3.488e^-5	0.8	SYNONYMOUS_CODING Dref
2R	14733513	2R_14733513_SNP [dm3] 2R_18846008_SNP [dm6]	C	T	3.530e^-5	0.8	DOWNSTREAM CG15100 INTRON CG15099	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
2R	10576591	2R_10576591_SNP [dm3] 2R_14689086_SNP [dm6]	T	C	3.664e^-5	0.8	INTRON mspo
3R	12345429	3R_12345429_SNP [dm3] 3R_16519707_SNP [dm6]	G	T	3.684e^-5	0.8	INTRON CG42342	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
2R	7449080	2R_7449080_SNP [dm3] 2R_11561575_SNP [dm6]	C	T	3.702e^-5	0.8	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9318728	2L_9318728_SNP [dm3] 2L_9318728_SNP [dm6]	T	C	3.790e^-5	0.8	INTERGENIC
X	18138990	X_18138990_DEL [dm3] X_18244957_DEL [dm6]	GTGTG	G	3.849e^-5	0.8	EXON CR45607	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9033676	3R_9033676_SNP [dm3] 3R_13207954_SNP [dm6]	C	G	3.864e^-5	0.8	DOWNSTREAM CG8483 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	14883274	2R_14883274_SNP [dm3] 2R_18995769_SNP [dm6]	T	G	3.890e^-5	0.8	DOWNSTREAM snoRNA:abba-a INTRON tn
X	15551620	X_15551620_SNP [dm3] X_15657587_SNP [dm6]	G	C	3.891e^-5	0.8	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	8437848	3L_8437848_SNP [dm3] 3L_8444748_SNP [dm6]	C	T	3.908e^-5	0.8	INTRON CG6983	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12345430	3R_12345430_SNP [dm3] 3R_16519708_SNP [dm6]	G	C	3.916e^-5	0.8	INTRON CG42342	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
X	14154208	X_14154208_SNP [dm3] X_14260175_SNP [dm6]	C	A	3.966e^-5	0.8	INTERGENIC
3L	3187461	3L_3187461_SNP [dm3] 3L_3187461_SNP [dm6]	T	A	4.042e^-5	0.8	UPSTREAM CG14957 DOWNSTREAM CG42494 & 2 others INTERGENIC
3R	24246893	3R_24246893_SNP [dm3] 3R_28421171_SNP [dm6]	C	A	4.090e^-5	0.8	INTRON beat-VI
2L	12156666	2L_12156666_SNP [dm3] 2L_12156666_SNP [dm6]	A	G	4.134e^-5	0.8	INTRON CG31760
2R	19675961	2R_19675961_SNP [dm3] 2R_23788438_SNP [dm6]	C	T	4.193e^-5	0.8	INTRON CG9850
3R	23984927	3R_23984927_SNP [dm3] 3R_28159205_SNP [dm6]	A	G	4.193e^-5	0.8	INTRON CG34354
3R	12706605	3R_12706605_SNP [dm3] 3R_16880883_SNP [dm6]	C	T	4.232e^-5	0.8	INTRON iab-8
3R	9076306	3R_9076306_SNP [dm3] 3R_13250584_SNP [dm6]	T	A	4.297e^-5	0.8	INTRON Ace
3R	21098076	3R_21098076_SNP [dm3] 3R_25272354_SNP [dm6]	T	G	4.415e^-5	0.8	NON_SYNONYMOUS_CODING CG11891 UTR_3_PRIME CG11889 DOWNSTREAM CG11889	TF binding site mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

mn_Surv_Azinpho_1_0 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results