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=3.163e^-16)
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

2211 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	16036130	3L_16036130_SNP [dm3] 3L_16043030_SNP [dm6]	C	T	1.752e^-6	0.807	UTR_5_PRIME th UPSTREAM th INTRON th	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_inv
3L	19590381	3L_19590381_SNP [dm3] 3L_19597281_SNP [dm6]	T	A	1.895e^-6	0.807	SYNONYMOUS_CODING ash1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	5997712	3L_5997712_SNP [dm3] 3L_6004612_SNP [dm6]	C	T	2.286e^-6	0.807	INTRON PVRAP	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	19649763	3R_19649763_INS [dm3] 3R_23824041_INS [dm6]	T	TGT	2.408e^-6	0.807	INTRON CG34355
3R	23964494	3R_23964494_SNP [dm3] 3R_28138772_SNP [dm6]	G	T	2.915e^-6	0.807	INTERGENIC
3L	8636367	3L_8636367_SNP [dm3] 3L_8643267_SNP [dm6]	G	A	3.723e^-6	0.807	SYNONYMOUS_CODING Cpr66D	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	9340954	3L_9340954_SNP [dm3] 3L_9347854_SNP [dm6]	T	C	4.089e^-6	0.807	SYNONYMOUS_CODING PGRP-LC UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC
3L	9746615	3L_9746615_SNP [dm3] 3L_9753515_SNP [dm6]	A	G	4.214e^-6	0.807	INTRON CG42268
2R	2718726	2R_2718726_SNP [dm3] 2R_6831221_SNP [dm6]	C	T	4.910e^-6	0.807	DOWNSTREAM CG34215 INTRON CG15236
3R	27135735	3R_27135735_SNP [dm3] 3R_31310013_SNP [dm6]	A	C	5.174e^-6	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	9340927	3L_9340927_SNP [dm3] 3L_9347827_SNP [dm6]	C	T	5.182e^-6	0.807	SYNONYMOUS_CODING PGRP-LC UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC
X	18011757	X_18011757_INS [dm3] X_18117724_INS [dm6]	T	TT	5.622e^-6	0.807	UPSTREAM wupA INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	16744235	2R_16744235_SNP [dm3] 2R_20856730_SNP [dm6]	G	T	5.791e^-6	0.807	INTERGENIC
3R	11652848	3R_11652848_SNP [dm3] 3R_15827126_SNP [dm6]	T	G	6.227e^-6	0.807	SYNONYMOUS_CODING CG4576 INTRON rec
2L	5974062	2L_5974062_SNP [dm3] 2L_5974062_SNP [dm6]	A	T	7.194e^-6	0.807	INTRON chic
3R	19216311	3R_19216311_SNP [dm3] 3R_23390589_SNP [dm6]	G	T	7.215e^-6	0.807	DOWNSTREAM CR43387 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	9950539	2L_9950539_SNP [dm3] 2L_9950539_SNP [dm6]	G	C	7.376e^-6	0.807	UPSTREAM mir-87 INTERGENIC
3L	9746792	3L_9746792_SNP [dm3] 3L_9753692_SNP [dm6]	C	T	8.987e^-6	0.807	INTRON CG42268
2R	16531028	2R_16531028_SNP [dm3] 2R_20643523_SNP [dm6]	T	C	9.183e^-6	0.807	UPSTREAM DMAP1 DOWNSTREAM CG11110 INTRON CG33785 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2R	1078372	2R_1078372_SNP [dm3] 2R_5190867_SNP [dm6]	C	A	9.308e^-6	0.807	INTRON Nipped-A	transposable element FlyBase
2L	14830196	2L_14830196_SNP [dm3] 2L_14830196_SNP [dm6]	T	C	9.440e^-6	0.807	INTERGENIC
2R	5401020	2R_5401020_SNP [dm3] 2R_9513515_SNP [dm6]	A	G	1.043e^-5	0.807	INTRON brp
3R	27135758	3R_27135758_INS [dm3] 3R_31310036_INS [dm6]	A	ACTGCTGCG	1.095e^-5	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	10413521	3L_10413521_SNP [dm3] 3L_10420421_SNP [dm6]	A	T	1.140e^-5	0.807	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9340957	3L_9340957_SNP [dm3] 3L_9347857_SNP [dm6]	T	C	1.171e^-5	0.807	SYNONYMOUS_CODING PGRP-LC UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC
2L	9209653	2L_9209653_SNP [dm3] 2L_9209653_SNP [dm6]	C	G	1.257e^-5	0.807	INTRON tai
3R	23964492	3R_23964492_SNP [dm3] 3R_28138770_SNP [dm6]	T	A	1.369e^-5	0.807	INTERGENIC
3R	23926119	3R_23926119_SNP [dm3] 3R_28100397_SNP [dm6]	C	A	1.393e^-5	0.807	INTERGENIC
2R	14808373	2R_14808373_SNP [dm3] 2R_18920868_SNP [dm6]	C	T	1.427e^-5	0.807	INTRON sano
2R	5943150	2R_5943150_SNP [dm3] 2R_10055645_SNP [dm6]	A	T	1.460e^-5	0.807	INTRON magu	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3R	24836863	3R_24836863_SNP [dm3] 3R_29011141_SNP [dm6]	C	T	1.487e^-5	0.807	INTRON wat
2L	14830212	2L_14830212_SNP [dm3] 2L_14830212_SNP [dm6]	C	T	1.503e^-5	0.807	INTERGENIC
2L	14830203	2L_14830203_SNP [dm3] 2L_14830203_SNP [dm6]	T	C	1.629e^-5	0.807	INTERGENIC
2L	16778469	2L_16778469_SNP [dm3] 2L_16778469_SNP [dm6]	G	T	1.650e^-5	0.807	NON_SYNONYMOUS_CODING Mhc INTRON Mhc
3L	9341302	3L_9341302_SNP [dm3] 3L_9348202_SNP [dm6]	T	G	1.701e^-5	0.807	UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC
2R	16744236	2R_16744236_DEL [dm3] 2R_20856731_DEL [dm6]	GG	G	1.742e^-5	0.807	INTERGENIC
3L	10357987	3L_10357987_SNP [dm3] 3L_10364887_SNP [dm6]	A	T	1.744e^-5	0.807	UPSTREAM mir-276a EXON CR44327
3L	10432767	3L_10432767_INS [dm3] 3L_10439667_INS [dm6]	A	AA	1.866e^-5	0.807	INTERGENIC
2L	14830210	2L_14830210_SNP [dm3] 2L_14830210_SNP [dm6]	T	A	1.909e^-5	0.807	INTERGENIC
2R	15027922	2R_15027922_SNP [dm3] 2R_19140417_SNP [dm6]	C	T	1.931e^-5	0.807	SYNONYMOUS_CODING CG15111	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	14752901	2R_14752901_SNP [dm3] 2R_18865396_SNP [dm6]	C	G	1.994e^-5	0.807	UPSTREAM Dpt & 1 other DOWNSTREAM CG43070 INTERGENIC
2L	10868856	2L_10868856_SNP [dm3] 2L_10868856_SNP [dm6]	C	G	2.019e^-5	0.807	INTERGENIC
2L	7578722	2L_7578722_SNP [dm3] 2L_7578722_SNP [dm6]	A	C	2.080e^-5	0.807	UTR_5_PRIME RapGAP1
3L	9697223	3L_9697223_INS [dm3] 3L_9704123_INS [dm6]	C	TTTATA	2.082e^-5	0.807	UPSTREAM CG16711 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	19649746	3R_19649746_SNP [dm3] 3R_23824024_SNP [dm6]	T	C	2.211e^-5	0.807	INTRON CG34355
3L	11104967	3L_11104967_SNP [dm3] 3L_11111867_SNP [dm6]	T	C	2.226e^-5	0.807	UTR_3_PRIME CG7638 DOWNSTREAM Sod
2L	14830187	2L_14830187_SNP [dm3] 2L_14830187_SNP [dm6]	T	G	2.301e^-5	0.807	INTERGENIC
2L	5849263	2L_5849263_SNP [dm3] 2L_5849263_SNP [dm6]	A	C	2.352e^-5	0.807	INTRON TrissinR
3L	9545597	3L_9545597_SNP [dm3] 3L_9552497_SNP [dm6]	C	A	2.439e^-5	0.807	INTRON CG42673
3R	14345445	3R_14345445_SNP [dm3] 3R_18519723_SNP [dm6]	T	A	2.565e^-5	0.807	INTRON fru
2R	2718605	2R_2718605_SNP [dm3] 2R_6831100_SNP [dm6]	T	G	2.628e^-5	0.807	DOWNSTREAM CG34215 INTRON CG15236
2R	18087115	2R_18087115_SNP [dm3] 2R_22199610_SNP [dm6]	A	C	2.670e^-5	0.807	INTRON Swim
3R	25290840	3R_25290840_SNP [dm3] 3R_29465118_SNP [dm6]	C	G	2.771e^-5	0.807	INTRON Ptp99A
2L	5973720	2L_5973720_SNP [dm3] 2L_5973720_SNP [dm6]	A	G	2.807e^-5	0.807	INTRON chic
2R	1358575	2R_1358575_SNP [dm3] 2R_5471070_SNP [dm6]	G	A	2.884e^-5	0.807	INTRON CG30440	TF binding site mE1_TFBS_cad mE1_TFBS_HSA transposable element FlyBase
2L	9079049	2L_9079049_SNP [dm3] 2L_9079049_SNP [dm6]	G	C	2.965e^-5	0.807	INTERGENIC
2R	18984195	2R_18984195_SNP [dm3] 2R_23096672_SNP [dm6]	A	G	3.004e^-5	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_hb
2R	17929804	2R_17929804_SNP [dm3] 2R_22042299_SNP [dm6]	A	G	3.044e^-5	0.807	SYNONYMOUS_CODING PpD5	TF binding site BDTNP1_TFBS_sna
2L	7366950	2L_7366950_SNP [dm3] 2L_7366950_SNP [dm6]	T	G	3.073e^-5	0.807	INTRON Wnt10
2R	1078285	2R_1078285_SNP [dm3] 2R_5190780_SNP [dm6]	A	G	3.124e^-5	0.807	INTRON Nipped-A	transposable element FlyBase
2R	1373724	2R_1373724_SNP [dm3] 2R_5486219_SNP [dm6]	G	C	3.140e^-5	0.807	INTRON CG30440	transposable element FlyBase
3L	11745867	3L_11745867_SNP [dm3] 3L_11752767_SNP [dm6]	G	T	3.167e^-5	0.807	DOWNSTREAM Gr68a INTRON CG6024
2L	14830188	2L_14830188_SNP [dm3] 2L_14830188_SNP [dm6]	C	A	3.274e^-5	0.807	INTERGENIC
3L	11102343	3L_11102343_SNP [dm3] 3L_11109243_SNP [dm6]	G	A	3.303e^-5	0.807	SYNONYMOUS_CODING CG34012 UPSTREAM CG7638 DOWNSTREAM CG12522
2R	17433764	2R_17433764_SNP [dm3] 2R_21546259_SNP [dm6]	G	A	3.380e^-5	0.807	UPSTREAM Egfr INTRON Egfr	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_Trl
3R	14345446	3R_14345446_SNP [dm3] 3R_18519724_SNP [dm6]	T	G	3.384e^-5	0.807	INTRON fru
3L	10853842	3L_10853842_SNP [dm3] 3L_10860742_SNP [dm6]	A	T	3.419e^-5	0.807	INTRON tna	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
X	9507797	X_9507797_SNP [dm3] X_9613764_SNP [dm6]	G	T	3.439e^-5	0.807	INTRON CG42797
3R	24836860	3R_24836860_SNP [dm3] 3R_29011138_SNP [dm6]	C	G	3.472e^-5	0.807	INTRON wat
2R	5943130	2R_5943130_DEL [dm3] 2R_10055625_DEL [dm6]	TA	T	3.486e^-5	0.807	INTRON magu	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	16778306	2L_16778306_SNP [dm3] 2L_16778306_SNP [dm6]	T	G	3.504e^-5	0.807	INTRON Mhc
2L	5848806	2L_5848806_SNP [dm3] 2L_5848806_SNP [dm6]	G	T	3.538e^-5	0.807	INTRON TrissinR
2R	14752706	2R_14752706_SNP [dm3] 2R_18865201_SNP [dm6]	G	C	3.579e^-5	0.807	UTR_5_PRIME CG43071 UPSTREAM Dpt DOWNSTREAM CG43070
2L	19129622	2L_19129622_SNP [dm3] 2L_19129622_SNP [dm6]	T	A	3.592e^-5	0.807	UTR_3_PRIME Aats-asn DOWNSTREAM Aats-asn & 1 other	TF binding site mE1_TFBS_cad
2R	14098872	2R_14098872_SNP [dm3] 2R_18211367_SNP [dm6]	G	A	3.608e^-5	0.807	DOWNSTREAM CR45147 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	16778314	2L_16778314_SNP [dm3] 2L_16778314_SNP [dm6]	T	C	3.639e^-5	0.807	INTRON Mhc
3R	26746203	3R_26746203_SNP [dm3] 3R_30920481_SNP [dm6]	T	C	3.658e^-5	0.807	INTRON Ptx1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2L	8982738	2L_8982738_INS [dm3] 2L_8982738_INS [dm6]	T	TT	3.713e^-5	0.807	INTRON CG13101
2L	4984901	2L_4984901_SNP [dm3] 2L_4984901_SNP [dm6]	C	T	3.750e^-5	0.807	SYNONYMOUS_CODING CG34126	TF binding site mE1_TFBS_chinmo
X	18017185	X_18017185_SNP [dm3] X_18123152_SNP [dm6]	A	G	3.791e^-5	0.807	DOWNSTREAM CR45606 INTERGENIC
2R	12604439	2R_12604439_SNP [dm3] 2R_16716934_SNP [dm6]	A	C	3.802e^-5	0.807	INTRON CG30463
2L	15534002	2L_15534002_SNP [dm3] 2L_15534002_SNP [dm6]	C	T	3.824e^-5	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19573384	2R_19573384_SNP [dm3] 2R_23685861_SNP [dm6]	T	A	3.920e^-5	0.807	UPSTREAM l_2_efl INTRON St3
3R	19649740	3R_19649740_SNP [dm3] 3R_23824018_SNP [dm6]	T	G	3.966e^-5	0.807	INTRON CG34355
2L	1239293	2L_1239293_SNP [dm3] 2L_1239293_SNP [dm6]	T	G	4.000e^-5	0.807	UPSTREAM CG5397 INTERGENIC
3R	24836848	3R_24836848_SNP [dm3] 3R_29011126_SNP [dm6]	G	A	4.057e^-5	0.807	INTRON wat
2R	1358734	2R_1358734_SNP [dm3] 2R_5471229_SNP [dm6]	G	C	4.070e^-5	0.807	INTRON CG30440	TF binding site mE1_TFBS_cad mE1_TFBS_HSA transposable element FlyBase
2R	1325455	2R_1325455_SNP [dm3] 2R_5437950_SNP [dm6]	T	A	4.114e^-5	0.807	INTRON laccase2
X	4615350	X_4615350_SNP [dm3] X_4721317_SNP [dm6]	C	T	4.207e^-5	0.807	INTRON Proc-R
2R	17260722	2R_17260722_SNP [dm3] 2R_21373217_SNP [dm6]	T	C	4.319e^-5	0.807	INTRON cv-2	TF binding site BDTNP1_TFBS_twi
2R	15838613	2R_15838613_SNP [dm3] 2R_19951108_SNP [dm6]	G	A	4.643e^-5	0.807	UPSTREAM CG10822 INTERGENIC
X	6952669	X_6952669_DEL [dm3] X_7058636_DEL [dm6]	TGACCTATGGGCATACA...	T	4.650e^-5	0.807	INTRON CG12541	TF binding site 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_eve mE1_TFBS_HSA
3R	4935239	3R_4935239_SNP [dm3] 3R_9109517_SNP [dm6]	A	G	4.663e^-5	0.807	INTRON pum
2L	5652592	2L_5652592_SNP [dm3] 2L_5652592_SNP [dm6]	C	T	4.673e^-5	0.807	INTRON CG31646
2R	19709451	2R_19709451_SNP [dm3] 2R_23821928_SNP [dm6]	G	A	4.715e^-5	0.807	INTRON CG5549	TF binding site mE1_TFBS_chinmo
2R	16531073	2R_16531073_SNP [dm3] 2R_20643568_SNP [dm6]	T	C	4.747e^-5	0.807	UPSTREAM DMAP1 INTRON CG33785 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	14695808	2R_14695808_SNP [dm3] 2R_18808303_SNP [dm6]	C	T	4.829e^-5	0.807	DOWNSTREAM CG15096 INTERGENIC
3L	10515325	3L_10515325_SNP [dm3] 3L_10522225_SNP [dm6]	T	C	4.855e^-5	0.807	INTRON A2bp1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA
X	15570203	X_15570203_SNP [dm3] X_15676170_SNP [dm6]	C	G	4.934e^-5	0.807	INTRON CG12708
2L	9078985	2L_9078985_SNP [dm3] 2L_9078985_SNP [dm6]	A	G	4.935e^-5	0.807	DOWNSTREAM CG12439 INTERGENIC

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By genomic position
Variant impact
Gene name

mn_Week5_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results