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=3.060e^-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

Covariate	p-value	Significance
In_2L_t	0.08109

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.0195	0.0813
In_2R_NS	7.0907	0.0289

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2092 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	1085642	3L_1085642_SNP [dm3] 3L_1085642_SNP [dm6]	T	A	3.144e^-8	0.059	INTRON bab1
3R	21217519	3R_21217519_SNP [dm3] 3R_25391797_SNP [dm6]	T	C	2.173e^-7	0.103	INTRON Fur1
X	9121129	X_9121129_SNP [dm3] X_9227096_SNP [dm6]	C	T	2.196e^-7	0.103	UPSTREAM Gr8a DOWNSTREAM CG15370 INTERGENIC
3L	1084990	3L_1084990_SNP [dm3] 3L_1084990_SNP [dm6]	C	G	2.203e^-7	0.103	INTRON bab1	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	1085137	3L_1085137_SNP [dm3] 3L_1085137_SNP [dm6]	G	T	4.669e^-7	0.159	INTRON bab1	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	27133512	3R_27133512_SNP [dm3] 3R_31307790_SNP [dm6]	C	G	5.092e^-7	0.159	INTERGENIC
3L	1085230	3L_1085230_SNP [dm3] 3L_1085230_SNP [dm6]	T	G	8.418e^-7	0.183	INTRON bab1	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	1244833	3L_1244833_SNP [dm3] 3L_1244833_SNP [dm6]	G	A	8.598e^-7	0.183	SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1244830	3L_1244830_SNP [dm3] 3L_1244830_SNP [dm6]	G	A	8.955e^-7	0.183	SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1242674	3L_1242674_SNP [dm3] 3L_1242674_SNP [dm6]	T	A	1.011e^-6	0.183	SYNONYMOUS_CODING Klp61F DOWNSTREAM CG9194	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1122911	3L_1122911_SNP [dm3] 3L_1122911_SNP [dm6]	G	T	1.076e^-6	0.183	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	1244839	3L_1244839_SNP [dm3] 3L_1244839_SNP [dm6]	G	A	1.657e^-6	0.241	SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1243096	3L_1243096_SNP [dm3] 3L_1243096_SNP [dm6]	A	C	1.671e^-6	0.241	NON_SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_sens
3L	1271857	3L_1271857_SNP [dm3] 3L_1271857_SNP [dm6]	G	T	1.880e^-6	0.252	INTRON CG9134
X	9121094	X_9121094_SNP [dm3] X_9227061_SNP [dm6]	T	C	2.367e^-6	0.296	UPSTREAM Gr8a DOWNSTREAM CG15370 INTERGENIC
3R	25420537	3R_25420537_SNP [dm3] 3R_29594815_SNP [dm6]	A	G	2.960e^-6	0.347	INTRON alph
3L	1230773	3L_1230773_SNP [dm3] 3L_1230773_SNP [dm6]	C	A	3.673e^-6	0.381	SYNONYMOUS_CODING mwh	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1090733	3L_1090733_SNP [dm3] 3L_1090733_SNP [dm6]	T	A	3.928e^-6	0.381	INTRON bab1	regulatory region REDfly_CRMs
3L	1243072	3L_1243072_SNP [dm3] 3L_1243072_SNP [dm6]	C	T	3.992e^-6	0.381	NON_SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_sens
3L	1271873	3L_1271873_SNP [dm3] 3L_1271873_SNP [dm6]	T	C	4.154e^-6	0.381	INTRON CG9134
3L	1245121	3L_1245121_SNP [dm3] 3L_1245121_SNP [dm6]	T	A	4.269e^-6	0.381	DOWNSTREAM CG32318 INTRON Klp61F	TF binding site mE1_TFBS_sens
3L	1242701	3L_1242701_SNP [dm3] 3L_1242701_SNP [dm6]	A	T	4.632e^-6	0.395	SYNONYMOUS_CODING Klp61F DOWNSTREAM CG9194	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	9496975	2L_9496975_SNP [dm3] 2L_9496975_SNP [dm6]	T	C	5.162e^-6	0.421	INTRON CG33298	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
3R	27143441	3R_27143441_SNP [dm3] 3R_31317719_SNP [dm6]	G	A	6.209e^-6	0.467	INTRON CG34347
3R	27138232	3R_27138232_SNP [dm3] 3R_31312510_SNP [dm6]	G	A	6.463e^-6	0.467	INTRON CG34347
X	15535738	X_15535738_SNP [dm3] X_15641705_SNP [dm6]	T	C	6.479e^-6	0.467	EXON CR44893
X	9121177	X_9121177_SNP [dm3] X_9227144_SNP [dm6]	C	T	7.165e^-6	0.471	UTR_5_PRIME Gr8a DOWNSTREAM CG15370
3R	27135131	3R_27135131_SNP [dm3] 3R_31309409_SNP [dm6]	C	A	7.269e^-6	0.471	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26935103	3R_26935103_SNP [dm3] 3R_31109381_SNP [dm6]	C	T	7.275e^-6	0.471	UPSTREAM CG11318 INTERGENIC
3L	1904606	3L_1904606_SNP [dm3] 3L_1904606_SNP [dm6]	A	T	7.896e^-6	0.478	INTRON CG1887	TF binding site mE1_TFBS_chinmo
3L	1267191	3L_1267191_SNP [dm3] 3L_1267191_SNP [dm6]	G	A	8.032e^-6	0.478	INTRON CG9134
3L	1257108	3L_1257108_SNP [dm3] 3L_1257108_SNP [dm6]	G	C	8.148e^-6	0.478	UTR_5_PRIME CG9134
3R	15500551	3R_15500551_SNP [dm3] 3R_19674829_SNP [dm6]	A	G	9.184e^-6	0.522	INTRON Naam
3R	17063120	3R_17063120_SNP [dm3] 3R_21237398_SNP [dm6]	T	C	9.882e^-6	0.522	UPSTREAM e INTERGENIC	regulatory region REDfly_CRMs
2L	22075281	2L_22075281_SNP [dm3] 2L_22075281_SNP [dm6]	A	T	9.979e^-6	0.522	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	15535734	X_15535734_SNP [dm3] X_15641701_SNP [dm6]	T	G	1.022e^-5	0.522	EXON CR44893
3L	1090783	3L_1090783_SNP [dm3] 3L_1090783_SNP [dm6]	T	A	1.050e^-5	0.522	INTRON bab1	regulatory region REDfly_CRMs
2R	15490188	2R_15490188_SNP [dm3] 2R_19602683_SNP [dm6]	G	A	1.058e^-5	0.522	UPSTREAM CR44473 INTRON sm
2R	19687195	2R_19687195_SNP [dm3] 2R_23799672_SNP [dm6]	C	G	1.120e^-5	0.53	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	1086181	3L_1086181_SNP [dm3] 3L_1086181_SNP [dm6]	G	A	1.194e^-5	0.53	INTRON bab1
3R	14358995	3R_14358995_SNP [dm3] 3R_18533273_SNP [dm6]	A	T	1.234e^-5	0.53	INTRON fru
3L	1268391	3L_1268391_SNP [dm3] 3L_1268391_SNP [dm6]	A	G	1.305e^-5	0.53	INTRON CG9134
3L	1092106	3L_1092106_SNP [dm3] 3L_1092106_SNP [dm6]	C	T	1.343e^-5	0.53	INTRON bab1	regulatory region REDfly_CRMs
3L	1085272	3L_1085272_SNP [dm3] 3L_1085272_SNP [dm6]	C	T	1.357e^-5	0.53	INTRON bab1	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	2537181	3L_2537181_SNP [dm3] 3L_2537181_SNP [dm6]	T	C	1.365e^-5	0.53	UPSTREAM Spn INTRON Spn	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	14249623	3L_14249623_SNP [dm3] 3L_14256523_SNP [dm6]	T	C	1.395e^-5	0.53	INTERGENIC
3L	1239438	3L_1239438_SNP [dm3] 3L_1239438_SNP [dm6]	G	C	1.436e^-5	0.53	INTRON CG9194	TF binding site mE1_TFBS_cad
3R	21217489	3R_21217489_SNP [dm3] 3R_25391767_SNP [dm6]	A	C	1.466e^-5	0.53	INTRON Fur1
3L	1268803	3L_1268803_SNP [dm3] 3L_1268803_SNP [dm6]	A	T	1.468e^-5	0.53	INTRON CG9134
2L	9497507	2L_9497507_SNP [dm3] 2L_9497507_SNP [dm6]	T	C	1.475e^-5	0.53	INTRON CG33298	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	20283209	3R_20283209_SNP [dm3] 3R_24457487_SNP [dm6]	T	G	1.482e^-5	0.53	UPSTREAM nAChRalpha1 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	1191631	3L_1191631_SNP [dm3] 3L_1191631_SNP [dm6]	T	C	1.495e^-5	0.53	INTRON Trh	TF binding site mE1_TFBS_cad
3L	1193607	3L_1193607_SNP [dm3] 3L_1193607_SNP [dm6]	C	G	1.555e^-5	0.53	UPSTREAM Trh INTERGENIC
3R	21217629	3R_21217629_SNP [dm3] 3R_25391907_SNP [dm6]	T	C	1.580e^-5	0.53	INTRON Fur1
3L	2324713	3L_2324713_SNP [dm3] 3L_2324713_SNP [dm6]	T	C	1.648e^-5	0.53	INTRON MsR1
3R	20283190	3R_20283190_SNP [dm3] 3R_24457468_SNP [dm6]	G	T	1.700e^-5	0.53	UPSTREAM nAChRalpha1 INTERGENIC	TF binding site mE1_TFBS_Trl
3R	27143473	3R_27143473_SNP [dm3] 3R_31317751_SNP [dm6]	T	C	1.711e^-5	0.53	INTRON CG34347
3L	1085552	3L_1085552_SNP [dm3] 3L_1085552_SNP [dm6]	G	A	1.746e^-5	0.53	INTRON bab1
3R	27135120	3R_27135120_SNP [dm3] 3R_31309398_SNP [dm6]	C	T	1.772e^-5	0.53	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	1242730	3L_1242730_SNP [dm3] 3L_1242730_SNP [dm6]	C	G	1.793e^-5	0.53	NON_SYNONYMOUS_CODING Klp61F DOWNSTREAM CG9194	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1268390	3L_1268390_SNP [dm3] 3L_1268390_SNP [dm6]	G	A	1.798e^-5	0.53	INTRON CG9134
3R	25416511	3R_25416511_SNP [dm3] 3R_29590789_SNP [dm6]	G	T	1.809e^-5	0.53	NON_SYNONYMOUS_CODING CG31041	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	21542838	3R_21542838_SNP [dm3] 3R_25717116_SNP [dm6]	G	A	1.809e^-5	0.53	INTRON LpR2
3L	1271833	3L_1271833_SNP [dm3] 3L_1271833_SNP [dm6]	A	C	1.842e^-5	0.53	INTRON CG9134
2L	1956864	2L_1956864_SNP [dm3] 2L_1956864_SNP [dm6]	G	A	1.859e^-5	0.53	INTRON erm	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	20628607	2L_20628607_SNP [dm3] 2L_20628607_SNP [dm6]	C	A	1.866e^-5	0.53	INTERGENIC
3L	1085809	3L_1085809_SNP [dm3] 3L_1085809_SNP [dm6]	T	C	1.972e^-5	0.551	INTRON bab1
3L	1250335	3L_1250335_SNP [dm3] 3L_1250335_SNP [dm6]	G	T	1.996e^-5	0.551	UTR_3_PRIME Sac1 UPSTREAM CG9129
3L	1266443	3L_1266443_SNP [dm3] 3L_1266443_SNP [dm6]	C	G	2.041e^-5	0.555	INTRON CG9134
3L	1085687	3L_1085687_SNP [dm3] 3L_1085687_SNP [dm6]	G	A	2.121e^-5	0.566	INTRON bab1
3L	1267306	3L_1267306_SNP [dm3] 3L_1267306_SNP [dm6]	T	C	2.177e^-5	0.566	INTRON CG9134
2R	10700370	2R_10700370_SNP [dm3] 2R_14812865_SNP [dm6]	G	C	2.180e^-5	0.566	INTERGENIC	regulatory region REDfly_CRMs
2R	19687188	2R_19687188_SNP [dm3] 2R_23799665_SNP [dm6]	A	G	2.202e^-5	0.566	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	17057231	3R_17057231_SNP [dm3] 3R_21231509_SNP [dm6]	A	G	2.300e^-5	0.573	SYNONYMOUS_CODING e	TF binding site mE1_TFBS_cad
3L	1244227	3L_1244227_SNP [dm3] 3L_1244227_SNP [dm6]	A	G	2.326e^-5	0.573	SYNONYMOUS_CODING Klp61F	TF binding site mE1_TFBS_sens
2R	9897501	2R_9897501_DEL [dm3] 2R_14009996_DEL [dm6]	CC	G	2.336e^-5	0.573	INTRON mam
3R	25156878	3R_25156878_SNP [dm3] 3R_29331156_SNP [dm6]	C	G	2.354e^-5	0.573	INTERGENIC
3L	1268394	3L_1268394_DEL [dm3] 3L_1268394_DEL [dm6]	GCCA	G	2.543e^-5	0.605	INTRON CG9134
3L	1268399	3L_1268399_SNP [dm3] 3L_1268399_SNP [dm6]	A	T	2.609e^-5	0.605	INTRON CG9134
3L	2537183	3L_2537183_SNP [dm3] 3L_2537183_SNP [dm6]	G	A	2.612e^-5	0.605	UPSTREAM Spn INTRON Spn	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	3601548	2R_3601548_SNP [dm3] 2R_7714043_SNP [dm6]	T	G	2.657e^-5	0.605	NON_SYNONYMOUS_CODING CG1942 UPSTREAM CG1946	TF binding site mE1_TFBS_cnc
2L	16369024	2L_16369024_SNP [dm3] 2L_16369024_SNP [dm6]	A	T	2.684e^-5	0.605	INTERGENIC
3L	1265993	3L_1265993_SNP [dm3] 3L_1265993_SNP [dm6]	T	A	2.692e^-5	0.605	UTR_5_PRIME CG9134 INTRON CG9134	TF binding site mE1_TFBS_Trl
3R	27579885	3R_27579885_DEL [dm3] 3R_31754163_DEL [dm6]	GTGAAATTCATCTAAG...	G	2.712e^-5	0.605	UPSTREAM mir-1014 INTRON salt
2R	10700329	2R_10700329_SNP [dm3] 2R_14812824_SNP [dm6]	C	G	2.743e^-5	0.605	INTERGENIC	regulatory region REDfly_CRMs
3L	1086802	3L_1086802_INS [dm3] 3L_1086802_INS [dm6]	TC	CTAT	2.883e^-5	0.629	INTRON bab1
3R	26391868	3R_26391868_SNP [dm3] 3R_30566146_SNP [dm6]	G	A	2.972e^-5	0.641	INTRON tmod
3L	1086767	3L_1086767_SNP [dm3] 3L_1086767_SNP [dm6]	A	G	3.170e^-5	0.676	INTRON bab1
3L	12152302	3L_12152302_SNP [dm3] 3L_12159202_SNP [dm6]	G	T	3.290e^-5	0.688	SYNONYMOUS_CODING CG9760
3R	25066836	3R_25066836_SNP [dm3] 3R_29241114_SNP [dm6]	C	T	3.319e^-5	0.688	SYNONYMOUS_CODING CG31445 UPSTREAM CG31427	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1268172	3L_1268172_SNP [dm3] 3L_1268172_SNP [dm6]	T	C	3.336e^-5	0.688	INTRON CG9134
3R	16494797	3R_16494797_SNP [dm3] 3R_20669075_SNP [dm6]	C	T	3.485e^-5	0.71	UPSTREAM Cpr92F INTERGENIC	TF binding site mE1_TFBS_cad
3L	1285196	3L_1285196_SNP [dm3] 3L_1285196_SNP [dm6]	G	T	3.546e^-5	0.71	INTRON CG32333
3R	13127277	3R_13127277_SNP [dm3] 3R_17301555_SNP [dm6]	T	A	3.678e^-5	0.71	INTERGENIC
3R	13127297	3R_13127297_SNP [dm3] 3R_17301575_SNP [dm6]	A	T	3.678e^-5	0.71	INTERGENIC
3L	1254360	3L_1254360_SNP [dm3] 3L_1254360_SNP [dm6]	C	T	3.687e^-5	0.71	UTR_5_PRIME CG9133 UTR_3_PRIME CG9130 INTRON CG9130 & 1 other	TF binding site mE1_TFBS_chinmo
2L	6050212	2L_6050212_SNP [dm3] 2L_6050212_SNP [dm6]	A	G	3.702e^-5	0.71	NON_SYNONYMOUS_CODING CG12393 UPSTREAM CG9135	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo
3R	20304801	3R_20304801_DEL [dm3] 3R_24479079_DEL [dm6]	AA	A	3.746e^-5	0.71	INTERGENIC
2R	10700307	2R_10700307_SNP [dm3] 2R_14812802_SNP [dm6]	T	C	3.748e^-5	0.71	INTERGENIC	regulatory region REDfly_CRMs
2L	1762040	2L_1762040_SNP [dm3] 2L_1762040_SNP [dm6]	T	A	3.827e^-5	0.717	INTERGENIC

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By genomic position
Variant impact
Gene name

AbdominaPigmentT6 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results