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=7.358e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1936 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	9676496	2R_9676496_SNP [dm3] 2R_13788991_SNP [dm6]	T	C	1.242e^-6	0.679	INTERGENIC
2R	5389944	2R_5389944_SNP [dm3] 2R_9502439_SNP [dm6]	C	A	1.249e^-6	0.679	NON_SYNONYMOUS_CODING Wnt2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	1354357	2R_1354357_SNP [dm3] 2R_5466852_SNP [dm6]	G	T	1.564e^-6	0.679	INTERGENIC	transposable element FlyBase
3L	10836895	3L_10836895_SNP [dm3] 3L_10843795_SNP [dm6]	A	G	1.636e^-6	0.679	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2R	14676098	2R_14676098_SNP [dm3] 2R_18788593_SNP [dm6]	C	T	1.860e^-6	0.679	INTRON CG15080
2R	7220740	2R_7220740_SNP [dm3] 2R_11333235_SNP [dm6]	C	T	3.474e^-6	0.679	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	16925265	X_16925265_SNP [dm3] X_17031232_SNP [dm6]	G	C	3.590e^-6	0.679	INTRON CG45002
3L	10836651	3L_10836651_SNP [dm3] 3L_10843551_SNP [dm6]	C	T	3.713e^-6	0.679	INTERGENIC	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20517634	3R_20517634_SNP [dm3] 3R_24691912_SNP [dm6]	C	T	4.045e^-6	0.679	SYNONYMOUS_CODING slo
2R	9679611	2R_9679611_DEL [dm3] 2R_13792106_DEL [dm6]	CC	C	4.289e^-6	0.679	EXON CR43811
2R	1354359	2R_1354359_SNP [dm3] 2R_5466854_SNP [dm6]	C	A	4.542e^-6	0.679	INTERGENIC	transposable element FlyBase
2R	12145282	2R_12145282_SNP [dm3] 2R_16257777_SNP [dm6]	C	A	5.504e^-6	0.679	INTRON CngA
3R	16300782	3R_16300782_SNP [dm3] 3R_20475060_SNP [dm6]	T	C	5.526e^-6	0.679	INTRON Gfrl
2R	9676653	2R_9676653_SNP [dm3] 2R_13789148_SNP [dm6]	G	A	5.639e^-6	0.679	INTERGENIC
2R	10011581	2R_10011581_SNP [dm3] 2R_14124076_SNP [dm6]	C	T	5.874e^-6	0.679	INTRON Prosap
2R	7220722	2R_7220722_SNP [dm3] 2R_11333217_SNP [dm6]	G	A	6.065e^-6	0.679	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10011586	2R_10011586_SNP [dm3] 2R_14124081_SNP [dm6]	A	T	6.557e^-6	0.679	INTRON Prosap
X	16925264	X_16925264_SNP [dm3] X_17031231_SNP [dm6]	G	A	6.607e^-6	0.679	INTRON CG45002
2R	9799311	2R_9799311_SNP [dm3] 2R_13911806_SNP [dm6]	C	T	7.923e^-6	0.679	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799329	2R_9799329_INS [dm3] 2R_13911824_INS [dm6]	A	TGATGGTG	7.967e^-6	0.679	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799332	2R_9799332_SNP [dm3] 2R_13911827_SNP [dm6]	A	G	7.967e^-6	0.679	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9799335	2R_9799335_SNP [dm3] 2R_13911830_SNP [dm6]	C	T	7.967e^-6	0.679	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9675820	2R_9675820_SNP [dm3] 2R_13788315_SNP [dm6]	T	A	8.407e^-6	0.686	DOWNSTREAM Cpr50Ca INTERGENIC
2L	8423456	2L_8423456_DEL [dm3] 2L_8423456_DEL [dm6]	TGCT	T	8.866e^-6	0.693	INTRON Akap200	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_Trl
2R	13384648	2R_13384648_SNP [dm3] 2R_17497143_SNP [dm6]	G	A	9.599e^-6	0.72	INTERGENIC
3L	12494166	3L_12494166_SNP [dm3] 3L_12501066_SNP [dm6]	C	T	1.045e^-5	0.731	UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
2R	7220794	2R_7220794_SNP [dm3] 2R_11333289_SNP [dm6]	T	C	1.068e^-5	0.731	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	12145295	2R_12145295_DEL [dm3] 2R_16257790_DEL [dm6]	ATTGA	A	1.091e^-5	0.731	INTRON CngA
2L	20423664	2L_20423664_SNP [dm3] 2L_20423664_SNP [dm6]	G	A	1.171e^-5	0.744	DOWNSTREAM Arpc2 INTRON CG15130
2R	12076005	2R_12076005_SNP [dm3] 2R_16188500_SNP [dm6]	C	T	1.256e^-5	0.744	INTRON clu	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	10836872	3L_10836872_SNP [dm3] 3L_10843772_SNP [dm6]	G	T	1.303e^-5	0.744	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
X	5014255	X_5014255_DEL [dm3] X_5120222_DEL [dm6]	ACCA	A	1.306e^-5	0.744	INTRON rg & 1 other
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	1.308e^-5	0.744	INTRON Spn
2R	1352419	2R_1352419_SNP [dm3] 2R_5464914_SNP [dm6]	G	T	1.477e^-5	0.794	INTERGENIC	transposable element FlyBase
X	6732826	X_6732826_SNP [dm3] X_6838793_SNP [dm6]	T	A	1.482e^-5	0.794	UTR_3_PRIME CG14435 DOWNSTREAM nonC & 1 other
3R	13660339	3R_13660339_SNP [dm3] 3R_17834617_SNP [dm6]	A	G	1.578e^-5	0.801	INTRON tinc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	7220854	2R_7220854_SNP [dm3] 2R_11333349_SNP [dm6]	T	C	1.623e^-5	0.801	SYNONYMOUS_CODING sha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	19207896	3R_19207896_SNP [dm3] 3R_23382174_SNP [dm6]	T	A	1.632e^-5	0.801	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6487290	2L_6487290_SNP [dm3] 2L_6487290_SNP [dm6]	A	G	1.667e^-5	0.801	UTR_3_PRIME DLP DOWNSTREAM KFase & 1 other
2R	12100255	2R_12100255_SNP [dm3] 2R_16212750_SNP [dm6]	T	C	1.732e^-5	0.802	INTRON mrj
2R	12073056	2R_12073056_SNP [dm3] 2R_16185551_SNP [dm6]	A	G	1.781e^-5	0.802	SYNONYMOUS_CODING CG8441 DOWNSTREAM Lis-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	22569694	2L_22569694_SNP [dm3] 2L_22676962_SNP [dm6]	A	G	1.874e^-5	0.802	INTRON CG40006
2L	20415082	2L_20415082_SNP [dm3] 2L_20415082_SNP [dm6]	T	A	1.885e^-5	0.802	UPSTREAM CG10947 DOWNSTREAM CG10949 INTERGENIC
2R	12074021	2R_12074021_SNP [dm3] 2R_16186516_SNP [dm6]	C	A	2.023e^-5	0.802	UPSTREAM clu & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Ubx
2R	12145306	2R_12145306_SNP [dm3] 2R_16257801_SNP [dm6]	A	G	2.079e^-5	0.802	INTRON CngA
X	9006441	X_9006441_INS [dm3] X_9112408_INS [dm6]	C	CTT	2.122e^-5	0.802	INTRON AP-1gamma
3L	5212948	3L_5212948_SNP [dm3] 3L_5219848_SNP [dm6]	T	C	2.125e^-5	0.802	INTRON shep
3R	8151847	3R_8151847_SNP [dm3] 3R_12326125_SNP [dm6]	C	T	2.172e^-5	0.802	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	5718115	2L_5718115_SNP [dm3] 2L_5718115_SNP [dm6]	A	C	2.228e^-5	0.802	DOWNSTREAM CG11149 & 1 other INTERGENIC
X	16947237	X_16947237_SNP [dm3] X_17053204_SNP [dm6]	C	G	2.229e^-5	0.802	INTRON CG45002
2L	10430998	2L_10430998_SNP [dm3] 2L_10430998_SNP [dm6]	T	A	2.253e^-5	0.802	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	9675960	2R_9675960_SNP [dm3] 2R_13788455_SNP [dm6]	G	A	2.259e^-5	0.802	DOWNSTREAM Cpr50Ca INTERGENIC
3R	9702120	3R_9702120_SNP [dm3] 3R_13876398_SNP [dm6]	G	A	2.273e^-5	0.802	INTRON E5	TF binding site BDTNP1_TFBS_dl
3R	8151852	3R_8151852_SNP [dm3] 3R_12326130_SNP [dm6]	C	G	2.308e^-5	0.802	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	7702077	2L_7702077_SNP [dm3] 2L_7702077_SNP [dm6]	A	G	2.367e^-5	0.807	UPSTREAM Tep2 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	10431178	2L_10431178_SNP [dm3] 2L_10431178_SNP [dm6]	A	T	2.446e^-5	0.809	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	9702820	3R_9702820_SNP [dm3] 3R_13877098_SNP [dm6]	C	T	2.528e^-5	0.809	UTR_5_PRIME E5	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
X	16947242	X_16947242_SNP [dm3] X_17053209_SNP [dm6]	A	G	2.534e^-5	0.809	INTRON CG45002
3L	18957937	3L_18957937_SNP [dm3] 3L_18964837_SNP [dm6]	A	C	2.717e^-5	0.809	INTERGENIC
3L	18957938	3L_18957938_SNP [dm3] 3L_18964838_SNP [dm6]	T	A	2.717e^-5	0.809	INTERGENIC
2R	19573478	2R_19573478_SNP [dm3] 2R_23685955_SNP [dm6]	C	T	2.782e^-5	0.809	UPSTREAM l_2_efl INTRON St3
3L	5216153	3L_5216153_SNP [dm3] 3L_5223053_SNP [dm6]	T	A	2.839e^-5	0.809	INTRON shep
2R	9798932	2R_9798932_SNP [dm3] 2R_13911427_SNP [dm6]	G	A	2.904e^-5	0.809	UPSTREAM shot INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9675391	2R_9675391_SNP [dm3] 2R_13787886_SNP [dm6]	G	A	2.914e^-5	0.809	DOWNSTREAM Cpr50Ca INTERGENIC
X	7547548	X_7547548_SNP [dm3] X_7653515_SNP [dm6]	C	T	2.925e^-5	0.809	INTRON ct
2R	9977790	2R_9977790_SNP [dm3] 2R_14090285_SNP [dm6]	T	A	3.007e^-5	0.809	UPSTREAM CG42287 & 1 other INTRON Prosap
X	16947256	X_16947256_SNP [dm3] X_17053223_SNP [dm6]	C	A	3.007e^-5	0.809	INTRON CG45002
3L	18957941	3L_18957941_SNP [dm3] 3L_18964841_SNP [dm6]	G	C	3.059e^-5	0.809	INTERGENIC
2R	14925367	2R_14925367_SNP [dm3] 2R_19037862_SNP [dm6]	A	G	3.126e^-5	0.809	INTERGENIC
X	16947190	X_16947190_SNP [dm3] X_17053157_SNP [dm6]	G	T	3.172e^-5	0.809	INTRON CG45002
2R	8620603	2R_8620603_SNP [dm3] 2R_12733098_SNP [dm6]	T	C	3.287e^-5	0.809	INTRON CG42663	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	6487218	2L_6487218_SNP [dm3] 2L_6487218_SNP [dm6]	A	G	3.324e^-5	0.809	UTR_3_PRIME DLP DOWNSTREAM KFase & 1 other
2R	6679800	2R_6679800_SNP [dm3] 2R_10792295_SNP [dm6]	T	G	3.460e^-5	0.809	INTRON CG33144 & 1 other
2L	19688097	2L_19688097_SNP [dm3] 2L_19688097_SNP [dm6]	T	A	3.463e^-5	0.809	INTRON Lar	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA transposable element FlyBase
2R	9680600	2R_9680600_SNP [dm3] 2R_13793095_SNP [dm6]	G	T	3.485e^-5	0.809	DOWNSTREAM CR43811 INTERGENIC
2R	9679289	2R_9679289_SNP [dm3] 2R_13791784_SNP [dm6]	T	G	3.517e^-5	0.809	UPSTREAM CR43811 INTERGENIC
2R	9675734	2R_9675734_SNP [dm3] 2R_13788229_SNP [dm6]	T	C	3.524e^-5	0.809	DOWNSTREAM Cpr50Ca INTERGENIC
3L	18957992	3L_18957992_SNP [dm3] 3L_18964892_SNP [dm6]	C	T	3.524e^-5	0.809	INTERGENIC
2R	14925188	2R_14925188_SNP [dm3] 2R_19037683_SNP [dm6]	A	G	3.555e^-5	0.809	INTERGENIC
2R	20191493	2R_20191493_SNP [dm3] 2R_24303970_SNP [dm6]	G	A	3.571e^-5	0.809	INTERGENIC	regulatory region REDfly_CRMs
2R	17163256	2R_17163256_SNP [dm3] 2R_21275751_SNP [dm6]	G	A	3.583e^-5	0.809	INTRON Rgk3
2R	16326263	2R_16326263_SNP [dm3] 2R_20438758_SNP [dm6]	G	A	3.609e^-5	0.809	INTRON CG12484
2R	9677964	2R_9677964_SNP [dm3] 2R_13790459_SNP [dm6]	A	T	3.628e^-5	0.809	INTERGENIC
X	16925193	X_16925193_SNP [dm3] X_17031160_SNP [dm6]	A	T	3.644e^-5	0.809	INTRON CG45002
3R	26490041	3R_26490041_SNP [dm3] 3R_30664319_SNP [dm6]	G	T	3.664e^-5	0.809	UPSTREAM CR45191 INTERGENIC
X	5014243	X_5014243_SNP [dm3] X_5120210_SNP [dm6]	G	C	3.720e^-5	0.811	INTRON rg & 1 other
2L	663580	2L_663580_SNP [dm3] 2L_663580_SNP [dm6]	G	C	3.814e^-5	0.813	INTRON ds
3R	8151848	3R_8151848_SNP [dm3] 3R_12326126_SNP [dm6]	T	G	3.876e^-5	0.813	DOWNSTREAM CG10013 INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	10431186	2L_10431186_SNP [dm3] 2L_10431186_SNP [dm6]	A	G	3.921e^-5	0.813	UPSTREAM TfIIB & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	4242277	3L_4242277_SNP [dm3] 3L_4242277_SNP [dm6]	T	C	3.963e^-5	0.813	SYNONYMOUS_CODING CG14997 UPSTREAM pav	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	15295921	X_15295921_DEL [dm3] X_15401888_DEL [dm6]	AA	A	3.978e^-5	0.813	INTRON Cngl
2R	17002143	2R_17002143_SNP [dm3] 2R_21114638_SNP [dm6]	A	C	3.988e^-5	0.813	INTRON ktub
2R	9680269	2R_9680269_SNP [dm3] 2R_13792764_SNP [dm6]	T	A	4.128e^-5	0.82	DOWNSTREAM CR43811 INTERGENIC
3L	10836873	3L_10836873_SNP [dm3] 3L_10843773_SNP [dm6]	A	G	4.135e^-5	0.82	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
X	16925175	X_16925175_SNP [dm3] X_17031142_SNP [dm6]	A	G	4.154e^-5	0.82	INTRON CG45002
2R	12075919	2R_12075919_SNP [dm3] 2R_16188414_SNP [dm6]	A	G	4.200e^-5	0.82	INTRON clu	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	18958040	3L_18958040_SNP [dm3] 3L_18964940_SNP [dm6]	T	C	4.356e^-5	0.838	INTERGENIC
3L	18958049	3L_18958049_SNP [dm3] 3L_18964949_SNP [dm6]	A	G	4.381e^-5	0.838	INTERGENIC
3L	12494061	3L_12494061_SNP [dm3] 3L_12500961_SNP [dm6]	T	C	4.489e^-5	0.845	NON_SYNONYMOUS_CODING CG10638 UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
2R	18864961	2R_18864961_INS [dm3] 2R_22977438_INS [dm6]	T	TAT	4.557e^-5	0.845	INTERGENIC

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By genomic position
Variant impact
Gene name

lsm_Week1_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results