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=1.317e^-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

Covariate	p-value	Significance
In_3R_K	0.09746
In_3R_Mo	0.06196

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1735 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	9.065e^-7	0.728	INTERGENIC
2R	14586562	2R_14586562_SNP [dm3] 2R_18699057_SNP [dm6]	G	T	9.180e^-7	0.728	INTRON Sik3
3L	3845577	3L_3845577_SNP [dm3] 3L_3845577_SNP [dm6]	G	A	2.611e^-6	0.728	UPSTREAM Awh INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
3L	3846377	3L_3846377_SNP [dm3] 3L_3846377_SNP [dm6]	A	T	2.611e^-6	0.728	UTR_5_PRIME Awh	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
2L	20327414	2L_20327414_SNP [dm3] 2L_20327414_SNP [dm6]	A	C	2.655e^-6	0.728	INTRON spir
3L	11353261	3L_11353261_SNP [dm3] 3L_11360161_SNP [dm6]	T	C	3.099e^-6	0.728	INTERGENIC
3L	3850746	3L_3850746_SNP [dm3] 3L_3850746_SNP [dm6]	A	T	3.665e^-6	0.728	INTRON Awh
2L	20336420	2L_20336420_SNP [dm3] 2L_20336420_SNP [dm6]	G	A	4.605e^-6	0.728	INTRON spir
2L	20327422	2L_20327422_SNP [dm3] 2L_20327422_SNP [dm6]	T	C	4.662e^-6	0.728	INTRON spir
3L	3850776	3L_3850776_SNP [dm3] 3L_3850776_SNP [dm6]	G	T	5.252e^-6	0.728	INTRON Awh
2L	20327389	2L_20327389_SNP [dm3] 2L_20327389_SNP [dm6]	A	C	5.338e^-6	0.728	INTRON spir
2L	20328771	2L_20328771_SNP [dm3] 2L_20328771_SNP [dm6]	G	A	5.338e^-6	0.728	INTRON spir	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	3850859	3L_3850859_SNP [dm3] 3L_3850859_SNP [dm6]	C	G	5.423e^-6	0.728	INTRON Awh
2L	20336245	2L_20336245_SNP [dm3] 2L_20336245_SNP [dm6]	G	A	5.480e^-6	0.728	INTRON spir
3L	3843493	3L_3843493_SNP [dm3] 3L_3843493_SNP [dm6]	T	C	6.423e^-6	0.784	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	17162267	2R_17162267_SNP [dm3] 2R_21274762_SNP [dm6]	G	A	7.027e^-6	0.784	INTRON Rgk3
3L	7395670	3L_7395670_SNP [dm3] 3L_7402570_SNP [dm6]	C	A	7.770e^-6	0.784	SYNONYMOUS_CODING CG8560 DOWNSTREAM CG18417	TF binding site mE1_TFBS_HSA
3L	3850930	3L_3850930_SNP [dm3] 3L_3850930_SNP [dm6]	T	G	8.280e^-6	0.784	INTRON Awh
2R	12580261	2R_12580261_SNP [dm3] 2R_16692756_SNP [dm6]	G	A	8.415e^-6	0.784	NON_SYNONYMOUS_CODING CG5210 INTRON CG30463	TF binding site mE1_TFBS_cad
3L	7397462	3L_7397462_SNP [dm3] 3L_7404362_SNP [dm6]	A	C	9.222e^-6	0.784	UPSTREAM CG8560 INTERGENIC
3L	12173728	3L_12173728_SNP [dm3] 3L_12180628_SNP [dm6]	T	C	9.396e^-6	0.784	INTRON CAH2
3L	1607506	3L_1607506_SNP [dm3] 3L_1607506_SNP [dm6]	C	A	9.930e^-6	0.784	SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	3533694	2R_3533694_SNP [dm3] 2R_7646189_SNP [dm6]	G	T	1.046e^-5	0.784	NON_SYNONYMOUS_CODING CG43340 INTRON CG43340
2L	20336415	2L_20336415_SNP [dm3] 2L_20336415_SNP [dm6]	C	G	1.062e^-5	0.784	INTRON spir
2L	4090261	2L_4090261_SNP [dm3] 2L_4090261_SNP [dm6]	T	C	1.134e^-5	0.784	INTRON ed	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	5211726	3L_5211726_SNP [dm3] 3L_5218626_SNP [dm6]	C	T	1.153e^-5	0.784	INTRON shep
2L	3239163	2L_3239163_SNP [dm3] 2L_3239163_SNP [dm6]	C	T	1.204e^-5	0.784	INTERGENIC
3L	7795479	3L_7795479_SNP [dm3] 3L_7802379_SNP [dm6]	C	T	1.214e^-5	0.784	INTRON CG32369
3L	5198319	3L_5198319_SNP [dm3] 3L_5205219_SNP [dm6]	C	T	1.223e^-5	0.784	INTRON shep
3R	14239453	3R_14239453_SNP [dm3] 3R_18413731_SNP [dm6]	T	G	1.298e^-5	0.805	UPSTREAM CG31122 DOWNSTREAM fru INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	11440754	2R_11440754_SNP [dm3] 2R_15553249_SNP [dm6]	C	G	1.424e^-5	0.838	INTERGENIC
3R	14239486	3R_14239486_INS [dm3] 3R_18413764_INS [dm6]	A	AGGATCT	1.540e^-5	0.838	UPSTREAM CG31122 DOWNSTREAM fru INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	20328945	2L_20328945_SNP [dm3] 2L_20328945_SNP [dm6]	C	T	1.560e^-5	0.838	INTRON spir	TF binding site mE1_TFBS_inv
X	7989580	X_7989580_SNP [dm3] X_8095547_SNP [dm6]	A	T	1.588e^-5	0.838	UTR_3_PRIME CG2258 DOWNSTREAM CG2258
2L	20331596	2L_20331596_SNP [dm3] 2L_20331596_SNP [dm6]	G	C	1.676e^-5	0.838	INTRON spir
2R	4976769	2R_4976769_SNP [dm3] 2R_9089264_SNP [dm6]	C	A	1.785e^-5	0.838	DOWNSTREAM CG8080 INTRON Dbp45A
2L	16898786	2L_16898786_SNP [dm3] 2L_16898786_SNP [dm6]	T	A	1.828e^-5	0.838	NON_SYNONYMOUS_CODING CG31805 UTR_3_PRIME CG31805 INTRON tweek	TF binding site mE1_TFBS_sens
X	10797562	X_10797562_SNP [dm3] X_10903529_SNP [dm6]	G	A	1.933e^-5	0.838	INTERGENIC	TF binding site mE1_TFBS_cnc
3L	3850491	3L_3850491_SNP [dm3] 3L_3850491_SNP [dm6]	T	A	1.934e^-5	0.838	INTRON Awh
X	22190223	X_22190223_SNP [dm3] X_22788387_SNP [dm6]	C	T	1.970e^-5	0.838	INTRON CR44997
2R	18889506	2R_18889506_SNP [dm3] 2R_23001983_SNP [dm6]	G	A	1.975e^-5	0.838	INTRON twi	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2L	16793694	2L_16793694_SNP [dm3] 2L_16793694_SNP [dm6]	T	C	2.008e^-5	0.838	UPSTREAM Ugt36Ba DOWNSTREAM CG17928 INTERGENIC
3L	7830614	3L_7830614_SNP [dm3] 3L_7837514_SNP [dm6]	A	T	2.009e^-5	0.838	INTRON Pdp1	regulatory region REDfly_CRMs
2L	20336492	2L_20336492_SNP [dm3] 2L_20336492_SNP [dm6]	G	C	2.042e^-5	0.838	SYNONYMOUS_CODING spir
2L	4091459	2L_4091459_SNP [dm3] 2L_4091459_SNP [dm6]	C	G	2.100e^-5	0.838	INTRON ed
2L	19341337	2L_19341337_SNP [dm3] 2L_19341337_SNP [dm6]	T	G	2.135e^-5	0.838	INTRON dnt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	4277814	3L_4277814_SNP [dm3] 3L_4277814_SNP [dm6]	T	G	2.142e^-5	0.838	UPSTREAM CG1311 DOWNSTREAM CG1273 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	4277789	3L_4277789_SNP [dm3] 3L_4277789_SNP [dm6]	G	A	2.169e^-5	0.838	UPSTREAM CG1311 DOWNSTREAM CG1273 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	3850886	3L_3850886_SNP [dm3] 3L_3850886_SNP [dm6]	C	T	2.298e^-5	0.838	INTRON Awh
2R	18889510	2R_18889510_SNP [dm3] 2R_23001987_SNP [dm6]	C	A	2.317e^-5	0.838	INTRON twi	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
2R	11440746	2R_11440746_SNP [dm3] 2R_15553241_SNP [dm6]	C	G	2.338e^-5	0.838	INTERGENIC
X	20889395	X_20889395_INS [dm3] X_21018368_INS [dm6]	G	GC	2.386e^-5	0.838	INTERGENIC
X	16366183	X_16366183_SNP [dm3] X_16472150_SNP [dm6]	T	C	2.418e^-5	0.838	INTRON para	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	20331580	2L_20331580_SNP [dm3] 2L_20331580_SNP [dm6]	T	G	2.433e^-5	0.838	INTRON spir
3L	17567392	3L_17567392_SNP [dm3] 3L_17574292_SNP [dm6]	A	G	2.576e^-5	0.863	INTRON Eip74EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	17401022	3L_17401022_SNP [dm3] 3L_17407922_SNP [dm6]	A	G	2.681e^-5	0.863	INTRON blot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	7830608	3L_7830608_SNP [dm3] 3L_7837508_SNP [dm6]	A	G	2.735e^-5	0.863	INTRON Pdp1	regulatory region REDfly_CRMs
3L	7830606	3L_7830606_SNP [dm3] 3L_7837506_SNP [dm6]	G	A	2.736e^-5	0.863	INTRON Pdp1	regulatory region REDfly_CRMs
3L	3843983	3L_3843983_SNP [dm3] 3L_3843983_SNP [dm6]	T	G	2.770e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	14149277	2R_14149277_SNP [dm3] 2R_18261772_SNP [dm6]	T	A	2.870e^-5	0.863	INTERGENIC
2L	6157868	2L_6157868_SNP [dm3] 2L_6157868_SNP [dm6]	T	C	2.886e^-5	0.863	INTERGENIC
2L	4346097	2L_4346097_SNP [dm3] 2L_4346097_SNP [dm6]	G	A	2.899e^-5	0.863	DOWNSTREAM Atet INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
X	22187737	X_22187737_SNP [dm3] X_22785901_SNP [dm6]	T	A	2.927e^-5	0.863	INTRON CR44997
2L	10926938	2L_10926938_SNP [dm3] 2L_10926938_SNP [dm6]	C	T	3.001e^-5	0.863	INTRON dpr2
X	5391821	X_5391821_SNP [dm3] X_5497788_SNP [dm6]	A	G	3.015e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	11924209	2L_11924209_SNP [dm3] 2L_11924209_SNP [dm6]	G	T	3.124e^-5	0.877	INTRON Pde1c
3L	1043215	3L_1043215_SNP [dm3] 3L_1043215_SNP [dm6]	C	G	3.157e^-5	0.877	INTRON bab1
X	20847874	X_20847874_SNP [dm3] X_20976847_SNP [dm6]	T	C	3.246e^-5	0.888	INTERGENIC
3L	7824958	3L_7824958_DEL [dm3] 3L_7831858_DEL [dm6]	TT	T	3.395e^-5	0.905	INTRON Pdp1
2L	20331677	2L_20331677_SNP [dm3] 2L_20331677_SNP [dm6]	A	G	3.404e^-5	0.905	INTRON spir
X	3875217	X_3875217_SNP [dm3] X_3981184_SNP [dm6]	G	C	3.534e^-5	0.914	INTERGENIC
2L	16794067	2L_16794067_SNP [dm3] 2L_16794067_SNP [dm6]	G	A	3.576e^-5	0.914	UPSTREAM Ugt36Ba DOWNSTREAM CG17928 INTERGENIC	TF binding site mE1_TFBS_Trl
2L	13252246	2L_13252246_SNP [dm3] 2L_13252246_SNP [dm6]	T	C	3.587e^-5	0.914	NON_SYNONYMOUS_CODING CG31728
2L	20328737	2L_20328737_SNP [dm3] 2L_20328737_SNP [dm6]	C	T	3.716e^-5	0.916	INTRON spir	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	2865980	2L_2865980_SNP [dm3] 2L_2865980_SNP [dm6]	G	A	3.845e^-5	0.916	INTRON CG2991
3L	12173757	3L_12173757_SNP [dm3] 3L_12180657_SNP [dm6]	A	C	3.874e^-5	0.916	INTRON CAH2
3L	12173758	3L_12173758_SNP [dm3] 3L_12180658_SNP [dm6]	C	T	3.874e^-5	0.916	INTRON CAH2
3L	12173772	3L_12173772_SNP [dm3] 3L_12180672_SNP [dm6]	G	A	3.874e^-5	0.916	INTRON CAH2
3R	6343070	3R_6343070_SNP [dm3] 3R_10517348_SNP [dm6]	C	T	3.915e^-5	0.916	INTRON hth	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	13160016	2L_13160016_SNP [dm3] 2L_13160016_SNP [dm6]	G	T	3.986e^-5	0.916	SYNONYMOUS_CODING Pk34A UPSTREAM CG5204	TF binding site mE1_TFBS_cad
X	8617865	X_8617865_SNP [dm3] X_8723832_SNP [dm6]	G	T	4.014e^-5	0.916	UPSTREAM CR43297 INTERGENIC
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	4.035e^-5	0.916	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	14951073	X_14951073_SNP [dm3] X_15057040_SNP [dm6]	T	C	4.180e^-5	0.931	SPLICE_SITE_REGION hiw INTRON hiw	TF binding site mE1_TFBS_chinmo
2R	14572427	2R_14572427_SNP [dm3] 2R_18684922_SNP [dm6]	G	C	4.201e^-5	0.931	SYNONYMOUS_CODING CG44433 UPSTREAM CG44434 & 1 other	TF binding site mE1_TFBS_sens
2L	20143400	2L_20143400_SNP [dm3] 2L_20143400_SNP [dm6]	T	C	4.304e^-5	0.935	INTERGENIC
2R	17162234	2R_17162234_SNP [dm3] 2R_21274729_SNP [dm6]	G	A	4.352e^-5	0.935	INTRON Rgk3
3R	23561416	3R_23561416_SNP [dm3] 3R_27735694_SNP [dm6]	A	G	4.566e^-5	0.935	UPSTREAM Ets98B INTERGENIC
2L	1024601	2L_1024601_SNP [dm3] 2L_1024601_SNP [dm6]	G	C	4.592e^-5	0.935	INTRON IA-2
3L	12173725	3L_12173725_SNP [dm3] 3L_12180625_SNP [dm6]	C	T	4.665e^-5	0.935	INTRON CAH2
3R	16817595	3R_16817595_SNP [dm3] 3R_20991873_SNP [dm6]	C	T	4.720e^-5	0.935	INTRON Calx	TF binding site mE1_TFBS_chinmo
2L	3238065	2L_3238065_INS [dm3] 2L_3238065_INS [dm6]	T	TTTT	4.906e^-5	0.935	INTERGENIC
X	5484220	X_5484220_SNP [dm3] X_5590187_SNP [dm6]	A	C	5.023e^-5	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7736799	3L_7736799_SNP [dm3] 3L_7743699_SNP [dm6]	T	C	5.048e^-5	0.935	UPSTREAM Snmp2 INTRON CG32373
2L	15950359	2L_15950359_SNP [dm3] 2L_15950359_SNP [dm6]	A	T	5.052e^-5	0.935	INTRON beat-Ib
2L	11660817	2L_11660817_SNP [dm3] 2L_11660817_SNP [dm6]	C	T	5.106e^-5	0.935	DOWNSTREAM CR44479 EXON CR44497
2L	11660965	2L_11660965_SNP [dm3] 2L_11660965_SNP [dm6]	T	A	5.106e^-5	0.935	UPSTREAM CR44497 DOWNSTREAM CR44479 INTERGENIC
X	7989741	X_7989741_SNP [dm3] X_8095708_SNP [dm6]	C	G	5.131e^-5	0.935	UTR_3_PRIME CG2258 DOWNSTREAM CG2258
2L	8098939	2L_8098939_SNP [dm3] 2L_8098939_SNP [dm6]	T	C	5.183e^-5	0.935	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	7830609	3L_7830609_SNP [dm3] 3L_7837509_SNP [dm6]	A	G	5.224e^-5	0.935	INTRON Pdp1	regulatory region REDfly_CRMs
X	3907145	X_3907145_SNP [dm3] X_4013112_SNP [dm6]	T	C	5.306e^-5	0.935	INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

pc_Acetobacteraceae phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results