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=1.191e^-4)
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

Covariate	χ²	p-value	Significance
In_3R_Mo	5.7142	0.0574

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2126 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	6937595	3L_6937595_SNP [dm3] 3L_6944495_SNP [dm6]	G	T	1.934e^-6	0.867	START_GAINED tow UTR_5_PRIME tow UPSTREAM tow	TF binding site mE1_TFBS_Trl
2R	17451264	2R_17451264_INS [dm3] 2R_21563759_INS [dm6]	T	TCCTAT	2.390e^-6	0.867	INTRON CG10440
2L	2795796	2L_2795796_SNP [dm3] 2L_2795796_SNP [dm6]	A	C	3.755e^-6	0.867	UPSTREAM Syt1 INTRON Syt1
2L	3267631	2L_3267631_DEL [dm3] 2L_3267631_DEL [dm6]	ATTTAAAATGGTGCATCGTA...	A	4.379e^-6	0.867	UPSTREAM CR44484 INTERGENIC
2L	6976575	2L_6976575_SNP [dm3] 2L_6976575_SNP [dm6]	C	T	5.685e^-6	0.867	SYNONYMOUS_CODING uif	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	19614642	2R_19614642_SNP [dm3] 2R_23727119_SNP [dm6]	A	G	8.406e^-6	0.867	INTRON Sesn
3L	3915959	3L_3915959_SNP [dm3] 3L_3915959_SNP [dm6]	C	T	8.587e^-6	0.867	INTRON Eip63F-1
2R	17451277	2R_17451277_SNP [dm3] 2R_21563772_SNP [dm6]	C	T	8.639e^-6	0.867	INTRON CG10440
3L	1729840	3L_1729840_SNP [dm3] 3L_1729840_SNP [dm6]	A	C	8.918e^-6	0.867	INTRON drpr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2R	17930646	2R_17930646_SNP [dm3] 2R_22043141_SNP [dm6]	C	A	9.405e^-6	0.867	UPSTREAM PpD5 INTERGENIC
2R	17103207	2R_17103207_SNP [dm3] 2R_21215702_SNP [dm6]	G	A	1.007e^-5	0.867	SYNONYMOUS_CODING CG15661 UPSTREAM CG4302
2L	22011282	2L_22011282_SNP [dm3] 2L_22011282_SNP [dm6]	G	A	1.069e^-5	0.867	INTERGENIC
X	9318757	X_9318757_SNP [dm3] X_9424724_SNP [dm6]	G	A	1.130e^-5	0.867	INTRON mgl
3R	26332114	3R_26332114_SNP [dm3] 3R_30506392_SNP [dm6]	G	A	1.216e^-5	0.867	UTR_5_PRIME CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
2L	2795820	2L_2795820_SNP [dm3] 2L_2795820_SNP [dm6]	C	T	1.271e^-5	0.867	UPSTREAM Syt1 INTRON Syt1
X	10933694	X_10933694_SNP [dm3] X_11039661_SNP [dm6]	G	T	1.398e^-5	0.867	INTRON CG42339	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20533371	3R_20533371_SNP [dm3] 3R_24707649_SNP [dm6]	T	C	1.473e^-5	0.867	UTR_3_PRIME slo
3L	1729723	3L_1729723_SNP [dm3] 3L_1729723_SNP [dm6]	C	T	1.484e^-5	0.867	INTRON drpr	TF binding site BDTNP1_TFBS_twi BDTNP1_TFBS_z
2R	16297786	2R_16297786_SNP [dm3] 2R_20410281_SNP [dm6]	G	C	1.551e^-5	0.867	INTERGENIC
3R	14547161	3R_14547161_SNP [dm3] 3R_18721439_SNP [dm6]	A	G	1.593e^-5	0.867	DOWNSTREAM CG34283 INTRON Cha
X	9459132	X_9459132_SNP [dm3] X_9565099_SNP [dm6]	T	C	1.620e^-5	0.867	SYNONYMOUS_CODING Cubn
X	1270435	X_1270435_SNP [dm3] X_1376402_SNP [dm6]	C	T	1.620e^-5	0.867	INTRON AMPKalpha	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	9840824	2L_9840824_SNP [dm3] 2L_9840824_SNP [dm6]	C	T	1.622e^-5	0.867	INTRON nAChRalpha6
2L	7636397	2L_7636397_SNP [dm3] 2L_7636397_SNP [dm6]	T	G	1.651e^-5	0.867	UPSTREAM CR44800 INTRON CR44799	TF binding site BDTNP1_TFBS_twi
2L	7654746	2L_7654746_DEL [dm3] 2L_7654746_DEL [dm6]	TGTAT	T	1.686e^-5	0.867	INTRON Slob
X	11963142	X_11963142_DEL [dm3] X_12069109_DEL [dm6]	TGCCTGCCTTTTGGCCTTTA...	T	1.696e^-5	0.867	INTRON CR43960 & 1 other EXON CR43961
3R	19776051	3R_19776051_SNP [dm3] 3R_23950329_SNP [dm6]	T	C	1.707e^-5	0.867	INTERGENIC
2L	22684667	2L_22684667_SNP [dm3] 2L_22791935_SNP [dm6]	G	C	1.891e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_cad
3L	3857159	3L_3857159_SNP [dm3] 3L_3857159_SNP [dm6]	C	T	1.975e^-5	0.867	INTRON Awh
3R	26332132	3R_26332132_SNP [dm3] 3R_30506410_SNP [dm6]	T	A	2.003e^-5	0.867	UTR_5_PRIME CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
3L	1034183	3L_1034183_SNP [dm3] 3L_1034183_SNP [dm6]	T	G	2.005e^-5	0.867	UPSTREAM CG9205 INTRON trio	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	14793531	2R_14793531_SNP [dm3] 2R_18906026_SNP [dm6]	T	C	2.132e^-5	0.867	INTRON sano
2L	7454496	2L_7454496_SNP [dm3] 2L_7454496_SNP [dm6]	C	A	2.176e^-5	0.867	UPSTREAM Gr28a DOWNSTREAM Gr28b INTERGENIC
2L	15341216	2L_15341216_SNP [dm3] 2L_15341216_SNP [dm6]	C	A	2.176e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_sens
2L	9058061	2L_9058061_SNP [dm3] 2L_9058061_SNP [dm6]	T	C	2.219e^-5	0.867	INTRON CG31708
X	9237816	X_9237816_SNP [dm3] X_9343783_SNP [dm6]	A	G	2.245e^-5	0.867	INTRON CG34449
X	10748626	X_10748626_SNP [dm3] X_10854593_SNP [dm6]	C	T	2.343e^-5	0.867	SYNONYMOUS_CODING feo DOWNSTREAM sofe	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	5006769	2L_5006769_SNP [dm3] 2L_5006769_SNP [dm6]	C	A	2.404e^-5	0.867	UPSTREAM Rtnl1 INTRON Rtnl1
X	17656359	X_17656359_INS [dm3] X_17762326_INS [dm6]	G	GGTGGGCTGTGGGCCAAAAG...	2.502e^-5	0.867	INTERGENIC
3R	26332126	3R_26332126_SNP [dm3] 3R_30506404_SNP [dm6]	C	T	2.522e^-5	0.867	UTR_5_PRIME CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
2L	7636408	2L_7636408_SNP [dm3] 2L_7636408_SNP [dm6]	G	A	2.663e^-5	0.867	UPSTREAM CR44800 INTRON CR44799	TF binding site BDTNP1_TFBS_twi
2L	22212887	2L_22212887_SNP [dm3] 2L_22212887_SNP [dm6]	C	T	2.718e^-5	0.867	NON_SYNONYMOUS_CODING Ir40a	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	26332116	3R_26332116_SNP [dm3] 3R_30506394_SNP [dm6]	A	C	2.742e^-5	0.867	UTR_5_PRIME CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
2L	7882958	2L_7882958_SNP [dm3] 2L_7882958_SNP [dm6]	T	C	2.903e^-5	0.867	DOWNSTREAM CG7102 INTERGENIC
3L	3772078	3L_3772078_SNP [dm3] 3L_3772078_SNP [dm6]	T	A	2.966e^-5	0.867	INTRON CG32264
2L	16900031	2L_16900031_SNP [dm3] 2L_16900031_SNP [dm6]	T	C	3.043e^-5	0.867	NON_SYNONYMOUS_CODING CG31805 DOWNSTREAM CG12288 INTRON tweek	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	14219427	3R_14219427_INS [dm3] 3R_18393705_INS [dm6]	T	TG	3.212e^-5	0.867	INTRON Vha100-2	TF binding site mE1_TFBS_cad
3L	16063703	3L_16063703_SNP [dm3] 3L_16070603_SNP [dm6]	G	A	3.222e^-5	0.867	INTRON Mbs
3L	3800094	3L_3800094_SNP [dm3] 3L_3800094_SNP [dm6]	T	C	3.266e^-5	0.867	SYNONYMOUS_CODING CG32264 INTRON CG32264	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17930849	2R_17930849_SNP [dm3] 2R_22043344_SNP [dm6]	C	A	3.291e^-5	0.867	UPSTREAM PpD5 INTERGENIC
3L	3952522	3L_3952522_DEL [dm3] 3L_3952522_DEL [dm6]	AAA	A	3.322e^-5	0.867	UTR_5_PRIME CG14984 UPSTREAM CG14984
3L	4401167	3L_4401167_INS [dm3] 3L_4401167_INS [dm6]	T	TGCCTT	3.456e^-5	0.867	INTRON slow	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	18423826	2R_18423826_SNP [dm3] 2R_22536321_SNP [dm6]	A	G	3.487e^-5	0.867	INTRON px
3L	7778011	3L_7778011_SNP [dm3] 3L_7784911_SNP [dm6]	A	G	3.614e^-5	0.867	INTRON CG32369
3L	1579412	3L_1579412_SNP [dm3] 3L_1579412_SNP [dm6]	A	G	3.658e^-5	0.867	INTRON CG13917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
2R	19941273	2R_19941273_SNP [dm3] 2R_24053750_SNP [dm6]	C	T	3.707e^-5	0.867	DOWNSTREAM sei INTRON ppk29	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	11816846	3R_11816846_SNP [dm3] 3R_15991124_SNP [dm6]	T	C	3.712e^-5	0.867	INTRON srp & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	17683801	3L_17683801_SNP [dm3] 3L_17690701_SNP [dm6]	A	C	3.787e^-5	0.867	INTRON Ccn
3L	5135211	3L_5135211_SNP [dm3] 3L_5142111_SNP [dm6]	A	T	3.800e^-5	0.867	UTR_5_PRIME CG4623 UPSTREAM CG10672
2L	7879689	2L_7879689_SNP [dm3] 2L_7879689_SNP [dm6]	G	A	3.860e^-5	0.867	UPSTREAM spz3 INTERGENIC	TF binding site mE1_TFBS_cad
X	2800634	X_2800634_SNP [dm3] X_2906601_SNP [dm6]	G	A	3.881e^-5	0.867	INTRON kirre
2R	17979671	2R_17979671_SNP [dm3] 2R_22092166_SNP [dm6]	G	C	3.884e^-5	0.867	NON_SYNONYMOUS_CODING CG11073 UPSTREAM CG44163	TF binding site mE1_TFBS_chinmo
2L	2907346	2L_2907346_SNP [dm3] 2L_2907346_SNP [dm6]	A	T	3.916e^-5	0.867	INTRON lilli	TF binding site mE1_TFBS_bab1
3R	7827936	3R_7827936_DEL [dm3] 3R_12002214_DEL [dm6]	GGGCATTG	G	4.025e^-5	0.867	INTRON Tk & 1 other
2R	2953121	2R_2953121_SNP [dm3] 2R_7065616_SNP [dm6]	T	G	4.124e^-5	0.867	INTRON Tsp42Er
2R	17930822	2R_17930822_SNP [dm3] 2R_22043317_SNP [dm6]	C	T	4.289e^-5	0.867	UPSTREAM PpD5 INTERGENIC
2L	1306580	2L_1306580_SNP [dm3] 2L_1306580_SNP [dm6]	C	T	4.340e^-5	0.867	INTERGENIC
2L	1306581	2L_1306581_SNP [dm3] 2L_1306581_SNP [dm6]	G	A	4.340e^-5	0.867	INTERGENIC
2R	20958564	2R_20958564_SNP [dm3] 2R_25071041_SNP [dm6]	A	T	4.428e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6174667	3L_6174667_SNP [dm3] 3L_6181567_SNP [dm6]	G	A	4.494e^-5	0.867	SYNONYMOUS_CODING CG10274 DOWNSTREAM D19B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens
3R	26332130	3R_26332130_SNP [dm3] 3R_30506408_SNP [dm6]	A	T	4.530e^-5	0.867	UTR_5_PRIME CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
X	14863927	X_14863927_SNP [dm3] X_14969894_SNP [dm6]	G	C	4.539e^-5	0.867	INTRON eag
2R	17930864	2R_17930864_SNP [dm3] 2R_22043359_SNP [dm6]	A	G	4.556e^-5	0.867	UPSTREAM PpD5 INTERGENIC
2L	6613732	2L_6613732_SNP [dm3] 2L_6613732_SNP [dm6]	G	A	4.646e^-5	0.867	INTRON CG11050
2L	9054304	2L_9054304_SNP [dm3] 2L_9054304_SNP [dm6]	T	C	4.732e^-5	0.867	INTRON CG31708
2R	17930865	2R_17930865_SNP [dm3] 2R_22043360_SNP [dm6]	A	G	4.746e^-5	0.867	UPSTREAM PpD5 INTERGENIC
2L	1112909	2L_1112909_SNP [dm3] 2L_1112909_SNP [dm6]	C	T	4.858e^-5	0.867	UPSTREAM CG14340 DOWNSTREAM CG14339 INTERGENIC
2L	9055896	2L_9055896_SNP [dm3] 2L_9055896_SNP [dm6]	G	A	4.861e^-5	0.867	INTRON CG31708
3R	11325799	3R_11325799_SNP [dm3] 3R_15500077_SNP [dm6]	C	A	4.879e^-5	0.867	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	7873061	2L_7873061_SNP [dm3] 2L_7873061_SNP [dm6]	A	G	4.980e^-5	0.867	UPSTREAM CR45364 DOWNSTREAM spz3 & 1 other INTERGENIC
2R	804798	2R_804798_SNP [dm3] 2R_4917293_SNP [dm6]	A	C	5.012e^-5	0.867	UPSTREAM Ir41a INTERGENIC
2L	1111238	2L_1111238_INS [dm3] 2L_1111238_INS [dm6]	T	TATA	5.108e^-5	0.867	INTRON CG14339
X	18462567	X_18462567_DEL [dm3] X_18568534_DEL [dm6]	ATTATGGTTAACT...	A	5.195e^-5	0.867	INTRON Bx	TF binding site mE1_TFBS_chinmo
2L	1111232	2L_1111232_SNP [dm3] 2L_1111232_SNP [dm6]	G	A	5.210e^-5	0.867	INTRON CG14339
2L	9055972	2L_9055972_SNP [dm3] 2L_9055972_SNP [dm6]	G	A	5.218e^-5	0.867	INTRON CG31708
2L	3737742	2L_3737742_SNP [dm3] 2L_3737742_SNP [dm6]	T	A	5.255e^-5	0.867	INTRON CG10019
3L	11688944	3L_11688944_SNP [dm3] 3L_11695844_SNP [dm6]	C	A	5.285e^-5	0.867	INTRON CG11652	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	8095054	2L_8095054_INS [dm3] 2L_8095054_INS [dm6]	A	ACTT	5.316e^-5	0.867	INTRON Bsg
2L	8095055	2L_8095055_DEL [dm3] 2L_8095055_DEL [dm6]	AATGGATT	A	5.330e^-5	0.867	INTRON Bsg
2L	9500406	2L_9500406_SNP [dm3] 2L_9500406_SNP [dm6]	T	C	5.350e^-5	0.867	INTRON CG33298
2L	12160225	2L_12160225_SNP [dm3] 2L_12160225_SNP [dm6]	T	G	5.366e^-5	0.867	INTRON CG31760	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26332302	3R_26332302_SNP [dm3] 3R_30506580_SNP [dm6]	C	G	5.394e^-5	0.867	SPLICE_SITE_REGION CG15539 UPSTREAM PH4alphaSG1 & 1 other INTRON CG15539
2R	13945755	2R_13945755_SNP [dm3] 2R_18058250_SNP [dm6]	C	A	5.400e^-5	0.867	EXON CR45314
2R	6361935	2R_6361935_SNP [dm3] 2R_10474430_SNP [dm6]	A	T	5.412e^-5	0.867	INTRON whd
3L	23847988	3L_23847988_SNP [dm3] 3L_23854888_SNP [dm6]	C	T	5.513e^-5	0.867	INTRON CG40470
X	12672167	X_12672167_SNP [dm3] X_12778134_SNP [dm6]	A	C	5.542e^-5	0.867	INTRON CG32647
3L	5898507	3L_5898507_SNP [dm3] 3L_5905407_SNP [dm6]	T	G	5.546e^-5	0.867	INTRON CG10486
2R	20646137	2R_20646137_SNP [dm3] 2R_24758614_SNP [dm6]	C	T	5.561e^-5	0.867	SYNONYMOUS_CODING spz6
X	3367716	X_3367716_SNP [dm3] X_3473683_SNP [dm6]	A	C	5.746e^-5	0.867	UPSTREAM CG12206 INTRON CR44999 & 1 other
3L	5898770	3L_5898770_SNP [dm3] 3L_5905670_SNP [dm6]	C	G	5.778e^-5	0.867	SYNONYMOUS_CODING CG10486 INTRON CG10486

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By genomic position
Variant impact
Gene name

AVG PPL1 neurons phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results