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=1.308e^-15)
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

2310 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	1.348e^-6	0.804	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
3R	14345445	3R_14345445_SNP [dm3] 3R_18519723_SNP [dm6]	T	A	2.710e^-6	0.804	INTRON fru
3R	19649763	3R_19649763_INS [dm3] 3R_23824041_INS [dm6]	T	TGT	2.943e^-6	0.804	INTRON CG34355
3R	14345446	3R_14345446_SNP [dm3] 3R_18519724_SNP [dm6]	T	G	3.477e^-6	0.804	INTRON fru
2R	12604439	2R_12604439_SNP [dm3] 2R_16716934_SNP [dm6]	A	C	3.544e^-6	0.804	INTRON CG30463
3R	11652848	3R_11652848_SNP [dm3] 3R_15827126_SNP [dm6]	T	G	3.926e^-6	0.804	SYNONYMOUS_CODING CG4576 INTRON rec
2R	14808373	2R_14808373_SNP [dm3] 2R_18920868_SNP [dm6]	C	T	4.051e^-6	0.804	INTRON sano
3L	19590381	3L_19590381_SNP [dm3] 3L_19597281_SNP [dm6]	T	A	4.232e^-6	0.804	SYNONYMOUS_CODING ash1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	23964494	3R_23964494_SNP [dm3] 3R_28138772_SNP [dm6]	G	T	4.376e^-6	0.804	INTERGENIC
3L	5997712	3L_5997712_SNP [dm3] 3L_6004612_SNP [dm6]	C	T	4.428e^-6	0.804	INTRON PVRAP	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	27135735	3R_27135735_SNP [dm3] 3R_31310013_SNP [dm6]	A	C	5.046e^-6	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	8636367	3L_8636367_SNP [dm3] 3L_8643267_SNP [dm6]	G	A	5.842e^-6	0.804	SYNONYMOUS_CODING Cpr66D	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2L	5709091	2L_5709091_SNP [dm3] 2L_5709091_SNP [dm6]	G	A	6.748e^-6	0.804	UPSTREAM CG7236 INTRON CG7236
3R	24430474	3R_24430474_SNP [dm3] 3R_28604752_SNP [dm6]	A	G	6.990e^-6	0.804	UTR_3_PRIME Hrb98DE INTRON Hrb98DE
X	15570203	X_15570203_SNP [dm3] X_15676170_SNP [dm6]	C	G	7.092e^-6	0.804	INTRON CG12708
2L	5709074	2L_5709074_SNP [dm3] 2L_5709074_SNP [dm6]	A	G	7.273e^-6	0.804	UPSTREAM CG7236 INTRON CG7236
3L	9341302	3L_9341302_SNP [dm3] 3L_9348202_SNP [dm6]	T	G	8.301e^-6	0.804	UTR_3_PRIME PGRP-LC DOWNSTREAM PGRP-LC
3R	19216311	3R_19216311_SNP [dm3] 3R_23390589_SNP [dm6]	G	T	9.496e^-6	0.804	DOWNSTREAM CR43387 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14752901	2R_14752901_SNP [dm3] 2R_18865396_SNP [dm6]	C	G	1.071e^-5	0.804	UPSTREAM Dpt & 1 other DOWNSTREAM CG43070 INTERGENIC
3R	19649746	3R_19649746_SNP [dm3] 3R_23824024_SNP [dm6]	T	C	1.097e^-5	0.804	INTRON CG34355
2R	16744235	2R_16744235_SNP [dm3] 2R_20856730_SNP [dm6]	G	T	1.130e^-5	0.804	INTERGENIC
2R	2718726	2R_2718726_SNP [dm3] 2R_6831221_SNP [dm6]	C	T	1.148e^-5	0.804	DOWNSTREAM CG34215 INTRON CG15236
X	16185356	X_16185356_SNP [dm3] X_16291323_SNP [dm6]	G	T	1.206e^-5	0.804	INTRON caz
3R	27135758	3R_27135758_INS [dm3] 3R_31310036_INS [dm6]	A	ACTGCTGCG	1.206e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	5998197	3L_5998197_SNP [dm3] 3L_6005097_SNP [dm6]	C	A	1.249e^-5	0.804	INTRON PVRAP	TF binding site mE1_TFBS_cad
2L	16778469	2L_16778469_SNP [dm3] 2L_16778469_SNP [dm6]	G	T	1.255e^-5	0.804	NON_SYNONYMOUS_CODING Mhc INTRON Mhc
3R	24427450	3R_24427450_SNP [dm3] 3R_28601728_SNP [dm6]	A	T	1.347e^-5	0.804	UPSTREAM snoRNA:Psi28S-3405b & 3 others DOWNSTREAM snoRNA:Psi28S-3405a INTRON Hrb98DE EXON snoRNA:Psi28S-3305a
2R	18225467	2R_18225467_SNP [dm3] 2R_22337962_SNP [dm6]	G	T	1.425e^-5	0.804	INTRON Liprin-gamma
3L	10357987	3L_10357987_SNP [dm3] 3L_10364887_SNP [dm6]	A	T	1.438e^-5	0.804	UPSTREAM mir-276a EXON CR44327
2L	5974062	2L_5974062_SNP [dm3] 2L_5974062_SNP [dm6]	A	T	1.474e^-5	0.804	INTRON chic
2L	9950539	2L_9950539_SNP [dm3] 2L_9950539_SNP [dm6]	G	C	1.669e^-5	0.804	UPSTREAM mir-87 INTERGENIC
2R	16744236	2R_16744236_DEL [dm3] 2R_20856731_DEL [dm6]	GG	G	1.750e^-5	0.804	INTERGENIC
3R	18324842	3R_18324842_INS [dm3] 3R_22499120_INS [dm6]	C	CC	1.801e^-5	0.804	INTRON Octbeta1R
2R	1078372	2R_1078372_SNP [dm3] 2R_5190867_SNP [dm6]	C	A	1.843e^-5	0.804	INTRON Nipped-A	transposable element FlyBase
3R	23964492	3R_23964492_SNP [dm3] 3R_28138770_SNP [dm6]	T	A	1.870e^-5	0.804	INTERGENIC
3R	23926119	3R_23926119_SNP [dm3] 3R_28100397_SNP [dm6]	C	A	1.872e^-5	0.804	INTERGENIC
3L	12544228	3L_12544228_SNP [dm3] 3L_12551128_SNP [dm6]	G	C	2.047e^-5	0.804	INTRON sowah	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	7125274	2L_7125274_SNP [dm3] 2L_7125274_SNP [dm6]	G	A	2.058e^-5	0.804	INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	26667352	3R_26667352_SNP [dm3] 3R_30841630_SNP [dm6]	T	A	2.125e^-5	0.804	UTR_3_PRIME CG15544
2L	16778306	2L_16778306_SNP [dm3] 2L_16778306_SNP [dm6]	T	G	2.317e^-5	0.804	INTRON Mhc
3R	8431661	3R_8431661_SNP [dm3] 3R_12605939_SNP [dm6]	A	T	2.324e^-5	0.804	INTERGENIC
3L	12283172	3L_12283172_SNP [dm3] 3L_12290072_SNP [dm6]	A	G	2.333e^-5	0.804	DOWNSTREAM CG4328 EXON CR45658	TF binding site BDTNP1_TFBS_prd
2R	17442555	2R_17442555_SNP [dm3] 2R_21555050_SNP [dm6]	C	A	2.365e^-5	0.804	SPLICE_SITE_REGION Egfr SYNONYMOUS_CODING Egfr	TF binding site mE1_TFBS_HSA
2L	16778314	2L_16778314_SNP [dm3] 2L_16778314_SNP [dm6]	T	C	2.397e^-5	0.804	INTRON Mhc
2L	9706768	2L_9706768_SNP [dm3] 2L_9706768_SNP [dm6]	A	T	2.423e^-5	0.804	UPSTREAM CG31710 INTRON pelo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	17260722	2R_17260722_SNP [dm3] 2R_21373217_SNP [dm6]	T	C	2.534e^-5	0.804	INTRON cv-2	TF binding site BDTNP1_TFBS_twi
2R	14695808	2R_14695808_SNP [dm3] 2R_18808303_SNP [dm6]	C	T	2.603e^-5	0.804	DOWNSTREAM CG15096 INTERGENIC
3R	27135746	3R_27135746_SNP [dm3] 3R_31310024_SNP [dm6]	G	C	2.733e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	10968631	X_10968631_SNP [dm3] X_11074598_SNP [dm6]	G	A	2.881e^-5	0.804	SYNONYMOUS_CODING sev	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	19874939	3L_19874939_SNP [dm3] 3L_19881839_SNP [dm6]	C	T	2.885e^-5	0.804	DOWNSTREAM Mi-2 & 1 other INTERGENIC
3R	13443823	3R_13443823_SNP [dm3] 3R_17618101_SNP [dm6]	A	C	2.919e^-5	0.804	UPSTREAM CG14326 DOWNSTREAM tRNA:P:90Ca & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	10432767	3L_10432767_INS [dm3] 3L_10439667_INS [dm6]	A	AA	3.103e^-5	0.804	INTERGENIC
2L	5243998	2L_5243998_SNP [dm3] 2L_5243998_SNP [dm6]	T	C	3.106e^-5	0.804	SYNONYMOUS_CODING tkv INTRON tkv EXON CR14033
2R	14695767	2R_14695767_SNP [dm3] 2R_18808262_SNP [dm6]	C	T	3.175e^-5	0.804	DOWNSTREAM CG15096 INTERGENIC	TF binding site mE1_TFBS_bab1
3R	27139119	3R_27139119_SNP [dm3] 3R_31313397_SNP [dm6]	C	A	3.181e^-5	0.804	INTRON CG34347	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	5401020	2R_5401020_SNP [dm3] 2R_9513515_SNP [dm6]	A	G	3.196e^-5	0.804	INTRON brp
X	15665822	X_15665822_SNP [dm3] X_15771789_SNP [dm6]	G	A	3.325e^-5	0.804	SYNONYMOUS_CODING CG33172	TF binding site mE1_TFBS_sens
3R	12031709	3R_12031709_SNP [dm3] 3R_16205987_SNP [dm6]	T	C	3.377e^-5	0.804	UPSTREAM mtSSB INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_zfh1
2R	14450334	2R_14450334_SNP [dm3] 2R_18562829_SNP [dm6]	T	C	3.405e^-5	0.804	INTRON GEFmeso	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11373190	2R_11373190_SNP [dm3] 2R_15485685_SNP [dm6]	A	T	3.443e^-5	0.804	DOWNSTREAM CG12964 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
X	20612452	X_20612452_SNP [dm3] X_20741425_SNP [dm6]	C	A	3.519e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_da
X	20612692	X_20612692_SNP [dm3] X_20741665_SNP [dm6]	T	C	3.533e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	10360567	3L_10360567_DEL [dm3] 3L_10367467_DEL [dm6]	AAGCATAATTA...	A	3.556e^-5	0.804	DOWNSTREAM CR44327 INTERGENIC
X	6952669	X_6952669_DEL [dm3] X_7058636_DEL [dm6]	TGACCTATGGGCATACA...	T	3.563e^-5	0.804	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	14834015	3R_14834015_SNP [dm3] 3R_19008293_SNP [dm6]	G	A	3.802e^-5	0.804	INTRON gukh	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	13976881	3R_13976881_SNP [dm3] 3R_18151159_SNP [dm6]	A	G	3.817e^-5	0.804	UPSTREAM CG14316 INTERGENIC
3L	10413521	3L_10413521_SNP [dm3] 3L_10420421_SNP [dm6]	A	T	3.822e^-5	0.804	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	5997888	3L_5997888_SNP [dm3] 3L_6004788_SNP [dm6]	C	T	4.013e^-5	0.804	INTRON PVRAP	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	10845140	3L_10845140_SNP [dm3] 3L_10852040_SNP [dm6]	T	G	4.023e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	6310024	X_6310024_MNP [dm3] X_6415991_MNP [dm6]	ACTT	CGGC	4.061e^-5	0.804	INTERGENIC
X	6310029	X_6310029_SNP [dm3] X_6415996_SNP [dm6]	T	A	4.061e^-5	0.804	INTERGENIC
X	6310034	X_6310034_MNP [dm3] X_6416001_MNP [dm6]	GAATG	CGCAA	4.061e^-5	0.804	INTERGENIC
X	6310041	X_6310041_SNP [dm3] X_6416008_SNP [dm6]	A	G	4.061e^-5	0.804	INTERGENIC
X	6310054	X_6310054_SNP [dm3] X_6416021_SNP [dm6]	G	T	4.061e^-5	0.804	INTERGENIC
X	15665817	X_15665817_SNP [dm3] X_15771784_SNP [dm6]	C	A	4.090e^-5	0.804	NON_SYNONYMOUS_CODING CG33172	TF binding site mE1_TFBS_sens
3L	9746615	3L_9746615_SNP [dm3] 3L_9753515_SNP [dm6]	A	G	4.102e^-5	0.804	INTRON CG42268
2L	8982738	2L_8982738_INS [dm3] 2L_8982738_INS [dm6]	T	TT	4.179e^-5	0.804	INTRON CG13101
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	4.179e^-5	0.804	INTRON Spn
2R	1080219	2R_1080219_SNP [dm3] 2R_5192714_SNP [dm6]	G	A	4.214e^-5	0.804	INTRON Nipped-A
2R	14168976	2R_14168976_SNP [dm3] 2R_18281471_SNP [dm6]	T	A	4.246e^-5	0.804	SYNONYMOUS_CODING sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	18548361	2R_18548361_SNP [dm3] 2R_22660856_SNP [dm6]	A	C	4.521e^-5	0.804	SYNONYMOUS_CODING CG42565 UTR_3_PRIME CG13510 & 1 other DOWNSTREAM CG13511	TF binding site mE1_TFBS_cad
2R	17929804	2R_17929804_SNP [dm3] 2R_22042299_SNP [dm6]	A	G	4.597e^-5	0.804	SYNONYMOUS_CODING PpD5	TF binding site BDTNP1_TFBS_sna
2L	10817728	2L_10817728_SNP [dm3] 2L_10817728_SNP [dm6]	G	A	4.627e^-5	0.804	INTRON Nos
2R	15027922	2R_15027922_SNP [dm3] 2R_19140417_SNP [dm6]	C	T	4.671e^-5	0.804	SYNONYMOUS_CODING CG15111	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	9342975	3L_9342975_SNP [dm3] 3L_9349875_SNP [dm6]	C	A	4.775e^-5	0.804	DOWNSTREAM UGP INTRON PGRP-LF
2L	13059910	2L_13059910_INS [dm3] 2L_13059910_INS [dm6]	T	TTTA	4.788e^-5	0.804	UTR_5_PRIME CG9932	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	19649740	3R_19649740_SNP [dm3] 3R_23824018_SNP [dm6]	T	G	4.863e^-5	0.804	INTRON CG34355
2R	18984195	2R_18984195_SNP [dm3] 2R_23096672_SNP [dm6]	A	G	5.012e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_hb
2R	14695777	2R_14695777_SNP [dm3] 2R_18808272_SNP [dm6]	A	G	5.077e^-5	0.804	DOWNSTREAM CG15096 INTERGENIC	TF binding site mE1_TFBS_bab1
2R	14169845	2R_14169845_SNP [dm3] 2R_18282340_SNP [dm6]	G	A	5.156e^-5	0.804	SYNONYMOUS_CODING sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11104967	3L_11104967_SNP [dm3] 3L_11111867_SNP [dm6]	T	C	5.170e^-5	0.804	UTR_3_PRIME CG7638 DOWNSTREAM Sod
2R	18087115	2R_18087115_SNP [dm3] 2R_22199610_SNP [dm6]	A	C	5.195e^-5	0.804	INTRON Swim
3R	18323780	3R_18323780_SNP [dm3] 3R_22498058_SNP [dm6]	C	T	5.263e^-5	0.804	INTRON Octbeta1R
3L	13298802	3L_13298802_SNP [dm3] 3L_13305702_SNP [dm6]	T	A	5.326e^-5	0.804	INTERGENIC
2R	11372410	2R_11372410_SNP [dm3] 2R_15484905_SNP [dm6]	G	T	5.345e^-5	0.804	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_Trl
2L	19129622	2L_19129622_SNP [dm3] 2L_19129622_SNP [dm6]	T	A	5.356e^-5	0.804	UTR_3_PRIME Aats-asn DOWNSTREAM Aats-asn & 1 other	TF binding site mE1_TFBS_cad
3L	9545597	3L_9545597_SNP [dm3] 3L_9552497_SNP [dm6]	C	A	5.514e^-5	0.804	INTRON CG42673
3R	16787474	3R_16787474_SNP [dm3] 3R_20961752_SNP [dm6]	G	C	5.519e^-5	0.804	INTRON Atpalpha
2R	789073	2R_789073_DEL [dm3] 2R_4901568_DEL [dm6]	AATTTGTATATAAATCATCA...	TCTGTTTGTAAATG...	5.656e^-5	0.804	INTRON CG44102
2L	4958840	2L_4958840_SNP [dm3] 2L_4958840_SNP [dm6]	T	G	5.709e^-5	0.804	DOWNSTREAM Marcal1 INTRON CG34124	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

lsm_Week5_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results