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=4.125e^-5)
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_2R_NS	0.0274

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	8.1759	0.0168

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2107 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
2L	1337347	2L_1337347_SNP [dm3] 2L_1337347_SNP [dm6]	A	C	2.051e^-6	0.862	INTERGENIC	TF binding site mE1_TFBS_inv
2L	21052421	2L_21052421_SNP [dm3] 2L_21052421_SNP [dm6]	A	C	2.124e^-6	0.862	UPSTREAM CG42238 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Ubx
2R	17154790	2R_17154790_SNP [dm3] 2R_21267285_SNP [dm6]	A	G	2.366e^-6	0.862	SYNONYMOUS_CODING CG30393 UPSTREAM CG30391 INTRON Rgk3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12374265	2R_12374265_SNP [dm3] 2R_16486760_SNP [dm6]	T	C	3.337e^-6	0.862	SYNONYMOUS_CODING CG33458
2R	2116391	2R_2116391_SNP [dm3] 2R_6228886_SNP [dm6]	C	T	3.656e^-6	0.862	UPSTREAM bin3 INTRON bin3	TF binding site BDTNP1_TFBS_dl
2R	17154921	2R_17154921_SNP [dm3] 2R_21267416_SNP [dm6]	G	A	3.821e^-6	0.862	SYNONYMOUS_CODING CG30393 INTRON Rgk3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	13657696	2R_13657696_SNP [dm3] 2R_17770191_SNP [dm6]	C	T	4.568e^-6	0.862	UPSTREAM CG18635 DOWNSTREAM CG6362 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	9598332	2L_9598332_SNP [dm3] 2L_9598332_SNP [dm6]	T	C	4.709e^-6	0.862	DOWNSTREAM CG4382 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi
X	4157387	X_4157387_SNP [dm3] X_4263354_SNP [dm6]	T	C	5.284e^-6	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	18110792	3L_18110792_SNP [dm3] 3L_18117692_SNP [dm6]	C	T	5.806e^-6	0.862	UTR_3_PRIME CG32195 INTRON CG7341
3L	9019867	3L_9019867_SNP [dm3] 3L_9026767_SNP [dm6]	C	A	6.187e^-6	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	1649169	2L_1649169_SNP [dm3] 2L_1649169_SNP [dm6]	A	G	6.424e^-6	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	17867233	3L_17867233_SNP [dm3] 3L_17874133_SNP [dm6]	G	T	6.882e^-6	0.862	UPSTREAM CR43087 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	18741574	2R_18741574_SNP [dm3] 2R_22854051_SNP [dm6]	C	T	7.456e^-6	0.862	UPSTREAM RpL23 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
2L	3708289	2L_3708289_SNP [dm3] 2L_3708289_SNP [dm6]	C	T	7.958e^-6	0.862	INTRON cutlet	TF binding site mE1_TFBS_cad
X	19752469	X_19752469_SNP [dm3] X_19858436_SNP [dm6]	C	A	1.010e^-5	0.862	SYNONYMOUS_CODING Nup205	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	9019892	3L_9019892_SNP [dm3] 3L_9026792_SNP [dm6]	T	A	1.029e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	3709184	2L_3709184_SNP [dm3] 2L_3709184_SNP [dm6]	G	A	1.112e^-5	0.862	SYNONYMOUS_CODING cutlet	TF binding site mE1_TFBS_cad
2L	3221835	2L_3221835_SNP [dm3] 2L_3221835_SNP [dm6]	T	G	1.122e^-5	0.862	INTERGENIC
3L	9019849	3L_9019849_SNP [dm3] 3L_9026749_SNP [dm6]	A	G	1.141e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	15035964	2R_15035964_SNP [dm3] 2R_19148459_SNP [dm6]	T	A	1.187e^-5	0.862	INTRON ena	TF binding site BDTNP1_TFBS_dl
3L	8021848	3L_8021848_SNP [dm3] 3L_8028748_SNP [dm6]	T	C	1.246e^-5	0.862	UPSTREAM tRNA:CR32370 INTRON nmo	TF binding site mE1_TFBS_sens
3L	10474978	3L_10474978_SNP [dm3] 3L_10481878_SNP [dm6]	G	A	1.299e^-5	0.862	UTR_5_PRIME A2bp1
3L	4338219	3L_4338219_SNP [dm3] 3L_4338219_SNP [dm6]	A	G	1.328e^-5	0.862	INTRON Cip4	TF binding site mE1_TFBS_inv
2R	20225490	2R_20225490_SNP [dm3] 2R_24337967_SNP [dm6]	T	C	1.349e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
X	4571596	X_4571596_SNP [dm3] X_4677563_SNP [dm6]	G	T	1.357e^-5	0.862	UPSTREAM rap INTRON rap	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	13651934	2R_13651934_SNP [dm3] 2R_17764429_SNP [dm6]	T	A	1.408e^-5	0.862	UTR_3_PRIME CG5009 DOWNSTREAM OstDelta
2R	14581186	2R_14581186_SNP [dm3] 2R_18693681_SNP [dm6]	A	C	1.430e^-5	0.862	INTRON Sik3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	3221896	2L_3221896_SNP [dm3] 2L_3221896_SNP [dm6]	C	T	1.433e^-5	0.862	INTERGENIC
3L	9019884	3L_9019884_SNP [dm3] 3L_9026784_SNP [dm6]	A	T	1.466e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	11633585	2R_11633585_SNP [dm3] 2R_15746080_SNP [dm6]	G	C	1.589e^-5	0.862	INTRON CG30089	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	9598299	2L_9598299_SNP [dm3] 2L_9598299_SNP [dm6]	G	A	1.598e^-5	0.862	DOWNSTREAM CG4382 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi
3L	9011421	3L_9011421_SNP [dm3] 3L_9018321_SNP [dm6]	G	A	1.606e^-5	0.862	INTRON Doc2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
3L	8020395	3L_8020395_SNP [dm3] 3L_8027295_SNP [dm6]	C	T	1.670e^-5	0.862	INTRON nmo	TF binding site mE1_TFBS_cad
2R	8334505	2R_8334505_SNP [dm3] 2R_12447000_SNP [dm6]	G	T	1.734e^-5	0.862	INTRON Dyb
2L	20389298	2L_20389298_SNP [dm3] 2L_20389298_SNP [dm6]	A	T	1.902e^-5	0.862	INTRON CG10947
2L	10495582	2L_10495582_SNP [dm3] 2L_10495582_SNP [dm6]	A	G	1.977e^-5	0.862	INTRON Myo31DF
2R	20227794	2R_20227794_SNP [dm3] 2R_24340271_SNP [dm6]	C	G	1.982e^-5	0.862	INTERGENIC
2R	13657644	2R_13657644_SNP [dm3] 2R_17770139_SNP [dm6]	C	T	2.062e^-5	0.862	UPSTREAM CG18635 DOWNSTREAM CG6362 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	10475241	3L_10475241_SNP [dm3] 3L_10482141_SNP [dm6]	C	G	2.185e^-5	0.862	INTRON A2bp1
2L	3709240	2L_3709240_SNP [dm3] 2L_3709240_SNP [dm6]	C	A	2.188e^-5	0.862	INTRON cutlet	TF binding site mE1_TFBS_cad
2R	11633588	2R_11633588_SNP [dm3] 2R_15746083_SNP [dm6]	C	T	2.304e^-5	0.862	INTRON CG30089	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	19482135	2R_19482135_SNP [dm3] 2R_23594612_SNP [dm6]	G	C	2.338e^-5	0.862	INTRON apt	TF binding site mE1_TFBS_sens
2L	6372607	2L_6372607_SNP [dm3] 2L_6372607_SNP [dm6]	G	C	2.369e^-5	0.862	UPSTREAM slam INTRON slam	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
3L	4969182	3L_4969182_SNP [dm3] 3L_4969182_SNP [dm6]	C	A	2.398e^-5	0.862	INTRON Con	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	3708210	2L_3708210_SNP [dm3] 2L_3708210_SNP [dm6]	G	A	2.457e^-5	0.862	SYNONYMOUS_CODING cutlet	TF binding site mE1_TFBS_cad
3L	8020947	3L_8020947_SNP [dm3] 3L_8027847_SNP [dm6]	G	A	2.487e^-5	0.862	DOWNSTREAM tRNA:CR32370 INTRON nmo	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	5027206	3R_5027206_DEL [dm3] 3R_9201484_DEL [dm6]	AGGGGCGA	A	2.541e^-5	0.862	INTRON pum	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	8268475	2L_8268475_SNP [dm3] 2L_8268475_SNP [dm6]	T	C	2.543e^-5	0.862	INTRON Btk29A	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	7508743	2R_7508743_SNP [dm3] 2R_11621238_SNP [dm6]	G	A	2.557e^-5	0.862	SYNONYMOUS_CODING CG9005	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo mE1_TFBS_HSA
X	20431538	X_20431538_SNP [dm3] X_20560511_SNP [dm6]	C	T	2.573e^-5	0.862	INTRON RunxB
3L	17297619	3L_17297619_SNP [dm3] 3L_17304519_SNP [dm6]	C	T	2.688e^-5	0.862	INTERGENIC
2R	6786638	2R_6786638_SNP [dm3] 2R_10899133_SNP [dm6]	T	A	2.750e^-5	0.862	UPSTREAM Rpb5 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens
3L	22924198	3L_22924198_SNP [dm3] 3L_22931098_SNP [dm6]	A	T	2.770e^-5	0.862	INTERGENIC
3L	1263619	3L_1263619_SNP [dm3] 3L_1263619_SNP [dm6]	G	C	2.796e^-5	0.862	INTRON CG9134
2R	19482133	2R_19482133_SNP [dm3] 2R_23594610_SNP [dm6]	A	G	2.798e^-5	0.862	INTRON apt	TF binding site mE1_TFBS_sens
3R	16010065	3R_16010065_SNP [dm3] 3R_20184343_SNP [dm6]	C	T	2.807e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	6942895	2L_6942895_SNP [dm3] 2L_6942895_SNP [dm6]	G	C	2.875e^-5	0.862	UPSTREAM CG18304 DOWNSTREAM CG10158 INTERGENIC
2L	15637005	2L_15637005_SNP [dm3] 2L_15637005_SNP [dm6]	A	G	2.878e^-5	0.862	INTERGENIC
2R	18342893	2R_18342893_SNP [dm3] 2R_22455388_SNP [dm6]	C	A	2.916e^-5	0.862	UTR_5_PRIME CG10384
3L	1263533	3L_1263533_SNP [dm3] 3L_1263533_SNP [dm6]	C	A	2.971e^-5	0.862	INTRON CG9134
2L	14670341	2L_14670341_SNP [dm3] 2L_14670341_SNP [dm6]	C	G	3.005e^-5	0.862	INTRON osp
2L	4008338	2L_4008338_SNP [dm3] 2L_4008338_SNP [dm6]	G	A	3.114e^-5	0.862	UPSTREAM CG43774 DOWNSTREAM CG43773 INTERGENIC
2L	3708954	2L_3708954_SNP [dm3] 2L_3708954_SNP [dm6]	T	C	3.160e^-5	0.862	INTRON cutlet	TF binding site mE1_TFBS_cad
2L	3199886	2L_3199886_SNP [dm3] 2L_3199886_SNP [dm6]	A	G	3.212e^-5	0.862	UPSTREAM CG34393 INTRON CG34393
3R	14884001	3R_14884001_SNP [dm3] 3R_19058279_SNP [dm6]	T	A	3.214e^-5	0.862	INTRON cdi	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10474283	3L_10474283_SNP [dm3] 3L_10481183_SNP [dm6]	C	T	3.244e^-5	0.862	UPSTREAM A2bp1 INTERGENIC
3L	18107754	3L_18107754_SNP [dm3] 3L_18114654_SNP [dm6]	C	T	3.295e^-5	0.862	SYNONYMOUS_CODING CG32195 INTRON CG7341	TF binding site mE1_TFBS_sens
2L	15637422	2L_15637422_SNP [dm3] 2L_15637422_SNP [dm6]	G	A	3.312e^-5	0.862	INTERGENIC
3L	8019127	3L_8019127_SNP [dm3] 3L_8026027_SNP [dm6]	A	G	3.328e^-5	0.862	INTRON nmo
2L	17416459	2L_17416459_SNP [dm3] 2L_17416459_SNP [dm6]	A	G	3.343e^-5	0.862	SYNONYMOUS_CODING Dif INTRON Dif
3L	1392582	3L_1392582_SNP [dm3] 3L_1392582_SNP [dm6]	T	C	3.359e^-5	0.862	INTRON Ptp61F	TF binding site mE1_TFBS_cad
2L	20392466	2L_20392466_SNP [dm3] 2L_20392466_SNP [dm6]	C	A	3.365e^-5	0.862	INTRON CG10947
2R	18741182	2R_18741182_SNP [dm3] 2R_22853659_SNP [dm6]	T	C	3.427e^-5	0.862	SYNONYMOUS_CODING CG13531 UPSTREAM RpL23	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	14509307	3L_14509307_SNP [dm3] 3L_14516207_SNP [dm6]	G	T	3.490e^-5	0.862	INTRON bbg
3R	12491303	3R_12491303_SNP [dm3] 3R_16665581_SNP [dm6]	T	C	3.597e^-5	0.862	INTRON Ubx
2L	6372516	2L_6372516_SNP [dm3] 2L_6372516_SNP [dm6]	G	C	3.600e^-5	0.862	UTR_5_PRIME slam UPSTREAM slam	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_cad
2L	3200108	2L_3200108_SNP [dm3] 2L_3200108_SNP [dm6]	C	T	3.615e^-5	0.862	UPSTREAM CG34393 INTRON CG34393
3L	14229560	3L_14229560_SNP [dm3] 3L_14236460_SNP [dm6]	A	G	3.682e^-5	0.862	UPSTREAM CG7906 & 1 other INTERGENIC
3L	14223046	3L_14223046_SNP [dm3] 3L_14229946_SNP [dm6]	C	G	3.846e^-5	0.862	UTR_5_PRIME nuf INTRON nuf
2R	12102290	2R_12102290_SNP [dm3] 2R_16214785_SNP [dm6]	A	T	4.096e^-5	0.862	INTRON mrj
2L	21926543	2L_21926543_SNP [dm3] 2L_21926543_SNP [dm6]	G	A	4.158e^-5	0.862	INTERGENIC
X	12856440	X_12856440_SNP [dm3] X_12962407_SNP [dm6]	G	A	4.321e^-5	0.862	INTERGENIC
3L	10474263	3L_10474263_SNP [dm3] 3L_10481163_SNP [dm6]	A	C	4.515e^-5	0.862	UPSTREAM A2bp1 INTERGENIC
X	20430305	X_20430305_SNP [dm3] X_20559278_SNP [dm6]	T	A	4.576e^-5	0.862	INTRON RunxB
X	3480882	X_3480882_SNP [dm3] X_3586849_SNP [dm6]	G	A	4.585e^-5	0.862	INTRON AstA-R1
3R	965200	3R_965200_SNP [dm3] 3R_5139478_SNP [dm6]	C	A	4.641e^-5	0.862	UPSTREAM CG12589 INTERGENIC
2L	6942917	2L_6942917_SNP [dm3] 2L_6942917_SNP [dm6]	G	A	4.672e^-5	0.862	UPSTREAM CG18304 DOWNSTREAM CG10158 INTERGENIC
2L	21050723	2L_21050723_SNP [dm3] 2L_21050723_SNP [dm6]	G	T	4.698e^-5	0.862	INTRON CG42238	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	10743302	X_10743302_SNP [dm3] X_10849269_SNP [dm6]	G	C	4.795e^-5	0.862	SYNONYMOUS_CODING CG2202 DOWNSTREAM CG17333	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	4107993	X_4107993_SNP [dm3] X_4213960_SNP [dm6]	G	A	5.004e^-5	0.862	DOWNSTREAM CG43288 INTERGENIC	TF binding site BDTNP1_TFBS_gt
2R	7512597	2R_7512597_SNP [dm3] 2R_11625092_SNP [dm6]	C	G	5.087e^-5	0.862	NON_SYNONYMOUS_CODING CG9005	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	17586787	2R_17586787_SNP [dm3] 2R_21699282_SNP [dm6]	C	T	5.125e^-5	0.862	INTRON HmgZ	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4651421	2L_4651421_SNP [dm3] 2L_4651421_SNP [dm6]	G	A	5.137e^-5	0.862	UTR_5_PRIME CG3355 UPSTREAM CG3355
3L	8021004	3L_8021004_INS [dm3] 3L_8027904_INS [dm6]	T	TACT	5.140e^-5	0.862	DOWNSTREAM tRNA:CR32370 INTRON nmo	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	9831585	2L_9831585_SNP [dm3] 2L_9831585_SNP [dm6]	C	T	5.146e^-5	0.862	INTRON nAChRalpha6
3L	15996860	3L_15996860_SNP [dm3] 3L_16003760_SNP [dm6]	G	C	5.343e^-5	0.862	INTRON CG5830	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
3R	21785923	3R_21785923_SNP [dm3] 3R_25960201_SNP [dm6]	C	T	5.348e^-5	0.862	SYNONYMOUS_CODING CG14540
3L	20618992	3L_20618992_SNP [dm3] 3L_20625892_SNP [dm6]	T	C	5.423e^-5	0.862	UPSTREAM CR44680 DOWNSTREAM CR44683 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16018033	2R_16018033_SNP [dm3] 2R_20130528_SNP [dm6]	G	A	5.510e^-5	0.862	INTERGENIC

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By genomic position
Variant impact
Gene name

Surv_AAmanitin_0_2ug phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results