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=2.577e^-12)
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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

7163 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	21079359	3L_21079359_SNP [dm3] 3L_21086259_SNP [dm6]	T	G	2.430e^-18	4.521e^-12	INTRON ko	regulatory region REDfly_CRMs
2R	17315862	2R_17315862_SNP [dm3] 2R_21428357_SNP [dm6]	C	G	7.168e^-18	6.668e^-12	INTRON Sdc
3L	18197536	3L_18197536_SNP [dm3] 3L_18204436_SNP [dm6]	T	C	3.193e^-16	1.980e^-10	DOWNSTREAM CG7320 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_HSA
2R	5979802	2R_5979802_SNP [dm3] 2R_10092297_SNP [dm6]	A	C	2.368e^-14	1.101e^-8	INTRON CG2269
2L	12154665	2L_12154665_SNP [dm3] 2L_12154665_SNP [dm6]	C	G	9.196e^-14	3.422e^-8	INTRON CG31760
3R	15828101	3R_15828101_SNP [dm3] 3R_20002379_SNP [dm6]	A	T	2.202e^-13	6.829e^-8	INTRON Hs6st	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	5999899	3R_5999899_DEL [dm3] 3R_10174177_DEL [dm6]	TGAGCCGCGAGGCGAGAAGG...	T	6.562e^-13	1.744e^-7	INTRON CG12814
3R	9889548	3R_9889548_SNP [dm3] 3R_14063826_SNP [dm6]	A	C	2.176e^-12	5.061e^-7	INTRON foxo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb
3R	9889566	3R_9889566_SNP [dm3] 3R_14063844_SNP [dm6]	T	C	3.848e^-12	7.955e^-7	INTRON foxo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb
3R	5993505	3R_5993505_SNP [dm3] 3R_10167783_SNP [dm6]	C	T	9.420e^-12	1.753e^-6	INTRON Best1
3L	12885289	3L_12885289_SNP [dm3] 3L_12892189_SNP [dm6]	T	C	1.318e^-11	1.886e^-6	UPSTREAM CG14118 DOWNSTREAM CG43894 INTERGENIC
3L	12885291	3L_12885291_SNP [dm3] 3L_12892191_SNP [dm6]	C	A	1.318e^-11	1.886e^-6	UPSTREAM CG14118 DOWNSTREAM CG43894 INTERGENIC
3L	12885301	3L_12885301_SNP [dm3] 3L_12892201_SNP [dm6]	A	T	1.318e^-11	1.886e^-6	UPSTREAM CG14118 DOWNSTREAM CG43894 INTERGENIC
3R	5995523	3R_5995523_SNP [dm3] 3R_10169801_SNP [dm6]	A	T	1.496e^-11	1.988e^-6	INTRON Best1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2R	14131491	2R_14131491_SNP [dm3] 2R_18243986_SNP [dm6]	G	C	2.886e^-11	3.580e^-6	INTERGENIC
2R	6225205	2R_6225205_SNP [dm3] 2R_10337700_SNP [dm6]	A	G	7.716e^-11	8.972e^-6	INTRON CG42732
2R	14131714	2R_14131714_SNP [dm3] 2R_18244209_SNP [dm6]	A	C	9.775e^-11	1.070e^-5	INTERGENIC
2R	6225000	2R_6225000_SNP [dm3] 2R_10337495_SNP [dm6]	T	A	1.114e^-10	1.151e^-5	INTRON CG42732
X	18452847	X_18452847_SNP [dm3] X_18558814_SNP [dm6]	C	G	1.317e^-10	1.290e^-5	INTRON Bx
2R	8876027	2R_8876027_SNP [dm3] 2R_12988522_SNP [dm6]	C	G	1.394e^-10	1.297e^-5	INTERGENIC
3L	5211726	3L_5211726_SNP [dm3] 3L_5218626_SNP [dm6]	C	T	1.809e^-10	1.348e^-5	INTRON shep
3R	18574242	3R_18574242_SNP [dm3] 3R_22748520_SNP [dm6]	C	G	1.830e^-10	1.348e^-5	SYNONYMOUS_CODING CG31139 UPSTREAM CG17141 DOWNSTREAM rumi	TF binding site mE1_TFBS_cad
3L	2922495	3L_2922495_SNP [dm3] 3L_2922495_SNP [dm6]	T	C	1.857e^-10	1.348e^-5	INTRON Shab
2R	14537007	2R_14537007_SNP [dm3] 2R_18649502_SNP [dm6]	T	C	1.884e^-10	1.348e^-5	INTRON SP2637
3L	8077974	3L_8077974_SNP [dm3] 3L_8084874_SNP [dm6]	C	T	1.884e^-10	1.348e^-5	INTRON Ect4	TF binding site BDTNP1_TFBS_sna
3R	15825590	3R_15825590_SNP [dm3] 3R_19999868_SNP [dm6]	G	A	1.884e^-10	1.348e^-5	INTRON Hs6st
2R	8133071	2R_8133071_SNP [dm3] 2R_12245566_SNP [dm6]	C	T	2.272e^-10	1.565e^-5	UPSTREAM CG43244 INTERGENIC
2R	8120330	2R_8120330_SNP [dm3] 2R_12232825_SNP [dm6]	C	T	2.521e^-10	1.585e^-5	INTERGENIC
3R	12035671	3R_12035671_SNP [dm3] 3R_16209949_SNP [dm6]	T	C	2.624e^-10	1.585e^-5	UPSTREAM CR45638 DOWNSTREAM CR45640 & 1 other INTERGENIC
3L	8078005	3L_8078005_SNP [dm3] 3L_8084905_SNP [dm6]	T	C	2.793e^-10	1.585e^-5	INTRON Ect4	TF binding site BDTNP1_TFBS_sna
3R	21573660	3R_21573660_SNP [dm3] 3R_25747938_SNP [dm6]	G	A	2.975e^-10	1.585e^-5	INTRON LpR1
3R	21691431	3R_21691431_SNP [dm3] 3R_25865709_SNP [dm6]	G	T	3.034e^-10	1.585e^-5	INTRON CG5890
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	3.089e^-10	1.585e^-5	UPSTREAM CG43244 INTERGENIC
2R	8133171	2R_8133171_SNP [dm3] 2R_12245666_SNP [dm6]	C	T	3.089e^-10	1.585e^-5	UPSTREAM CG43244 INTERGENIC
2R	8133273	2R_8133273_DEL [dm3] 2R_12245768_DEL [dm6]	ACT	A	3.089e^-10	1.585e^-5	DOWNSTREAM CR44315 INTERGENIC
3R	22143461	3R_22143461_SNP [dm3] 3R_26317739_SNP [dm6]	A	C	3.137e^-10	1.585e^-5	UPSTREAM CG33970 INTERGENIC
2L	5792290	2L_5792290_SNP [dm3] 2L_5792290_SNP [dm6]	G	A	3.236e^-10	1.585e^-5	INTRON CG9171
2R	14762848	2R_14762848_SNP [dm3] 2R_18875343_SNP [dm6]	G	A	3.270e^-10	1.585e^-5	INTERGENIC
2R	8133105	2R_8133105_SNP [dm3] 2R_12245600_SNP [dm6]	A	C	3.331e^-10	1.585e^-5	UPSTREAM CG43244 INTERGENIC
2R	14762846	2R_14762846_SNP [dm3] 2R_18875341_SNP [dm6]	G	A	3.433e^-10	1.585e^-5	INTERGENIC
3R	24771802	3R_24771802_SNP [dm3] 3R_28946080_SNP [dm6]	C	T	3.552e^-10	1.585e^-5	INTRON CG14521
2R	8623667	2R_8623667_SNP [dm3] 2R_12736162_SNP [dm6]	G	A	3.701e^-10	1.585e^-5	INTRON CG42663	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	5995605	3R_5995605_SNP [dm3] 3R_10169883_SNP [dm6]	T	C	3.704e^-10	1.585e^-5	INTRON Best1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2L	8647954	2L_8647954_SNP [dm3] 2L_8647954_SNP [dm6]	A	G	3.748e^-10	1.585e^-5	INTRON Sema-1a
3R	12035634	3R_12035634_SNP [dm3] 3R_16209912_SNP [dm6]	A	T	3.891e^-10	1.609e^-5	UPSTREAM CR45639 & 1 other DOWNSTREAM CR45640 & 1 other INTERGENIC
2R	4910740	2R_4910740_SNP [dm3] 2R_9023235_SNP [dm6]	G	A	4.333e^-10	1.753e^-5	NON_SYNONYMOUS_CODING CG8170	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2R	8892727	2R_8892727_SNP [dm3] 2R_13005222_SNP [dm6]	T	A	4.589e^-10	1.779e^-5	INTRON Su_z_2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	15902881	3R_15902881_SNP [dm3] 3R_20077159_SNP [dm6]	G	A	4.589e^-10	1.779e^-5	INTERGENIC
X	12304374	X_12304374_SNP [dm3] X_12410341_SNP [dm6]	A	G	5.359e^-10	2.029e^-5	DOWNSTREAM CG2574 & 1 other INTERGENIC
3L	16205933	3L_16205933_SNP [dm3] 3L_16212833_SNP [dm6]	G	T	5.544e^-10	2.029e^-5	DOWNSTREAM CG13073 INTERGENIC	TF binding site mE1_TFBS_Stat92E
2R	5981461	2R_5981461_SNP [dm3] 2R_10093956_SNP [dm6]	A	G	5.562e^-10	2.029e^-5	NON_SYNONYMOUS_CODING CG2269	TF binding site mE1_TFBS_cad
2R	8623665	2R_8623665_INS [dm3] 2R_12736160_INS [dm6]	G	GTTGCCCAG	7.414e^-10	2.628e^-5	INTRON CG42663	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	9268999	3R_9268999_SNP [dm3] 3R_13443277_SNP [dm6]	G	C	7.485e^-10	2.628e^-5	EXON CR45679
2R	5991218	2R_5991218_SNP [dm3] 2R_10103713_SNP [dm6]	T	A	8.900e^-10	3.066e^-5	UPSTREAM 14-3-3zeta INTRON 14-3-3zeta	TF binding site BDTNP1_TFBS_dl
2R	5992985	2R_5992985_INS [dm3] 2R_10105480_INS [dm6]	T	TA	9.107e^-10	3.081e^-5	INTRON 14-3-3zeta	TF binding site mE1_TFBS_cad
3R	9985696	3R_9985696_SNP [dm3] 3R_14159974_SNP [dm6]	G	A	9.972e^-10	3.313e^-5	NON_SYNONYMOUS_CODING CG31327
3L	18199313	3L_18199313_SNP [dm3] 3L_18206213_SNP [dm6]	T	C	1.154e^-9	3.768e^-5	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2R	5985471	2R_5985471_SNP [dm3] 2R_10097966_SNP [dm6]	T	C	1.301e^-9	4.173e^-5	SYNONYMOUS_CODING Jra DOWNSTREAM RpLP0-like	TF binding site mE1_TFBS_inv mE1_TFBS_sens
2L	14715641	2L_14715641_SNP [dm3] 2L_14715641_SNP [dm6]	T	C	1.370e^-9	4.321e^-5	INTERGENIC
2R	14763347	2R_14763347_SNP [dm3] 2R_18875842_SNP [dm6]	C	T	1.440e^-9	4.466e^-5	INTERGENIC
3R	6007386	3R_6007386_SNP [dm3] 3R_10181664_SNP [dm6]	A	T	1.492e^-9	4.550e^-5	INTRON CG12814
3R	18215850	3R_18215850_SNP [dm3] 3R_22390128_SNP [dm6]	C	G	1.568e^-9	4.704e^-5	UTR_5_PRIME CG7059 UPSTREAM CG5379 & 1 other INTRON CG7059	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14434378	2R_14434378_SNP [dm3] 2R_18546873_SNP [dm6]	G	A	1.763e^-9	5.207e^-5	SYNONYMOUS_CODING Rgk2
2R	5984018	2R_5984018_SNP [dm3] 2R_10096513_SNP [dm6]	G	A	1.862e^-9	5.363e^-5	UTR_5_PRIME Jra UPSTREAM Jra DOWNSTREAM CG2269	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_kn mE1_TFBS_run mE1_TFBS_Ubx
3L	2323208	3L_2323208_DEL [dm3] 3L_2323208_DEL [dm6]	TGA	T	1.878e^-9	5.363e^-5	INTRON MsR1
2R	5990060	2R_5990060_SNP [dm3] 2R_10102555_SNP [dm6]	G	C	1.903e^-9	5.363e^-5	UPSTREAM 14-3-3zeta INTRON 14-3-3zeta	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	17315817	2R_17315817_SNP [dm3] 2R_21428312_SNP [dm6]	T	C	2.186e^-9	6.071e^-5	INTRON Sdc
3R	5997082	3R_5997082_SNP [dm3] 3R_10171360_SNP [dm6]	C	G	2.290e^-9	6.264e^-5	UTR_3_PRIME CG12814 UPSTREAM Best1	TF binding site BDTNP1_TFBS_dl
2L	11989738	2L_11989738_SNP [dm3] 2L_11989738_SNP [dm6]	G	T	2.435e^-9	6.565e^-5	SYNONYMOUS_CODING zuc UPSTREAM dgt2 DOWNSTREAM CG34163	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
2R	16950665	2R_16950665_SNP [dm3] 2R_21063160_SNP [dm6]	C	G	2.470e^-9	6.565e^-5	NON_SYNONYMOUS_CODING Cht8 DOWNSTREAM Cht12	TF binding site mE1_TFBS_chinmo
2R	14762835	2R_14762835_SNP [dm3] 2R_18875330_SNP [dm6]	T	A	2.576e^-9	6.749e^-5	INTERGENIC
2R	6225072	2R_6225072_DEL [dm3] 2R_10337567_DEL [dm6]	TC	G	3.033e^-9	7.837e^-5	INTRON CG42732
3L	2323186	3L_2323186_SNP [dm3] 3L_2323186_SNP [dm6]	T	A	3.315e^-9	8.115e^-5	INTRON MsR1
3L	2323190	3L_2323190_SNP [dm3] 3L_2323190_SNP [dm6]	G	C	3.315e^-9	8.115e^-5	INTRON MsR1
3L	2323192	3L_2323192_MNP [dm3] 3L_2323192_MNP [dm6]	TTAC	GCTT	3.315e^-9	8.115e^-5	INTRON MsR1
3L	2323203	3L_2323203_SNP [dm3] 3L_2323203_SNP [dm6]	T	C	3.315e^-9	8.115e^-5	INTRON MsR1
2R	18908798	2R_18908798_SNP [dm3] 2R_23021275_SNP [dm6]	A	G	3.469e^-9	8.381e^-5	INTRON twi & 1 other	TF binding site BDTNP1_TFBS_dl
3R	5996556	3R_5996556_SNP [dm3] 3R_10170834_SNP [dm6]	G	A	3.818e^-9	9.108e^-5	UPSTREAM Best1 DOWNSTREAM CG12814 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3R	3121944	3R_3121944_SNP [dm3] 3R_7296222_SNP [dm6]	C	A	4.544e^-9	1.069e^-4	INTRON rn
2R	7678655	2R_7678655_SNP [dm3] 2R_11791150_SNP [dm6]	T	A	4.597e^-9	1.069e^-4	INTRON ths	TF binding site BDTNP1_TFBS_dl
3L	2323197	3L_2323197_DEL [dm3] 3L_2323197_DEL [dm6]	AAAAT	A	4.885e^-9	1.122e^-4	INTRON MsR1
2R	15281279	2R_15281279_SNP [dm3] 2R_19393774_SNP [dm6]	G	T	5.416e^-9	1.229e^-4	SYNONYMOUS_CODING SdhA	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	10150358	3R_10150358_SNP [dm3] 3R_14324636_SNP [dm6]	C	T	5.727e^-9	1.284e^-4	SYNONYMOUS_CODING Afti	TF binding site mE1_TFBS_sens
3R	26063317	3R_26063317_SNP [dm3] 3R_30237595_SNP [dm6]	C	G	5.951e^-9	1.318e^-4	SPLICE_SITE_REGION CG43448 INTRON CG43448	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	600755	2L_600755_SNP [dm3] 2L_600755_SNP [dm6]	G	A	6.050e^-9	1.324e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	18452799	X_18452799_SNP [dm3] X_18558766_SNP [dm6]	G	T	6.230e^-9	1.332e^-4	INTRON Bx
X	18452805	X_18452805_INS [dm3] X_18558772_INS [dm6]	C	CC	6.230e^-9	1.332e^-4	INTRON Bx
X	12304723	X_12304723_SNP [dm3] X_12410690_SNP [dm6]	G	A	6.721e^-9	1.421e^-4	DOWNSTREAM CG2574 & 1 other INTERGENIC
3R	9776501	3R_9776501_SNP [dm3] 3R_13950779_SNP [dm6]	A	G	7.167e^-9	1.484e^-4	SYNONYMOUS_CODING CG9926
3R	3798346	3R_3798346_SNP [dm3] 3R_7972624_SNP [dm6]	A	T	7.178e^-9	1.484e^-4	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	23561416	3R_23561416_SNP [dm3] 3R_27735694_SNP [dm6]	A	G	7.817e^-9	1.598e^-4	UPSTREAM Ets98B INTERGENIC
2L	20074059	2L_20074059_SNP [dm3] 2L_20074059_SNP [dm6]	G	A	8.005e^-9	1.619e^-4	SYNONYMOUS_CODING pr DOWNSTREAM bwa	TF binding site mE1_TFBS_sens
3R	3797824	3R_3797824_SNP [dm3] 3R_7972102_SNP [dm6]	T	C	8.331e^-9	1.667e^-4	INTERGENIC
2L	15581654	2L_15581654_SNP [dm3] 2L_15581654_SNP [dm6]	T	C	1.007e^-8	1.893e^-4	INTRON kek3
2L	15581685	2L_15581685_SNP [dm3] 2L_15581685_SNP [dm6]	A	T	1.007e^-8	1.893e^-4	INTRON kek3
2L	15581747	2L_15581747_SNP [dm3] 2L_15581747_SNP [dm6]	T	C	1.007e^-8	1.893e^-4	INTRON kek3
2L	15581800	2L_15581800_SNP [dm3] 2L_15581800_SNP [dm6]	C	G	1.007e^-8	1.893e^-4	INTRON kek3
2L	15583531	2L_15583531_SNP [dm3] 2L_15583531_SNP [dm6]	A	T	1.007e^-8	1.893e^-4	UTR_3_PRIME kek3
2L	15584156	2L_15584156_SNP [dm3] 2L_15584156_SNP [dm6]	A	G	1.007e^-8	1.893e^-4	DOWNSTREAM kek3 INTERGENIC
3L	18199310	3L_18199310_SNP [dm3] 3L_18206210_SNP [dm6]	C	T	1.072e^-8	1.994e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv

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By genomic position
Variant impact
Gene name

Microbiota_OTU127 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results