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=4.170e^-9)
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

Covariate	p-value	Significance
In_2L_t	0.0001218
In_2R_NS	0.0587515
In_3R_P	0.0707850

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	9.5174	0.0086

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2361 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	14592781	3L_14592781_SNP [dm3] 3L_14599681_SNP [dm6]	G	T	8.756e^-7	0.608	UPSTREAM HGTX INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	18577629	3L_18577629_SNP [dm3] 3L_18584529_SNP [dm6]	G	A	1.139e^-6	0.608	DOWNSTREAM CR45435 INTERGENIC
2L	19324776	2L_19324776_SNP [dm3] 2L_19324776_SNP [dm6]	G	T	1.317e^-6	0.608	EXON CR45700	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	2066038	2R_2066038_SNP [dm3] 2R_6178533_SNP [dm6]	T	A	1.735e^-6	0.608	DOWNSTREAM tRNA:R2:42Aa INTERGENIC	regulatory region REDfly_CRMs
2R	12435213	2R_12435213_SNP [dm3] 2R_16547708_SNP [dm6]	A	G	1.955e^-6	0.608	INTERGENIC
2R	16994061	2R_16994061_SNP [dm3] 2R_21106556_SNP [dm6]	T	G	2.419e^-6	0.608	INTRON ktub
2L	19324779	2L_19324779_SNP [dm3] 2L_19324779_SNP [dm6]	G	A	2.628e^-6	0.608	EXON CR45700	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	5812552	3L_5812552_SNP [dm3] 3L_5819452_SNP [dm6]	C	A	2.800e^-6	0.608	INTRON vn
3L	5812559	3L_5812559_SNP [dm3] 3L_5819459_SNP [dm6]	C	A	2.918e^-6	0.608	INTRON vn
3R	4961130	3R_4961130_INS [dm3] 3R_9135408_INS [dm6]	G	GG	3.941e^-6	0.629	INTRON pum
3L	18071363	3L_18071363_SNP [dm3] 3L_18078263_SNP [dm6]	T	A	4.733e^-6	0.629	DOWNSTREAM CR45392 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	18071365	3L_18071365_SNP [dm3] 3L_18078265_SNP [dm6]	A	T	4.733e^-6	0.629	DOWNSTREAM CR45392 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	1830512	2R_1830512_SNP [dm3] 2R_5943007_SNP [dm6]	A	G	4.897e^-6	0.629	INTERGENIC
2R	16994062	2R_16994062_SNP [dm3] 2R_21106557_SNP [dm6]	G	T	5.109e^-6	0.629	INTRON ktub
X	10019999	X_10019999_SNP [dm3] X_10125966_SNP [dm6]	C	T	5.311e^-6	0.629	INTRON CR44894 & 1 other
3L	12165879	3L_12165879_SNP [dm3] 3L_12172779_SNP [dm6]	A	T	5.959e^-6	0.629	INTRON Rh7
2R	16994059	2R_16994059_SNP [dm3] 2R_21106554_SNP [dm6]	T	A	6.140e^-6	0.629	INTRON ktub
3R	2957640	3R_2957640_SNP [dm3] 3R_7131918_SNP [dm6]	A	T	6.845e^-6	0.629	SPLICE_SITE_REGION CG31493 SYNONYMOUS_CODING CG31493 UPSTREAM tRNA:CR31491 INTRON CG31493
X	13444081	X_13444081_SNP [dm3] X_13550048_SNP [dm6]	G	A	7.077e^-6	0.629	INTERGENIC
3L	13019640	3L_13019640_SNP [dm3] 3L_13026540_SNP [dm6]	T	G	7.404e^-6	0.629	UPSTREAM Zmynd10 INTERGENIC
3L	5810288	3L_5810288_SNP [dm3] 3L_5817188_SNP [dm6]	A	T	7.519e^-6	0.629	INTRON vn	regulatory region REDfly_CRMs
2L	3408526	2L_3408526_SNP [dm3] 2L_3408526_SNP [dm6]	A	G	7.969e^-6	0.629	INTRON pgant2
2L	20690724	2L_20690724_SNP [dm3] 2L_20690724_SNP [dm6]	A	T	8.129e^-6	0.629	INTRON Hr38	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
X	16522370	X_16522370_SNP [dm3] X_16628337_SNP [dm6]	G	A	8.211e^-6	0.629	SYNONYMOUS_CODING Rok	TF binding site mE1_TFBS_chinmo
2R	16175623	2R_16175623_SNP [dm3] 2R_20288118_SNP [dm6]	A	G	8.531e^-6	0.629	SYNONYMOUS_CODING CG34199 DOWNSTREAM Cpr56F
2L	20762989	2L_20762989_SNP [dm3] 2L_20762989_SNP [dm6]	T	C	8.726e^-6	0.629	DOWNSTREAM dia INTRON dia	TF binding site mE1_TFBS_HSA
2L	3926353	2L_3926353_SNP [dm3] 2L_3926353_SNP [dm6]	C	A	9.361e^-6	0.647	INTRON fred	TF binding site mE1_TFBS_bab1
3R	11990909	3R_11990909_SNP [dm3] 3R_16165187_SNP [dm6]	A	T	9.666e^-6	0.647	INTRON CG6006
3L	8503867	3L_8503867_SNP [dm3] 3L_8510767_SNP [dm6]	G	A	1.115e^-5	0.713	NON_SYNONYMOUS_CODING CG6745	TF binding site mE1_TFBS_sens
3L	11068397	3L_11068397_SNP [dm3] 3L_11075297_SNP [dm6]	A	T	1.269e^-5	0.713	NON_SYNONYMOUS_CODING CG7839 UPSTREAM l_3_01239	TF binding site mE1_TFBS_sens
2R	19719293	2R_19719293_SNP [dm3] 2R_23831770_SNP [dm6]	C	G	1.273e^-5	0.713	INTRON CG5549
2L	20762983	2L_20762983_SNP [dm3] 2L_20762983_SNP [dm6]	C	A	1.284e^-5	0.713	DOWNSTREAM dia INTRON dia	TF binding site mE1_TFBS_HSA
2R	8504375	2R_8504375_SNP [dm3] 2R_12616870_SNP [dm6]	T	G	1.342e^-5	0.713	SYNONYMOUS_CODING Galphaq UTR_3_PRIME CG45086	TF binding site mE1_TFBS_sens
2R	16994055	2R_16994055_DEL [dm3] 2R_21106550_DEL [dm6]	AT	A	1.348e^-5	0.713	INTRON ktub
3L	12482750	3L_12482750_SNP [dm3] 3L_12489650_SNP [dm6]	A	C	1.357e^-5	0.713	UPSTREAM CR45681 INTRON CG10660	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	18490711	3L_18490711_SNP [dm3] 3L_18497611_SNP [dm6]	T	C	1.369e^-5	0.713	INTRON AstC-R2	TF binding site BDTNP1_TFBS_twi
2L	4789881	2L_4789881_SNP [dm3] 2L_4789881_SNP [dm6]	G	A	1.411e^-5	0.715	INTRON CG15630
3L	15249826	3L_15249826_INS [dm3] 3L_15256726_INS [dm6]	C	ACTT	1.636e^-5	0.783	INTERGENIC
3L	9678679	3L_9678679_SNP [dm3] 3L_9685579_SNP [dm6]	G	T	1.669e^-5	0.783	NON_SYNONYMOUS_CODING CG16719 INTRON CG6767	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	8747098	3L_8747098_SNP [dm3] 3L_8753998_SNP [dm6]	T	A	1.844e^-5	0.783	UTR_5_PRIME Fhos UPSTREAM Fhos
2R	12608881	2R_12608881_SNP [dm3] 2R_16721376_SNP [dm6]	C	G	1.894e^-5	0.783	INTRON CG30463	TF binding site mE1_TFBS_inv
X	471714	X_471714_SNP [dm3] X_577681_SNP [dm6]	T	G	2.050e^-5	0.783	UTR_3_PRIME Appl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
3R	9575068	3R_9575068_SNP [dm3] 3R_13749346_SNP [dm6]	C	T	2.121e^-5	0.783	INTRON CG34383	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	1173082	X_1173082_SNP [dm3] X_1279049_SNP [dm6]	A	T	2.290e^-5	0.783	INTERGENIC
2L	6903262	2L_6903262_SNP [dm3] 2L_6903262_SNP [dm6]	T	C	2.304e^-5	0.783	SYNONYMOUS_CODING Nlg2
2L	8143941	2L_8143941_SNP [dm3] 2L_8143941_SNP [dm6]	C	T	2.380e^-5	0.783	DOWNSTREAM CG42763 INTRON CG8552 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15249791	3L_15249791_SNP [dm3] 3L_15256691_SNP [dm6]	G	A	2.423e^-5	0.783	INTERGENIC
3R	10775839	3R_10775839_SNP [dm3] 3R_14950117_SNP [dm6]	C	A	2.523e^-5	0.783	INTERGENIC
2R	6181881	2R_6181881_SNP [dm3] 2R_10294376_SNP [dm6]	T	C	2.559e^-5	0.783	INTRON CAP	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	18628743	2L_18628743_SNP [dm3] 2L_18628743_SNP [dm6]	A	T	2.677e^-5	0.783	INTRON MESR3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	13444064	X_13444064_SNP [dm3] X_13550031_SNP [dm6]	C	T	2.775e^-5	0.783	INTERGENIC
2R	12807397	2R_12807397_SNP [dm3] 2R_16919892_SNP [dm6]	A	C	2.781e^-5	0.783	INTERGENIC
3R	3150641	3R_3150641_SNP [dm3] 3R_7324919_SNP [dm6]	T	G	2.922e^-5	0.783	UPSTREAM CG44335 INTERGENIC
X	13444096	X_13444096_SNP [dm3] X_13550063_SNP [dm6]	C	T	2.931e^-5	0.783	INTERGENIC
2R	10505946	2R_10505946_SNP [dm3] 2R_14618441_SNP [dm6]	G	A	3.093e^-5	0.783	UPSTREAM Sec61beta & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	19714934	2R_19714934_SNP [dm3] 2R_23827411_SNP [dm6]	G	A	3.140e^-5	0.783	INTRON CG5549	TF binding site mE1_TFBS_inv
2R	16175545	2R_16175545_SNP [dm3] 2R_20288040_SNP [dm6]	A	G	3.153e^-5	0.783	SYNONYMOUS_CODING CG34199 UPSTREAM CG16868 DOWNSTREAM Cpr56F
2R	16994041	2R_16994041_SNP [dm3] 2R_21106536_SNP [dm6]	T	A	3.238e^-5	0.783	INTRON ktub
3L	14798382	3L_14798382_SNP [dm3] 3L_14805282_SNP [dm6]	A	G	3.330e^-5	0.783	UTR_5_PRIME CG17839
2L	3924618	2L_3924618_SNP [dm3] 2L_3924618_SNP [dm6]	C	T	3.348e^-5	0.783	INTRON fred
2L	9189774	2L_9189774_SNP [dm3] 2L_9189774_SNP [dm6]	C	T	3.395e^-5	0.783	INTRON tai
2R	17022265	2R_17022265_DEL [dm3] 2R_21134760_DEL [dm6]	ACATA	A	3.430e^-5	0.783	INTRON Magi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17022278	2R_17022278_SNP [dm3] 2R_21134773_SNP [dm6]	A	C	3.430e^-5	0.783	INTRON Magi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16916682	2R_16916682_SNP [dm3] 2R_21029177_SNP [dm6]	T	A	3.490e^-5	0.783	DOWNSTREAM CR45148 INTERGENIC
2R	17110852	2R_17110852_SNP [dm3] 2R_21223347_SNP [dm6]	G	A	3.600e^-5	0.783	INTRON ASPP
X	7909444	X_7909444_SNP [dm3] X_8015411_SNP [dm6]	G	A	3.620e^-5	0.783	INTRON Tbh
2L	7629859	2L_7629859_SNP [dm3] 2L_7629859_SNP [dm6]	C	T	3.645e^-5	0.783	INTERGENIC
2L	4789896	2L_4789896_SNP [dm3] 2L_4789896_SNP [dm6]	C	T	3.666e^-5	0.783	INTRON CG15630
X	3516236	X_3516236_SNP [dm3] X_3622203_SNP [dm6]	A	C	3.681e^-5	0.783	INTRON AstA-R1
3R	27058663	3R_27058663_SNP [dm3] 3R_31232941_SNP [dm6]	T	C	3.741e^-5	0.783	SYNONYMOUS_CODING CG15564 UPSTREAM CG15563	TF binding site mE1_TFBS_chinmo
2R	5876150	2R_5876150_SNP [dm3] 2R_9988645_SNP [dm6]	T	G	3.745e^-5	0.783	UPSTREAM TER94 EXON CR45324	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	21729884	2L_21729884_SNP [dm3] 2L_21729884_SNP [dm6]	T	G	3.822e^-5	0.783	DOWNSTREAM CG31619 INTERGENIC	transposable element FlyBase
3R	3262533	3R_3262533_SNP [dm3] 3R_7436811_SNP [dm6]	C	A	3.848e^-5	0.783	INTERGENIC
3L	18071370	3L_18071370_SNP [dm3] 3L_18078270_SNP [dm6]	C	A	3.873e^-5	0.783	DOWNSTREAM CR45392 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	19714907	2R_19714907_INS [dm3] 2R_23827384_INS [dm6]	C	CTCCCCCA	3.914e^-5	0.783	INTRON CG5549	TF binding site mE1_TFBS_inv
3L	12356469	3L_12356469_SNP [dm3] 3L_12363369_SNP [dm6]	G	A	3.976e^-5	0.783	INTERGENIC
3L	16691025	3L_16691025_SNP [dm3] 3L_16697925_SNP [dm6]	G	A	4.116e^-5	0.783	DOWNSTREAM CR45179 INTRON Lasp & 1 other
X	6455628	X_6455628_SNP [dm3] X_6561595_SNP [dm6]	G	T	4.124e^-5	0.783	INTRON CG34417	TF binding site mE1_TFBS_sens
2R	12434445	2R_12434445_SNP [dm3] 2R_16546940_SNP [dm6]	T	G	4.141e^-5	0.783	INTERGENIC
X	17272588	X_17272588_SNP [dm3] X_17378555_SNP [dm6]	T	G	4.142e^-5	0.783	EXON CR43491
X	13444087	X_13444087_SNP [dm3] X_13550054_SNP [dm6]	A	G	4.145e^-5	0.783	INTERGENIC
3L	2806678	3L_2806678_SNP [dm3] 3L_2806678_SNP [dm6]	C	G	4.175e^-5	0.783	INTRON CG43444	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	17411416	2R_17411416_SNP [dm3] 2R_21523911_SNP [dm6]	T	C	4.176e^-5	0.783	INTRON Egfr	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_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
3L	9935321	3L_9935321_SNP [dm3] 3L_9942221_SNP [dm6]	G	A	4.214e^-5	0.783	INTRON CG34356
3R	3216520	3R_3216520_SNP [dm3] 3R_7390798_SNP [dm6]	A	C	4.276e^-5	0.783	UPSTREAM CG42650 INTERGENIC
2R	17022895	2R_17022895_SNP [dm3] 2R_21135390_SNP [dm6]	C	T	4.312e^-5	0.783	INTRON Magi	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25158853	3R_25158853_SNP [dm3] 3R_29333131_SNP [dm6]	G	T	4.320e^-5	0.783	INTERGENIC
3L	9113341	3L_9113341_SNP [dm3] 3L_9120241_SNP [dm6]	A	C	4.441e^-5	0.783	INTRON bol
2L	838639	2L_838639_SNP [dm3] 2L_838639_SNP [dm6]	G	T	4.483e^-5	0.783	INTRON drongo	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
3R	2955189	3R_2955189_SNP [dm3] 3R_7129467_SNP [dm6]	G	T	4.499e^-5	0.783	UTR_5_PRIME CG31248 UPSTREAM tRNA:CR31494 DOWNSTREAM CR42875
3R	27526525	3R_27526525_SNP [dm3] 3R_31700803_SNP [dm6]	A	G	4.502e^-5	0.783	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	9311557	2L_9311557_SNP [dm3] 2L_9311557_SNP [dm6]	T	C	4.503e^-5	0.783	INTERGENIC
3R	11990934	3R_11990934_DEL [dm3] 3R_16165212_DEL [dm6]	TTTTA	T	4.526e^-5	0.783	INTRON CG6006
2R	14077089	2R_14077089_SNP [dm3] 2R_18189584_SNP [dm6]	T	G	4.545e^-5	0.783	UTR_3_PRIME CG14500 INTRON CG33958
3L	2349722	3L_2349722_SNP [dm3] 3L_2349722_SNP [dm6]	T	C	4.577e^-5	0.783	INTERGENIC
3R	27133612	3R_27133612_SNP [dm3] 3R_31307890_SNP [dm6]	A	G	4.587e^-5	0.783	INTERGENIC
3R	21438345	3R_21438345_SNP [dm3] 3R_25612623_SNP [dm6]	G	A	4.637e^-5	0.783	INTRON Npl4
2L	3858903	2L_3858903_SNP [dm3] 2L_3858903_SNP [dm6]	T	C	4.747e^-5	0.783	INTERGENIC
2R	8669121	2R_8669121_SNP [dm3] 2R_12781616_SNP [dm6]	A	C	4.794e^-5	0.783	INTRON sca	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	16347680	3L_16347680_SNP [dm3] 3L_16354580_SNP [dm6]	T	C	4.871e^-5	0.783	UPSTREAM Pdh DOWNSTREAM CG45057 INTERGENIC

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By genomic position
Variant impact
Gene name

Sample.size Experience 3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results