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=6.577e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_2R_NS	0.06343
In_3R_K	0.05493

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2468 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	12797662	2L_12797662_SNP [dm3] 2L_12797662_SNP [dm6]	C	G	1.461e^-7	0.18	INTERGENIC
2L	12797679	2L_12797679_SNP [dm3] 2L_12797679_SNP [dm6]	G	T	2.321e^-7	0.18	INTERGENIC
3L	11486883	3L_11486883_SNP [dm3] 3L_11493783_SNP [dm6]	C	T	3.981e^-7	0.18	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	11486233	3L_11486233_SNP [dm3] 3L_11493133_SNP [dm6]	G	A	5.018e^-7	0.18	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	12797294	2L_12797294_SNP [dm3] 2L_12797294_SNP [dm6]	G	A	5.231e^-7	0.18	INTERGENIC
3L	11485602	3L_11485602_SNP [dm3] 3L_11492502_SNP [dm6]	G	T	6.144e^-7	0.18	INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	12797646	2L_12797646_SNP [dm3] 2L_12797646_SNP [dm6]	C	T	6.823e^-7	0.18	INTERGENIC
2L	12799611	2L_12799611_SNP [dm3] 2L_12799611_SNP [dm6]	T	C	7.764e^-7	0.18	INTERGENIC
3L	11486384	3L_11486384_SNP [dm3] 3L_11493284_SNP [dm6]	T	C	9.154e^-7	0.18	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	11486774	3L_11486774_SNP [dm3] 3L_11493674_SNP [dm6]	C	T	9.596e^-7	0.18	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	11486237	3L_11486237_SNP [dm3] 3L_11493137_SNP [dm6]	A	T	1.269e^-6	0.189	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	12994349	X_12994349_SNP [dm3] X_13100316_SNP [dm6]	C	T	1.288e^-6	0.189	INTRON CG43313
3L	11485541	3L_11485541_SNP [dm3] 3L_11492441_SNP [dm6]	G	T	1.309e^-6	0.189	INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	11486451	3L_11486451_SNP [dm3] 3L_11493351_SNP [dm6]	C	A	1.511e^-6	0.202	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	12718175	2L_12718175_SNP [dm3] 2L_12718175_SNP [dm6]	T	A	2.382e^-6	0.246	UPSTREAM MRP INTRON CG5792	TF binding site mE1_TFBS_Trl
3L	11486235	3L_11486235_SNP [dm3] 3L_11493135_SNP [dm6]	A	G	2.433e^-6	0.246	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	12718259	2L_12718259_SNP [dm3] 2L_12718259_SNP [dm6]	G	A	2.453e^-6	0.246	UPSTREAM MRP INTRON CG5792	TF binding site mE1_TFBS_Trl
2L	12799498	2L_12799498_SNP [dm3] 2L_12799498_SNP [dm6]	C	T	2.506e^-6	0.246	INTERGENIC
3R	2101021	3R_2101021_SNP [dm3] 3R_6275299_SNP [dm6]	T	C	2.707e^-6	0.246	INTERGENIC
3L	11485392	3L_11485392_SNP [dm3] 3L_11492292_SNP [dm6]	G	C	2.749e^-6	0.246	INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	12797629	2L_12797629_SNP [dm3] 2L_12797629_SNP [dm6]	G	C	2.814e^-6	0.246	INTERGENIC
3L	11486247	3L_11486247_SNP [dm3] 3L_11493147_SNP [dm6]	A	C	3.285e^-6	0.246	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	11486441	3L_11486441_DEL [dm3] 3L_11493341_DEL [dm6]	AT	A	3.308e^-6	0.246	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	11486366	3L_11486366_SNP [dm3] 3L_11493266_SNP [dm6]	G	A	3.327e^-6	0.246	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7127891	2R_7127891_SNP [dm3] 2R_11240386_SNP [dm6]	G	T	3.371e^-6	0.246	UPSTREAM CG13215 INTERGENIC
2R	15400867	2R_15400867_SNP [dm3] 2R_19513362_SNP [dm6]	G	A	3.518e^-6	0.246	SYNONYMOUS_CODING Ir56d
2R	12708962	2R_12708962_SNP [dm3] 2R_16821457_SNP [dm6]	G	A	3.541e^-6	0.246	INTERGENIC
3L	11486181	3L_11486181_SNP [dm3] 3L_11493081_SNP [dm6]	G	T	3.844e^-6	0.258	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	15777852	2L_15777852_DEL [dm3] 2L_15777852_DEL [dm6]	ACA	G	4.725e^-6	0.282	UPSTREAM CG43760 INTERGENIC	TF binding site mE1_TFBS_kn
2L	12797735	2L_12797735_SNP [dm3] 2L_12797735_SNP [dm6]	A	T	4.767e^-6	0.282	INTERGENIC
2L	12799708	2L_12799708_SNP [dm3] 2L_12799708_SNP [dm6]	G	A	4.794e^-6	0.282	INTERGENIC
2R	2069605	2R_2069605_SNP [dm3] 2R_6182100_SNP [dm6]	G	A	4.831e^-6	0.282	UTR_3_PRIME Ptr UPSTREAM CG11211	regulatory region REDfly_CRMs
2L	12799499	2L_12799499_SNP [dm3] 2L_12799499_SNP [dm6]	C	T	4.957e^-6	0.282	INTERGENIC
3R	17825112	3R_17825112_INS [dm3] 3R_21999390_INS [dm6]	A	AA	5.358e^-6	0.296	INTRON Eip93F
2R	2066410	2R_2066410_SNP [dm3] 2R_6178905_SNP [dm6]	T	C	5.748e^-6	0.301	UPSTREAM tRNA:R2:42Aa & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2L	15777856	2L_15777856_SNP [dm3] 2L_15777856_SNP [dm6]	A	G	6.217e^-6	0.301	INTERGENIC	TF binding site mE1_TFBS_kn
2L	6565965	2L_6565965_SNP [dm3] 2L_6565965_SNP [dm6]	A	G	6.279e^-6	0.301	SYNONYMOUS_CODING CG13766	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA
2R	2438803	2R_2438803_SNP [dm3] 2R_6551298_SNP [dm6]	T	A	6.345e^-6	0.301	INTRON jing
2R	12713591	2R_12713591_SNP [dm3] 2R_16826086_SNP [dm6]	C	T	6.533e^-6	0.301	SYNONYMOUS_CODING CG34459 UPSTREAM CG34460	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	5339034	2R_5339034_SNP [dm3] 2R_9451529_SNP [dm6]	A	T	6.540e^-6	0.301	INTRON Camta
3R	18649686	3R_18649686_SNP [dm3] 3R_22823964_SNP [dm6]	C	G	6.648e^-6	0.301	EXON CR44350	TF binding site mE1_TFBS_inv
2L	6380408	2L_6380408_DEL [dm3] 2L_6380408_DEL [dm6]	CCTT	C	6.742e^-6	0.301	UPSTREAM CG9507 INTRON CG42368
3L	4840590	3L_4840590_SNP [dm3] 3L_4840590_SNP [dm6]	G	C	7.498e^-6	0.322	UPSTREAM CG13707 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3R	14416131	3R_14416131_SNP [dm3] 3R_18590409_SNP [dm6]	C	T	7.729e^-6	0.322	SYNONYMOUS_CODING CG7694 UPSTREAM qin DOWNSTREAM fray
3L	10562794	3L_10562794_SNP [dm3] 3L_10569694_SNP [dm6]	T	A	7.967e^-6	0.322	INTRON A2bp1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	11083549	3R_11083549_DEL [dm3] 3R_15257827_DEL [dm6]	TT	T	8.043e^-6	0.322	DOWNSTREAM eIF-2gamma & 1 other INTERGENIC
2L	6380416	2L_6380416_SNP [dm3] 2L_6380416_SNP [dm6]	A	C	8.220e^-6	0.322	UPSTREAM CG9507 INTRON CG42368
3R	18650373	3R_18650373_SNP [dm3] 3R_22824651_SNP [dm6]	T	C	8.411e^-6	0.322	EXON CR44350	TF binding site mE1_TFBS_inv
X	4434810	X_4434810_SNP [dm3] X_4540777_SNP [dm6]	T	C	8.414e^-6	0.322	UPSTREAM CHOp24 & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA
3R	14416236	3R_14416236_SNP [dm3] 3R_18590514_SNP [dm6]	C	A	8.966e^-6	0.336	UPSTREAM qin INTRON CG7694
3L	4415899	3L_4415899_SNP [dm3] 3L_4415899_SNP [dm6]	G	A	9.524e^-6	0.35	INTRON DOR
3L	2683052	3L_2683052_SNP [dm3] 3L_2683052_SNP [dm6]	G	A	9.821e^-6	0.354	INTRON Fife
2R	12708964	2R_12708964_SNP [dm3] 2R_16821459_SNP [dm6]	T	A	1.046e^-5	0.369	INTERGENIC
X	4434808	X_4434808_SNP [dm3] X_4540775_SNP [dm6]	C	T	1.064e^-5	0.369	UPSTREAM CHOp24 & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA
3L	11486292	3L_11486292_SNP [dm3] 3L_11493192_SNP [dm6]	T	A	1.092e^-5	0.369	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	16028663	3R_16028663_SNP [dm3] 3R_20202941_SNP [dm6]	C	T	1.102e^-5	0.369	INTERGENIC
2L	4757791	2L_4757791_DEL [dm3] 2L_4757791_DEL [dm6]	TTTCGCT	T	1.124e^-5	0.37	INTRON CG15630
2L	4788231	2L_4788231_SNP [dm3] 2L_4788231_SNP [dm6]	G	C	1.184e^-5	0.379	INTRON CG15630
3R	18644308	3R_18644308_SNP [dm3] 3R_22818586_SNP [dm6]	G	A	1.235e^-5	0.379	INTERGENIC
2L	12804680	2L_12804680_SNP [dm3] 2L_12804680_SNP [dm6]	T	G	1.239e^-5	0.379	INTERGENIC
3L	16744393	3L_16744393_SNP [dm3] 3L_16751293_SNP [dm6]	A	G	1.262e^-5	0.379	INTERGENIC
3L	11486466	3L_11486466_SNP [dm3] 3L_11493366_SNP [dm6]	A	T	1.273e^-5	0.379	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	15777860	2L_15777860_SNP [dm3] 2L_15777860_SNP [dm6]	A	G	1.300e^-5	0.379	INTERGENIC	TF binding site mE1_TFBS_kn
2L	9831234	2L_9831234_SNP [dm3] 2L_9831234_SNP [dm6]	C	T	1.307e^-5	0.379	INTRON nAChRalpha6
2L	12721998	2L_12721998_SNP [dm3] 2L_12721998_SNP [dm6]	A	T	1.314e^-5	0.379	UPSTREAM MRP & 1 other INTRON MRP	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Ubx
3L	10562766	3L_10562766_SNP [dm3] 3L_10569666_SNP [dm6]	A	G	1.432e^-5	0.407	INTRON A2bp1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	11486106	3L_11486106_SNP [dm3] 3L_11493006_SNP [dm6]	T	G	1.473e^-5	0.412	UPSTREAM chrb INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	13035259	3R_13035259_SNP [dm3] 3R_17209537_SNP [dm6]	A	G	1.493e^-5	0.412	INTERGENIC
2R	2075854	2R_2075854_SNP [dm3] 2R_6188349_SNP [dm6]	T	A	1.524e^-5	0.414	UTR_3_PRIME Ptr INTRON Ptr	TF binding site mE1_TFBS_inv
X	13411608	X_13411608_SNP [dm3] X_13517575_SNP [dm6]	T	A	1.556e^-5	0.416	INTRON Neto	TF binding site BDTNP1_TFBS_dl
X	4434811	X_4434811_SNP [dm3] X_4540778_SNP [dm6]	G	T	1.575e^-5	0.416	UPSTREAM CHOp24 & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA
3L	11484827	3L_11484827_DEL [dm3] 3L_11491727_DEL [dm6]	GG	G	1.650e^-5	0.43	INTRON chrb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	4434794	X_4434794_SNP [dm3] X_4540761_SNP [dm6]	C	A	1.675e^-5	0.43	UPSTREAM CHOp24 & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA
X	12531590	X_12531590_SNP [dm3] X_12637557_SNP [dm6]	A	G	1.695e^-5	0.43	SYNONYMOUS_CODING Tomosyn	TF binding site BDTNP1_TFBS_dl
2L	3698438	2L_3698438_SNP [dm3] 2L_3698438_SNP [dm6]	C	A	1.719e^-5	0.43	UPSTREAM CG3604 DOWNSTREAM CG10031 INTERGENIC
2L	9514668	2L_9514668_SNP [dm3] 2L_9514668_SNP [dm6]	A	G	1.846e^-5	0.45	INTRON CG33298
3L	11861950	3L_11861950_SNP [dm3] 3L_11868850_SNP [dm6]	C	T	1.866e^-5	0.45	INTRON CG44837
3L	4840591	3L_4840591_DEL [dm3] 3L_4840591_DEL [dm6]	GG	G	1.870e^-5	0.45	UPSTREAM CG13707 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	4840608	3L_4840608_SNP [dm3] 3L_4840608_SNP [dm6]	C	A	1.967e^-5	0.467	UPSTREAM CG13707 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2L	20549199	2L_20549199_SNP [dm3] 2L_20549199_SNP [dm6]	A	G	2.090e^-5	0.49	INTERGENIC
2L	17550377	2L_17550377_SNP [dm3] 2L_17550377_SNP [dm6]	A	G	2.141e^-5	0.496	INTERGENIC
2L	13838508	2L_13838508_SNP [dm3] 2L_13838508_SNP [dm6]	T	G	2.279e^-5	0.521	DOWNSTREAM CG33307 INTRON CenG1A	TF binding site mE1_TFBS_HSA
3L	10562762	3L_10562762_SNP [dm3] 3L_10569662_SNP [dm6]	T	C	2.325e^-5	0.522	INTRON A2bp1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	12795673	2L_12795673_SNP [dm3] 2L_12795673_SNP [dm6]	G	T	2.357e^-5	0.522	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	1839314	2R_1839314_SNP [dm3] 2R_5951809_SNP [dm6]	A	T	2.393e^-5	0.522	INTERGENIC	transposable element FlyBase
2L	12771300	2L_12771300_SNP [dm3] 2L_12771300_SNP [dm6]	C	T	2.399e^-5	0.522	INTERGENIC
3L	13268744	3L_13268744_SNP [dm3] 3L_13275644_SNP [dm6]	C	G	2.424e^-5	0.522	UTR_5_PRIME caps	TF binding site mE1_TFBS_chinmo
X	18953837	X_18953837_DEL [dm3] X_19059804_DEL [dm6]	AAG	A	2.464e^-5	0.525	INTRON CG14190
2L	9514331	2L_9514331_SNP [dm3] 2L_9514331_SNP [dm6]	C	T	2.743e^-5	0.547	INTRON CG33298
3R	10300223	3R_10300223_SNP [dm3] 3R_14474501_SNP [dm6]	C	T	2.794e^-5	0.547	INTRON cv-c	TF binding site mE1_TFBS_cad
3R	23448644	3R_23448644_INS [dm3] 3R_27622922_INS [dm6]	T	TT	2.904e^-5	0.547	DOWNSTREAM CG5612 INTRON Tusp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	1839313	2R_1839313_SNP [dm3] 2R_5951808_SNP [dm6]	T	A	2.936e^-5	0.547	INTERGENIC	transposable element FlyBase
2R	2860248	2R_2860248_SNP [dm3] 2R_6972743_SNP [dm6]	G	C	2.946e^-5	0.547	INTRON Cyp6u1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	12798114	2L_12798114_SNP [dm3] 2L_12798114_SNP [dm6]	C	A	2.957e^-5	0.547	INTERGENIC
X	18953831	X_18953831_DEL [dm3] X_19059798_DEL [dm6]	AAGTG	C	2.957e^-5	0.547	INTRON CG14190
2R	18235721	2R_18235721_SNP [dm3] 2R_22348216_SNP [dm6]	G	T	2.976e^-5	0.547	UPSTREAM CG11298 INTRON Liprin-gamma
2L	12721737	2L_12721737_SNP [dm3] 2L_12721737_SNP [dm6]	C	T	2.982e^-5	0.547	UTR_5_PRIME CG5792 UPSTREAM MRP INTRON MRP	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
X	13411553	X_13411553_SNP [dm3] X_13517520_SNP [dm6]	G	T	2.985e^-5	0.547	INTRON Neto	TF binding site BDTNP1_TFBS_dl
X	13411607	X_13411607_SNP [dm3] X_13517574_SNP [dm6]	T	C	3.023e^-5	0.547	INTRON Neto	TF binding site BDTNP1_TFBS_dl
2R	14015181	2R_14015181_SNP [dm3] 2R_18127676_SNP [dm6]	T	C	3.033e^-5	0.547	UPSTREAM Dip3 INTRON Spn55B	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

lsm_Lifespan phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results