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=1.501e^-13)
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_3R_Mo	0.05716

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	5.625	0.0601

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

5258 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
X	10957741	X_10957741_DEL [dm3] X_11063708_DEL [dm6]	TGCA	T	4.529e^-20	7.122e^-14	UPSTREAM CG1537 INTERGENIC
2R	9802372	2R_9802372_SNP [dm3] 2R_13914867_SNP [dm6]	A	T	7.657e^-20	7.122e^-14	INTRON shot
X	10957685	X_10957685_SNP [dm3] X_11063652_SNP [dm6]	G	A	3.334e^-17	2.068e^-11	UPSTREAM CG1537 INTERGENIC
X	14954380	X_14954380_SNP [dm3] X_15060347_SNP [dm6]	T	A	9.421e^-17	3.751e^-11	SYNONYMOUS_CODING hiw	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	10957751	X_10957751_SNP [dm3] X_11063718_SNP [dm6]	C	G	1.008e^-16	3.751e^-11	UPSTREAM CG1537 INTERGENIC
3R	2516927	3R_2516927_SNP [dm3] 3R_6691205_SNP [dm6]	T	A	2.049e^-15	6.352e^-10	SYNONYMOUS_CODING Ccp84Ae UPSTREAM Ccp84Af
X	10957965	X_10957965_SNP [dm3] X_11063932_SNP [dm6]	T	C	1.585e^-14	4.213e^-9	UPSTREAM CG1537 INTERGENIC
3R	5465852	3R_5465852_SNP [dm3] 3R_9640130_SNP [dm6]	G	A	6.109e^-14	1.421e^-8	UPSTREAM Dh44 INTRON Dh44
3L	24109846	3L_24109846_DEL [dm3] 3L_24116746_DEL [dm6]	TACC	T	2.291e^-13	4.736e^-8	INTRON Snap25
3L	24109851	3L_24109851_DEL [dm3] 3L_24116751_DEL [dm6]	CCCA	C	4.466e^-13	7.553e^-8	INTRON Snap25
3L	24109857	3L_24109857_DEL [dm3] 3L_24116757_DEL [dm6]	AGCGC	A	4.466e^-13	7.553e^-8	INTRON Snap25
2R	6825911	2R_6825911_SNP [dm3] 2R_10938406_SNP [dm6]	C	T	2.875e^-12	4.385e^-7	DOWNSTREAM Spn47C INTERGENIC
X	19721676	X_19721676_SNP [dm3] X_19827643_SNP [dm6]	C	A	4.254e^-12	4.385e^-7	INTERGENIC
2L	9420280	2L_9420280_SNP [dm3] 2L_9420280_SNP [dm6]	A	T	4.335e^-12	4.385e^-7	INTRON Mco1
2R	9802355	2R_9802355_DEL [dm3] 2R_13914850_DEL [dm6]	GAG	G	4.410e^-12	4.385e^-7	INTRON shot
2L	4165316	2L_4165316_SNP [dm3] 2L_4165316_SNP [dm6]	T	C	4.447e^-12	4.385e^-7	SYNONYMOUS_CODING Or24a
X	10957731	X_10957731_SNP [dm3] X_11063698_SNP [dm6]	G	C	4.470e^-12	4.385e^-7	UPSTREAM CG1537 INTERGENIC
X	10957738	X_10957738_MNP [dm3] X_11063705_MNP [dm6]	GCT	AAA	4.470e^-12	4.385e^-7	UPSTREAM CG1537 INTERGENIC
2R	900208	2R_900208_DEL [dm3] 2R_5012703_DEL [dm6]	AT	A	4.478e^-12	4.385e^-7	INTRON Ir41a	transposable element FlyBase
2L	9419771	2L_9419771_SNP [dm3] 2L_9419771_SNP [dm6]	T	A	6.266e^-12	5.544e^-7	INTRON Mco1
2L	9419854	2L_9419854_SNP [dm3] 2L_9419854_SNP [dm6]	A	T	6.266e^-12	5.544e^-7	INTRON Mco1
X	10957721	X_10957721_SNP [dm3] X_11063688_SNP [dm6]	A	C	6.556e^-12	5.544e^-7	UPSTREAM CG1537 INTERGENIC
X	12997588	X_12997588_SNP [dm3] X_13103555_SNP [dm6]	G	C	9.180e^-12	7.107e^-7	INTRON CG43313
X	2388150	X_2388150_SNP [dm3] X_2494117_SNP [dm6]	T	C	9.519e^-12	7.107e^-7	INTRON trol
X	10957728	X_10957728_SNP [dm3] X_11063695_SNP [dm6]	A	G	9.549e^-12	7.107e^-7	UPSTREAM CG1537 INTERGENIC
2R	9652382	2R_9652382_SNP [dm3] 2R_13764877_SNP [dm6]	G	T	1.001e^-11	7.162e^-7	INTERGENIC
2L	8856431	2L_8856431_SNP [dm3] 2L_8856431_SNP [dm6]	G	A	1.213e^-11	8.359e^-7	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	3091303	2R_3091303_SNP [dm3] 2R_7203798_SNP [dm6]	G	T	1.401e^-11	9.310e^-7	INTRON pk
X	2388012	X_2388012_SNP [dm3] X_2493979_SNP [dm6]	A	G	1.465e^-11	9.400e^-7	INTRON trol
2R	11693784	2R_11693784_SNP [dm3] 2R_15806279_SNP [dm6]	G	C	1.993e^-11	1.236e^-6	INTRON tun & 1 other
2L	8847267	2L_8847267_SNP [dm3] 2L_8847267_SNP [dm6]	C	G	2.895e^-11	1.737e^-6	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
2R	9403418	2R_9403418_SNP [dm3] 2R_13515913_SNP [dm6]	C	T	3.197e^-11	1.859e^-6	SYNONYMOUS_CODING CG13330 UTR_3_PRIME Vmat	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	125913	3L_125913_DEL [dm3] 3L_125913_DEL [dm6]	AAAC	A	3.425e^-11	1.931e^-6	UPSTREAM CR45401 DOWNSTREAM CR45402 INTERGENIC
2R	11696133	2R_11696133_SNP [dm3] 2R_15808628_SNP [dm6]	G	A	3.531e^-11	1.932e^-6	INTRON tun & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	1371173	2L_1371173_SNP [dm3] 2L_1371173_SNP [dm6]	C	T	4.628e^-11	2.460e^-6	INTERGENIC	TF binding site BDTNP1_TFBS_Med
2L	4110394	2L_4110394_SNP [dm3] 2L_4110394_SNP [dm6]	A	T	7.092e^-11	3.665e^-6	INTRON ed
3L	15486719	3L_15486719_SNP [dm3] 3L_15493619_SNP [dm6]	A	T	7.790e^-11	3.917e^-6	INTRON CG12355	TF binding site mE1_TFBS_Trl
2R	18080405	2R_18080405_DEL [dm3] 2R_22192900_DEL [dm6]	AGCCACAGA	A	9.830e^-11	4.813e^-6	INTRON Swim
3L	11794843	3L_11794843_INS [dm3] 3L_11801743_INS [dm6]	T	TATTATATATATAT...	1.298e^-10	6.194e^-6	UPSTREAM CG10361 & 1 other DOWNSTREAM CG42255 INTERGENIC
X	10957265	X_10957265_INS [dm3] X_11063232_INS [dm6]	T	TCTGCATCT	1.897e^-10	8.822e^-6	UPSTREAM CG1537 INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	7363731	2L_7363731_DEL [dm3] 2L_7363731_DEL [dm6]	TTAAGGTTGTCTATATT...	T	2.538e^-10	1.152e^-5	SPLICE_SITE_DONOR Wnt10 SPLICE_SITE_REGION Wnt10 UTR_5_PRIME Wnt10 INTRON Wnt10 INTRAGENIC Wnt10
3L	23294962	3L_23294962_SNP [dm3] 3L_23301862_SNP [dm6]	T	A	2.744e^-10	1.215e^-5	INTERGENIC	transposable element FlyBase
2L	11427661	2L_11427661_SNP [dm3] 2L_11427661_SNP [dm6]	G	T	3.128e^-10	1.293e^-5	INTERGENIC
2R	3814257	2R_3814257_SNP [dm3] 2R_7926752_SNP [dm6]	T	C	3.128e^-10	1.293e^-5	SYNONYMOUS_CODING CG8791 UPSTREAM CG8791
3L	9051175	3L_9051175_SNP [dm3] 3L_9058075_SNP [dm6]	G	A	3.128e^-10	1.293e^-5	UPSTREAM Argk INTRON Argk	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	1490386	3L_1490386_DEL [dm3] 3L_1490386_DEL [dm6]	CACACGATTTTTTGGC...	C	3.304e^-10	1.336e^-5	UPSTREAM stet DOWNSTREAM CG12084 INTERGENIC	TF binding site mE1_TFBS_sbb transposable element FlyBase
2L	13191642	2L_13191642_SNP [dm3] 2L_13191642_SNP [dm6]	G	T	4.021e^-10	1.592e^-5	UPSTREAM Edem2 INTRON CG16974	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	3810089	2R_3810089_SNP [dm3] 2R_7922584_SNP [dm6]	T	C	4.303e^-10	1.609e^-5	START_GAINED Or43b UTR_5_PRIME Or43b DOWNSTREAM Kdm4A	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	25368027	3R_25368027_SNP [dm3] 3R_29542305_SNP [dm6]	A	G	4.392e^-10	1.609e^-5	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
X	17073019	X_17073019_SNP [dm3] X_17178986_SNP [dm6]	C	A	4.392e^-10	1.609e^-5	INTRON baz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	16694461	2L_16694461_SNP [dm3] 2L_16694461_SNP [dm6]	C	A	4.411e^-10	1.609e^-5	INTRON grp
2L	4108538	2L_4108538_SNP [dm3] 2L_4108538_SNP [dm6]	A	G	5.935e^-10	2.123e^-5	INTRON ed
X	13522808	X_13522808_SNP [dm3] X_13628775_SNP [dm6]	T	G	9.841e^-10	3.455e^-5	INTRON NFAT
2L	8232101	2L_8232101_SNP [dm3] 2L_8232101_SNP [dm6]	G	A	1.136e^-9	3.913e^-5	INTRON Pvr
3R	5441324	3R_5441324_SNP [dm3] 3R_9615602_SNP [dm6]	A	C	1.231e^-9	4.166e^-5	INTRON CG8312	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	21468344	3L_21468344_SNP [dm3] 3L_21475244_SNP [dm6]	C	A	1.291e^-9	4.290e^-5	SYNONYMOUS_CODING croc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	16688783	2L_16688783_SNP [dm3] 2L_16688783_SNP [dm6]	A	T	1.388e^-9	4.532e^-5	INTRON grp	TF binding site BDTNP1_TFBS_twi
2R	17539	2R_17539_SNP [dm3] 2R_4130034_SNP [dm6]	C	T	1.498e^-9	4.805e^-5	UPSTREAM CG17683 INTERGENIC
2R	1308684	2R_1308684_SNP [dm3] 2R_5421179_SNP [dm6]	G	T	1.573e^-9	4.960e^-5	INTRON laccase2	transposable element FlyBase
2L	1286280	2L_1286280_SNP [dm3] 2L_1286280_SNP [dm6]	C	T	1.697e^-9	5.202e^-5	SYNONYMOUS_CODING robo3	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
3L	21194704	3L_21194704_SNP [dm3] 3L_21201604_SNP [dm6]	G	T	1.706e^-9	5.202e^-5	UPSTREAM CG33056 INTRON CG33054 & 1 other
2L	7138152	2L_7138152_SNP [dm3] 2L_7138152_SNP [dm6]	G	T	2.182e^-9	6.548e^-5	INTRON Pvf3	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	2347970	3R_2347970_SNP [dm3] 3R_6522248_SNP [dm6]	G	A	2.360e^-9	6.970e^-5	INTERGENIC
3L	21713207	3L_21713207_SNP [dm3] 3L_21720107_SNP [dm6]	C	G	2.408e^-9	6.999e^-5	INTERGENIC
2R	10037	2R_10037_SNP [dm3] 2R_4122532_SNP [dm6]	A	C	2.482e^-9	7.104e^-5	INTERGENIC
3L	21429169	3L_21429169_SNP [dm3] 3L_21436069_SNP [dm6]	T	G	2.607e^-9	7.243e^-5	INTRON Aef1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	14262884	2R_14262884_SNP [dm3] 2R_18375379_SNP [dm6]	C	T	2.608e^-9	7.243e^-5	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	21762081	3L_21762081_SNP [dm3] 3L_21768981_SNP [dm6]	A	G	2.909e^-9	7.911e^-5	UPSTREAM CG7370 INTRON Syn1 & 1 other
2R	7138880	2R_7138880_SNP [dm3] 2R_11251375_SNP [dm6]	A	C	2.934e^-9	7.911e^-5	SYNONYMOUS_CODING Or47a DOWNSTREAM Cpr47Ea	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	11302175	2L_11302175_SNP [dm3] 2L_11302175_SNP [dm6]	T	C	3.821e^-9	1.016e^-4	INTERGENIC
X	15997076	X_15997076_INS [dm3] X_16103043_INS [dm6]	T	TT	4.666e^-9	1.223e^-4	UTR_5_PRIME CG42353 & 1 other INTRON CG42354 & 1 other	TF binding site BDTNP1_TFBS_dl
2R	14537876	2R_14537876_SNP [dm3] 2R_18650371_SNP [dm6]	G	A	4.865e^-9	1.257e^-4	INTRON SP2637
2L	8871097	2L_8871097_SNP [dm3] 2L_8871097_SNP [dm6]	C	T	5.178e^-9	1.320e^-4	INTERGENIC
3L	9059614	3L_9059614_SNP [dm3] 3L_9066514_SNP [dm6]	C	A	5.544e^-9	1.380e^-4	UPSTREAM Argk DOWNSTREAM CG4911 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	17614549	2R_17614549_SNP [dm3] 2R_21727044_SNP [dm6]	C	G	5.563e^-9	1.380e^-4	DOWNSTREAM CR44750 INTERGENIC	transposable element FlyBase
2R	17398110	2R_17398110_SNP [dm3] 2R_21510605_SNP [dm6]	G	A	7.234e^-9	1.748e^-4	INTRON MESK2	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	18030699	2R_18030699_DEL [dm3] 2R_22143194_DEL [dm6]	CATTTTCATGAAAA...	C	7.234e^-9	1.748e^-4	INTRON a	TF binding site BDTNP1_TFBS_twi
2L	9422410	2L_9422410_SNP [dm3] 2L_9422410_SNP [dm6]	A	G	7.996e^-9	1.846e^-4	INTRON Mco1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	10957664	X_10957664_INS [dm3] X_11063631_INS [dm6]	T	TTT	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957699	X_10957699_SNP [dm3] X_11063666_SNP [dm6]	T	A	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957704	X_10957704_SNP [dm3] X_11063671_SNP [dm6]	C	T	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957709	X_10957709_SNP [dm3] X_11063676_SNP [dm6]	G	A	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957719	X_10957719_SNP [dm3] X_11063686_SNP [dm6]	C	T	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957723	X_10957723_DEL [dm3] X_11063690_DEL [dm6]	AAA	A	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
X	10957727	X_10957727_SNP [dm3] X_11063694_SNP [dm6]	A	T	8.432e^-9	1.846e^-4	UPSTREAM CG1537 INTERGENIC
2R	18030735	2R_18030735_SNP [dm3] 2R_22143230_SNP [dm6]	G	C	9.327e^-9	2.018e^-4	INTRON a	TF binding site BDTNP1_TFBS_twi
2L	10443746	2L_10443746_SNP [dm3] 2L_10443746_SNP [dm6]	T	C	1.030e^-8	2.136e^-4	INTRON loh	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9426054	2L_9426054_SNP [dm3] 2L_9426054_SNP [dm6]	G	T	1.047e^-8	2.136e^-4	NON_SYNONYMOUS_CODING Mco1 UPSTREAM Fbp2
2R	10350657	2R_10350657_SNP [dm3] 2R_14463152_SNP [dm6]	G	A	1.066e^-8	2.136e^-4	SYNONYMOUS_CODING Oaz	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	10350658	2R_10350658_SNP [dm3] 2R_14463153_SNP [dm6]	G	A	1.066e^-8	2.136e^-4	NON_SYNONYMOUS_CODING Oaz	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	8174188	2R_8174188_SNP [dm3] 2R_12286683_SNP [dm6]	C	G	1.066e^-8	2.136e^-4	INTRON CG42700
X	5903923	X_5903923_SNP [dm3] X_6009890_SNP [dm6]	T	A	1.066e^-8	2.136e^-4	INTRON mab-21
2L	10872248	2L_10872248_SNP [dm3] 2L_10872248_SNP [dm6]	C	T	1.068e^-8	2.136e^-4	EXON CR45454
X	10957662	X_10957662_SNP [dm3] X_11063629_SNP [dm6]	A	G	1.113e^-8	2.202e^-4	UPSTREAM CG1537 INTERGENIC
2L	9439997	2L_9439997_DEL [dm3] 2L_9439997_DEL [dm6]	TAGTAACTTATAATTTAGAA...	T	1.188e^-8	2.326e^-4	DOWNSTREAM CG33723 INTRON numb
2R	19993383	2R_19993383_SNP [dm3] 2R_24105860_SNP [dm6]	C	T	1.237e^-8	2.397e^-4	NON_SYNONYMOUS_CODING enok	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	4799946	2L_4799946_SNP [dm3] 2L_4799946_SNP [dm6]	A	T	1.285e^-8	2.464e^-4	INTRON Clect27	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	17812295	2R_17812295_SNP [dm3] 2R_21924790_SNP [dm6]	G	A	1.361e^-8	2.584e^-4	INTRON Fili
3L	12473709	3L_12473709_SNP [dm3] 3L_12480609_SNP [dm6]	C	A	1.549e^-8	2.911e^-4	INTRON CG10663
X	10867624	X_10867624_INS [dm3] X_10973591_INS [dm6]	G	GCGAG	1.612e^-8	2.999e^-4	INTRON CG42339

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By genomic position
Variant impact
Gene name

Microbiota_OTU137 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results