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=5.161e^-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

937 significant hits at p-value < 0.001.

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	12107801	3L_12107801_SNP [dm3] 3L_12114701_SNP [dm6]	A	G	1.718e^-5	0.867	INTERGENIC
X	20467196	X_20467196_SNP [dm3] X_20596169_SNP [dm6]	C	A	1.718e^-5	0.867	INTRON RunxA
X	13439484	X_13439484_SNP [dm3] X_13545451_SNP [dm6]	G	A	2.052e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
2R	20934857	2R_20934857_SNP [dm3] 2R_25047334_SNP [dm6]	A	G	2.099e^-5	0.867	INTRON gsb-n	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2R	12432566	2R_12432566_SNP [dm3] 2R_16545061_SNP [dm6]	A	G	2.309e^-5	0.867	INTERGENIC
X	15151565	X_15151565_SNP [dm3] X_15257532_SNP [dm6]	G	A	2.337e^-5	0.867	INTERGENIC
2R	15998536	2R_15998536_SNP [dm3] 2R_20111031_SNP [dm6]	C	G	3.048e^-5	0.867	UPSTREAM 18w INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_zfh1
X	3047189	X_3047189_SNP [dm3] X_3153156_SNP [dm6]	A	T	3.048e^-5	0.867	INTRON N	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	3047209	X_3047209_SNP [dm3] X_3153176_SNP [dm6]	C	T	3.048e^-5	0.867	INTRON N	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	10455292	3L_10455292_SNP [dm3] 3L_10462192_SNP [dm6]	T	C	3.187e^-5	0.867	SYNONYMOUS_CODING Gem3	TF binding site mE1_TFBS_sens
2L	2053277	2L_2053277_SNP [dm3] 2L_2053277_SNP [dm6]	C	T	3.674e^-5	0.867	INTERGENIC
2L	2355935	2L_2355935_DEL [dm3] 2L_2355935_DEL [dm6]	ATGAAGA	A	3.674e^-5	0.867	INTRON CG9967 & 1 other
2R	8846262	2R_8846262_SNP [dm3] 2R_12958757_SNP [dm6]	T	G	3.957e^-5	0.867	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	3046522	3L_3046522_SNP [dm3] 3L_3046522_SNP [dm6]	A	G	3.957e^-5	0.867	UPSTREAM Sk2 INTRON scramb2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	13439472	X_13439472_SNP [dm3] X_13545439_SNP [dm6]	C	A	3.957e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
X	13439474	X_13439474_SNP [dm3] X_13545441_SNP [dm6]	A	C	3.957e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
X	13439488	X_13439488_SNP [dm3] X_13545455_SNP [dm6]	T	C	3.957e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
X	13439495	X_13439495_SNP [dm3] X_13545462_SNP [dm6]	A	T	3.957e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
2R	1721610	2R_1721610_SNP [dm3] 2R_5834105_SNP [dm6]	A	C	4.005e^-5	0.867	INTRON dpr12
2R	9790949	2R_9790949_SNP [dm3] 2R_13903444_SNP [dm6]	C	T	4.186e^-5	0.867	SYNONYMOUS_CODING shot	TF binding site BDTNP1_TFBS_prd
X	16297099	X_16297099_SNP [dm3] X_16403066_SNP [dm6]	G	A	4.186e^-5	0.867	INTRON CG9981	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	8559959	X_8559959_SNP [dm3] X_8665926_SNP [dm6]	T	C	4.186e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	11520916	3L_11520916_SNP [dm3] 3L_11527816_SNP [dm6]	T	C	4.203e^-5	0.867	SPLICE_SITE_REGION Mob2 UTR_5_PRIME Mob2 INTRON Mob2	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	18133985	3L_18133985_SNP [dm3] 3L_18140885_SNP [dm6]	T	C	4.203e^-5	0.867	INTRON gk
3L	1005300	3L_1005300_SNP [dm3] 3L_1005300_SNP [dm6]	T	A	4.253e^-5	0.867	INTRON trio
3L	3046481	3L_3046481_SNP [dm3] 3L_3046481_SNP [dm6]	A	G	4.588e^-5	0.867	UPSTREAM Sk2 INTRON scramb2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	238051	2R_238051_SNP [dm3] 2R_4350546_SNP [dm6]	T	C	5.254e^-5	0.867	SPLICE_SITE_REGION Gprk1 INTRON Gprk1
2L	15228808	2L_15228808_SNP [dm3] 2L_15228808_SNP [dm6]	A	T	5.628e^-5	0.867	UTR_3_PRIME ZnT35C
3L	10454574	3L_10454574_DEL [dm3] 3L_10461474_DEL [dm6]	TAAG	T	5.883e^-5	0.867	CODON_DELETION Gem3
2R	119278	2R_119278_SNP [dm3] 2R_4231773_SNP [dm6]	T	C	5.917e^-5	0.867	INTERGENIC
2R	123225	2R_123225_SNP [dm3] 2R_4235720_SNP [dm6]	C	G	5.917e^-5	0.867	DOWNSTREAM IntS3 INTERGENIC
2R	174069	2R_174069_SNP [dm3] 2R_4286564_SNP [dm6]	A	C	5.917e^-5	0.867	INTERGENIC
2R	187445	2R_187445_DEL [dm3] 2R_4299940_DEL [dm6]	CC	C	5.917e^-5	0.867	INTERGENIC
2R	195945	2R_195945_SNP [dm3] 2R_4308440_SNP [dm6]	T	C	5.917e^-5	0.867	INTERGENIC
2R	209617	2R_209617_SNP [dm3] 2R_4322112_SNP [dm6]	C	T	5.917e^-5	0.867	DOWNSTREAM Gprk1 INTERGENIC
2R	216417	2R_216417_SNP [dm3] 2R_4328912_SNP [dm6]	G	T	5.917e^-5	0.867	INTRON Gprk1
2R	216508	2R_216508_SNP [dm3] 2R_4329003_SNP [dm6]	C	T	5.917e^-5	0.867	INTRON Gprk1
2R	228562	2R_228562_SNP [dm3] 2R_4341057_SNP [dm6]	A	G	5.917e^-5	0.867	INTRON Gprk1
2R	234692	2R_234692_SNP [dm3] 2R_4347187_SNP [dm6]	C	T	5.917e^-5	0.867	INTRON Gprk1
2R	236138	2R_236138_SNP [dm3] 2R_4348633_SNP [dm6]	G	A	5.917e^-5	0.867	INTRON Gprk1
2R	238925	2R_238925_SNP [dm3] 2R_4351420_SNP [dm6]	T	G	5.917e^-5	0.867	INTRON Gprk1
2R	263803	2R_263803_SNP [dm3] 2R_4376298_SNP [dm6]	C	A	5.917e^-5	0.867	INTRON Gprk1
2R	276622	2R_276622_SNP [dm3] 2R_4389117_SNP [dm6]	T	A	5.917e^-5	0.867	INTRON Gprk1
2R	284982	2R_284982_MNP [dm3] 2R_4397477_MNP [dm6]	AGAATTT	TCTTAGA	5.917e^-5	0.867	INTRON Gprk1	TF binding site mE1_TFBS_cad
2R	288951	2R_288951_SNP [dm3] 2R_4401446_SNP [dm6]	G	A	5.917e^-5	0.867	INTRON Gprk1
2R	293117	2R_293117_SNP [dm3] 2R_4405612_SNP [dm6]	C	T	5.917e^-5	0.867	INTRON Gprk1
2R	294944	2R_294944_SNP [dm3] 2R_4407439_SNP [dm6]	G	T	5.917e^-5	0.867	INTRON Gprk1
2R	294945	2R_294945_SNP [dm3] 2R_4407440_SNP [dm6]	T	A	5.917e^-5	0.867	INTRON Gprk1
2R	297929	2R_297929_SNP [dm3] 2R_4410424_SNP [dm6]	C	T	5.917e^-5	0.867	INTRON Gprk1
2R	301623	2R_301623_DEL [dm3] 2R_4414118_DEL [dm6]	TTT	T	5.917e^-5	0.867	INTRON Gprk1
2R	314372	2R_314372_DEL [dm3] 2R_4426867_DEL [dm6]	ATTGGA	A	5.917e^-5	0.867	INTRON Gprk1
3L	6770288	3L_6770288_SNP [dm3] 3L_6777188_SNP [dm6]	C	G	5.917e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	13439480	X_13439480_SNP [dm3] X_13545447_SNP [dm6]	T	C	5.947e^-5	0.867	DOWNSTREAM Cpr12A INTERGENIC
3L	7083413	3L_7083413_DEL [dm3] 3L_7090313_DEL [dm6]	AA	A	6.123e^-5	0.867	INTERGENIC
2L	1461857	2L_1461857_SNP [dm3] 2L_1461857_SNP [dm6]	G	A	6.242e^-5	0.867	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	10797237	3L_10797237_SNP [dm3] 3L_10804137_SNP [dm6]	C	T	6.555e^-5	0.867	EXON CR44347
3L	10797240	3L_10797240_SNP [dm3] 3L_10804140_SNP [dm6]	A	T	6.555e^-5	0.867	EXON CR44347
2L	20864331	2L_20864331_SNP [dm3] 2L_20864331_SNP [dm6]	A	G	6.823e^-5	0.867	UPSTREAM CR9337 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sbb
3L	7087336	3L_7087336_SNP [dm3] 3L_7094236_SNP [dm6]	C	T	7.607e^-5	0.867	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC
3L	1005298	3L_1005298_SNP [dm3] 3L_1005298_SNP [dm6]	T	C	7.988e^-5	0.867	INTRON trio
3L	1005321	3L_1005321_SNP [dm3] 3L_1005321_SNP [dm6]	A	C	7.988e^-5	0.867	INTRON trio
X	15813072	X_15813072_SNP [dm3] X_15919039_SNP [dm6]	A	C	7.988e^-5	0.867	SYNONYMOUS_CODING CG8909
2R	9793053	2R_9793053_SNP [dm3] 2R_13905548_SNP [dm6]	G	A	8.162e^-5	0.867	INTRON shot
2L	7484615	2L_7484615_INS [dm3] 2L_7484615_INS [dm6]	T	TAT	8.469e^-5	0.867	INTRON Ziz	TF binding site mE1_TFBS_inv
2R	16073754	2R_16073754_SNP [dm3] 2R_20186249_SNP [dm6]	A	G	9.045e^-5	0.867	INTERGENIC
3L	18850205	3L_18850205_SNP [dm3] 3L_18857105_SNP [dm6]	C	T	9.061e^-5	0.867	EXON CR45388
X	20467316	X_20467316_SNP [dm3] X_20596289_SNP [dm6]	C	T	9.061e^-5	0.867	INTRON RunxA
3R	18077710	3R_18077710_SNP [dm3] 3R_22251988_SNP [dm6]	A	G	9.236e^-5	0.867	INTRON SKIP
3R	21289246	3R_21289246_SNP [dm3] 3R_25463524_SNP [dm6]	G	A	9.715e^-5	0.867	INTRON Fur1
2R	266292	2R_266292_SNP [dm3] 2R_4378787_SNP [dm6]	T	C	9.793e^-5	0.867	NON_SYNONYMOUS_CODING Gprk1
3L	19049372	3L_19049372_SNP [dm3] 3L_19056272_SNP [dm6]	A	T	9.793e^-5	0.867	INTERGENIC
3L	19049373	3L_19049373_SNP [dm3] 3L_19056273_SNP [dm6]	C	G	9.793e^-5	0.867	INTERGENIC
3L	19049376	3L_19049376_DEL [dm3] 3L_19056276_DEL [dm6]	ATC	A	9.793e^-5	0.867	INTERGENIC
3L	19049380	3L_19049380_INS [dm3] 3L_19056280_INS [dm6]	A	ACTTGC	9.793e^-5	0.867	INTERGENIC
3L	10134679	3L_10134679_SNP [dm3] 3L_10141579_SNP [dm6]	G	T	1.021e^-4	0.867	INTERGENIC
2L	16541881	2L_16541881_SNP [dm3] 2L_16541881_SNP [dm6]	T	G	1.040e^-4	0.867	UPSTREAM CG31816 INTERGENIC
2L	16541885	2L_16541885_SNP [dm3] 2L_16541885_SNP [dm6]	A	T	1.040e^-4	0.867	UPSTREAM CG31816 INTERGENIC
2R	198036	2R_198036_SNP [dm3] 2R_4310531_SNP [dm6]	T	A	1.044e^-4	0.867	INTERGENIC
3L	10134684	3L_10134684_SNP [dm3] 3L_10141584_SNP [dm6]	G	T	1.048e^-4	0.867	INTERGENIC
3L	14105388	3L_14105388_DEL [dm3] 3L_14112288_DEL [dm6]	AT	C	1.048e^-4	0.867	DOWNSTREAM Sox21b INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_zfh1
3R	6736381	3R_6736381_SNP [dm3] 3R_10910659_SNP [dm6]	T	C	1.068e^-4	0.867	INTERGENIC
2L	13966015	2L_13966015_SNP [dm3] 2L_13966015_SNP [dm6]	G	A	1.078e^-4	0.867	SPLICE_SITE_REGION NimB2 DOWNSTREAM NimB1 INTRON NimB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	13966017	2L_13966017_SNP [dm3] 2L_13966017_SNP [dm6]	T	A	1.078e^-4	0.867	SPLICE_SITE_REGION NimB2 DOWNSTREAM NimB1 INTRON NimB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	13966021	2L_13966021_SNP [dm3] 2L_13966021_SNP [dm6]	A	C	1.078e^-4	0.867	DOWNSTREAM NimB1 INTRON NimB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9264818	2R_9264818_SNP [dm3] 2R_13377313_SNP [dm6]	C	T	1.091e^-4	0.867	NON_SYNONYMOUS_CODING CG10814	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1005288	3L_1005288_SNP [dm3] 3L_1005288_SNP [dm6]	C	A	1.157e^-4	0.867	INTRON trio
3L	8672802	3L_8672802_SNP [dm3] 3L_8679702_SNP [dm6]	A	T	1.159e^-4	0.867	DOWNSTREAM h INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
X	20467213	X_20467213_SNP [dm3] X_20596186_SNP [dm6]	T	G	1.211e^-4	0.867	INTRON RunxA
2L	13966035	2L_13966035_SNP [dm3] 2L_13966035_SNP [dm6]	T	G	1.228e^-4	0.867	DOWNSTREAM NimB1 INTRON NimB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11524104	3L_11524104_SNP [dm3] 3L_11531004_SNP [dm6]	T	C	1.271e^-4	0.867	INTRON Mob2
X	17152811	X_17152811_SNP [dm3] X_17258778_SNP [dm6]	A	C	1.276e^-4	0.867	UPSTREAM f INTRON f	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	13932432	2R_13932432_SNP [dm3] 2R_18044927_SNP [dm6]	T	G	1.280e^-4	0.867	NON_SYNONYMOUS_CODING CG5770
2L	13423840	2L_13423840_SNP [dm3] 2L_13423840_SNP [dm6]	T	A	1.313e^-4	0.867	INTRON CG42784
2L	13423856	2L_13423856_SNP [dm3] 2L_13423856_SNP [dm6]	G	C	1.313e^-4	0.867	INTRON CG42784
2L	13423901	2L_13423901_SNP [dm3] 2L_13423901_SNP [dm6]	T	C	1.313e^-4	0.867	INTRON CG42784
2L	13931640	2L_13931640_SNP [dm3] 2L_13931640_SNP [dm6]	A	T	1.313e^-4	0.867	UPSTREAM CG42711 DOWNSTREAM CG16885 INTRON Ance-3
3L	7713969	3L_7713969_SNP [dm3] 3L_7720869_SNP [dm6]	A	G	1.317e^-4	0.867	SYNONYMOUS_CODING CG12262 DOWNSTREAM CG7457 INTRON CG32373	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	7087491	3L_7087491_SNP [dm3] 3L_7094391_SNP [dm6]	C	T	1.328e^-4	0.867	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC
4	1114303	4_1114303_SNP [dm3] 4_1093677_SNP [dm6]	T	A	1.344e^-4	0.867	INTRON sv	transposable element FlyBase
2R	121910	2R_121910_SNP [dm3] 2R_4234405_SNP [dm6]	G	A	1.361e^-4	0.867	INTERGENIC

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By genomic position
Variant impact
Gene name

RepOutput_Day12 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results